Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z A a (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.layers.esen.nn.radial.PolynomialEnvelope attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) a_sigma() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) AA_NAME_NUMBER (in module MolecularDiffusion.data.component.pmdm_data) ablate_frame_updates (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCP attribute) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCP2 attribute) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) ablate_scalars (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) ablate_vectors (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) AC2BO() (in module MolecularDiffusion.utils.xyz2mol.converter) AC2mol() (in module MolecularDiffusion.utils.xyz2mol.converter) accuracy() (in module MolecularDiffusion.modules.tasks.metrics) act (MolecularDiffusion.modules.layers.equiformer_v2.activation.S2Activation attribute) (MolecularDiffusion.modules.layers.equiformer_v2.activation.ScaledSmoothLeakyReLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2.activation.ScaledSwiGLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2.activation.SwiGLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.S2Activation attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.ScaledSmoothLeakyReLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.ScaledSwiGLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.SwiGLU attribute) (MolecularDiffusion.modules.layers.esen.esen_block.SpectralAtomwise attribute) (MolecularDiffusion.modules.layers.esen.nn.activation.S2Activation attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.PosUpdate attribute) (MolecularDiffusion.modules.models.chefnmr.layers.Mlp attribute) (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) (MolecularDiffusion.modules.models.etflow.torchmd.GatedEquivariantBlock attribute) (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.Mlp attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.GatedEquivariantBlock attribute) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.SiLUSmearing attribute) act_class_mapping (in module MolecularDiffusion.modules.models.etflow.torchmd) act_dense_correct_bool (MolecularDiffusion.modules.models.ditmc.dit.DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) act_dropout (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer attribute) act_fn (MolecularDiffusion.modules.models.apo2mol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.ditmc.dit.DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.readout.EquivariantReadout attribute) (MolecularDiffusion.modules.models.ditmc.readout.SimpleReadout attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) act_fn_in (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) act_fn_obj (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) act_fn_out (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) act_gates (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Gate attribute) act_layer (MolecularDiffusion.modules.models.loqi.fn_model.MLP attribute) act_scalars (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Gate attribute) act_type (MolecularDiffusion.modules.layers.esen.esen_block.Edgewise attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) activate (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) Activation (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) activation (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) (MolecularDiffusion.modules.models.goflow.ops.Dense attribute) (MolecularDiffusion.modules.models.goflow.ops.EdgeInit attribute) (MolecularDiffusion.modules.models.goflow.outputs.SNNDense attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.OneLayerActivation attribute) (MolecularDiffusion.modules.models.pmdm.common.MultiLayerPerceptron attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) activation_checkpointing (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) activation_fn (MolecularDiffusion.modules.models.ditmc.layers.E3MLP attribute) (MolecularDiffusion.modules.models.ditmc.layers.MLP attribute) ACTIVATION_MAPPING (in module MolecularDiffusion.modules.models.oareactdiff.leftnet) activation_type (MolecularDiffusion.modules.layers.tabasco.transition.Transition attribute) (MolecularDiffusion.runmodes.train.tasks_transformer.ModelTaskFactory attribute) acts (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Activation attribute) actvn (MolecularDiffusion.modules.layers.vn.vn_layers.ResnetBlockFC attribute) (MolecularDiffusion.modules.models.diffsmol.shape_ae.DecoderInner attribute) actvn_0 (MolecularDiffusion.modules.layers.vn.vn_layers.VNResnetBlockFC attribute) actvn_1 (MolecularDiffusion.modules.layers.vn.vn_layers.VNResnetBlockFC attribute) actvn_c (MolecularDiffusion.modules.models.diffsmol.shape_ae.VNResnetEncoder attribute) ada_dense (MolecularDiffusion.modules.models.ditmc.dit.DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.readout.EquivariantReadout attribute) (MolecularDiffusion.modules.models.ditmc.readout.SimpleReadout attribute) adaln_beta (MolecularDiffusion.modules.layers.tabasco.attention.AdaLNAttention attribute) (MolecularDiffusion.modules.layers.tabasco.attention.CrossAdaLNAttention attribute) adaLN_edge_modulation (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) adaln_gamma (MolecularDiffusion.modules.layers.tabasco.attention.AdaLNAttention attribute) (MolecularDiffusion.modules.layers.tabasco.attention.CrossAdaLNAttention attribute) adaLN_modulation (MolecularDiffusion.modules.models.chefnmr.layers.DiTBlock attribute) (MolecularDiffusion.modules.models.chefnmr.layers.FinalLayer attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiTBlock attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.FinalLayer attribute) (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) AdaLNAttention (class in MolecularDiffusion.modules.layers.tabasco.attention) adapter (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTask attribute) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask attribute) adapter_indices (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer attribute) (MolecularDiffusion.modules.models.tabasco_egnn.egnn_backbone.EGNNBackbone attribute) (MolecularDiffusion.modules.models.tabasco_equiformer.equiformer_backbone.EquiformerV2TabascoBackbone attribute) (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone attribute) adapter_module (MolecularDiffusion.modules.models.egcl.EGNN attribute) add() (in module MolecularDiffusion.modules.layers.e3x.features) (MolecularDiffusion.callbacks.train_helper.Queue method) (MolecularDiffusion.utils.geom_analyzer.Histogram_cont method) (MolecularDiffusion.utils.geom_analyzer.Histogram_discrete method) add_cmd() (in module MolecularDiffusion.cli.zoo) add_edge() (MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly.RDKitMoleculeAssembly method) add_fragment() (MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly.RDKitMoleculeAssembly method) add_h_unit() (in module MolecularDiffusion.runmodes.data.augmentation) add_n_nodes (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDPocketGenerator attribute) add_node() (MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly.RDKitMoleculeAssembly method) add_noise() (MolecularDiffusion.modules.tasks.diffusion_nextmol.Graph3DBatchToNextMolAdapter method) add_noise_to_quaternion() (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D method) add_param_group() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer method) add_sinusoid_posenc (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) (MolecularDiffusion.modules.models.transformer_dynamics.TransformerDynamics attribute) (MolecularDiffusion.runmodes.train.tasks_transformer.ModelTaskFactory attribute) add_smooth_lddt_loss (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) add_time (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) add_to_parser() (MolecularDiffusion.cli.data.VariadicOption method) add_virtual_edges_to_edge_index() (in module MolecularDiffusion.modules.models.shepherd_arch.utils) add_virtual_node_x1 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) add_virtual_node_x2 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) add_virtual_node_x3 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) add_virtual_node_x4 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) adj_from_node_mask() (in module MolecularDiffusion.modules.models.syncogen.models.semla_utils) adj_to_attn_mask() (in module MolecularDiffusion.modules.models.syncogen.models.semla) (in module MolecularDiffusion.modules.models.syncogen.models.semla_pharm) adjacency_from_bonds() (in module MolecularDiffusion.modules.models.ditmc.graph_features) adjust_bias() (in module MolecularDiffusion.utils.torch) adjust_state_dict() (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory method) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory method) adjust_weights() (in module MolecularDiffusion.utils.torch) affine (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantLayerNormArray attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantLayerNormArray attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantRMSNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantLayerNormArray attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNorm attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNormV2 attribute) affine_weight (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantDegreeLayerScale attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantDegreeLayerScale attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantDegreeLayerScale attribute) aggregate() (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention method) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPMessagePassing method) (MolecularDiffusion.modules.models.goflow.gotennet.GATA method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiMessage method) aggregate_node_error() (in module MolecularDiffusion.modules.models.ditmc.flow_matching) aggregation_method (MolecularDiffusion.modules.layers.conv.EquivariantBlock attribute) (MolecularDiffusion.modules.layers.conv.EquivariantUpdate attribute) (MolecularDiffusion.modules.layers.conv.GCL attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.EquivariantBlock attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.GCL attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EGNN attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.difflinker.egnn.GCL attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EGNN attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.GCL attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.GCL attribute) (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EGNN attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.geoldm.egnn.GCL attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.EquivariantBlock attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.GCL attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) align_atoms() (in module MolecularDiffusion.runmodes.data.preparation) align_bool (MolecularDiffusion.modules.models.ditmc.flow_matching.FlowMatching attribute) align_loss (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) align_prior() (in module MolecularDiffusion.modules.models.loqi.interpolant) align_target_with_reference() (in module MolecularDiffusion.utils.geom_constraint) all_open_reaction_centers() (MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly.RDKitMoleculeAssembly method) all_pairs_edges() (in module MolecularDiffusion.modules.models.ditmc.graph_features) all_parameters() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer method) allow_n_bonds (in module MolecularDiffusion.utils.geom_constant) allow_unknown (MolecularDiffusion.data.component.feature.NodeFeaturizer attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) allowed_bonds (in module MolecularDiffusion.utils.geom_analyzer) allowed_shape (in module MolecularDiffusion.utils.geom_constant) ALPHA (in module MolecularDiffusion.utils.shepherd_score.score.constants) alpha (MolecularDiffusion.modules.layers.equiformer_v2.activation.SmoothLeakyReLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.SmoothLeakyReLU attribute) (MolecularDiffusion.modules.models.etflow.flow.HarmonicSampler attribute) (MolecularDiffusion.modules.models.etflow.torchmd.ExpNormalSmearing attribute) (MolecularDiffusion.modules.models.goflow.ops.ExpNormalSmearing attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.SmoothLeakyReLU attribute) alpha() (in module MolecularDiffusion.modules.models.equifm.paths) (MolecularDiffusion.modules.models.difflinker.edm.EDM method) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) (MolecularDiffusion.modules.models.oareactdiff.schedule.DiffSchedule method) ALPHA_DEFAULT (in module MolecularDiffusion.utils.geom_metrics) alpha_drop (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) alpha_dropout (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) alpha_t() (MolecularDiffusion.modules.models.flowmol.interpolant_scheduler.InterpolantScheduler method) alpha_t_prime() (MolecularDiffusion.modules.models.flowmol.interpolant_scheduler.InterpolantScheduler method) alphas (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) alphas_cumprod (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) alphas_cumprod_prev (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) analyze() (in module MolecularDiffusion.cli.analyze) analyze_and_save() (in module MolecularDiffusion.runmodes.train.eval) analyze_node_distribution() (in module MolecularDiffusion.utils.geom_analyzer) anchors_context (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) ang (in module MolecularDiffusion.modules.models.diffsmol.shape_utils) angle_between_vecs() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca) angle_between_vecs_np() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca_np) angle_emb (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) ANGLE_RELAX (in module MolecularDiffusion.runmodes.train.eval) ANGSTROM_TO_BOHR (in module MolecularDiffusion.runmodes.analyze.xtb_electronic) annealing_coef (MolecularDiffusion.modules.models.syncogen.diffusion.sampling.integrators.euler.EulerIntegrator attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) annotate_cmd() (in module MolecularDiffusion.cli.data) annotate_db() (in module MolecularDiffusion.runmodes.data.preparation) antithetic_sampling (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) APO2MOL_ATOM_VOCAB (in module MolecularDiffusion.data.component.apo2mol_data) apo2mol_collate() (in module MolecularDiffusion.data.component.apo2mol_data) Apo2MolDataModule (class in MolecularDiffusion.data.component.apo2mol_data) Apo2MolDataset (class in MolecularDiffusion.data.component.apo2mol_data) Apo2MolDiffusionTask (class in MolecularDiffusion.modules.tasks.diffusion_apo2mol) Apo2MolPocketGenerator (class in MolecularDiffusion.modules.tasks.diffusion_apo2mol) append_gt_array() (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator method) append_pred_array() (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator method) apply() (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) apply_coef() (MolecularDiffusion.modules.models.syncogen.diffusion.loss.base.LossBase method) apply_edge_givens() (in module MolecularDiffusion.modules.models.syncogen.api.ops.graph_ops) (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph method) apply_mask() (in module MolecularDiffusion.modules.models.tabasco.utils.tensor_ops) (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates method) apply_noise() (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel method) apply_random_rotation() (in module MolecularDiffusion.modules.models.tabasco.data.transforms) apply_rotation_augmentation() (in module MolecularDiffusion.utils.geom_utils) apply_SE3_transform() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.se3) apply_SE3_transform_np() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.se3_np) apply_SO3_transform() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.se3) apply_SO3_transform_np() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.se3_np) apply_t_threshold() (MolecularDiffusion.modules.models.syncogen.diffusion.loss.base.LossBase method) apply_time_weight() (MolecularDiffusion.modules.models.syncogen.diffusion.loss.base.LossBase method) apply_transforms_tensor() (in module MolecularDiffusion.modules.models.apo2mol.residue_ops) apply_transforms_tensor_batch() (in module MolecularDiffusion.modules.models.apo2mol.residue_ops) area_under_prc() (in module MolecularDiffusion.modules.tasks.metrics) area_under_roc() (in module MolecularDiffusion.modules.tasks.metrics) aromatic_flags (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) as_mask() (in module MolecularDiffusion.modules.layers.functional) ase_db_path (MolecularDiffusion.runmodes.train.data.DataModule attribute) ase_ops_group() (in module MolecularDiffusion.cli.data) AseAtomsAdaptor (in module MolecularDiffusion.modules.layers.atomic_data) assemble_nodemask() (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet static method) assert_correctly_masked() (in module MolecularDiffusion.modules.models.difflinker.utils) (in module MolecularDiffusion.modules.models.jodo.utils) (in module MolecularDiffusion.modules.models.midi.diffusion_utils) (in module MolecularDiffusion.utils.geom_utils) assert_mean_zero() (in module MolecularDiffusion.utils.geom_utils) assert_mean_zero_with_mask() (in module MolecularDiffusion.modules.models.difflinker.utils) (in module MolecularDiffusion.modules.models.jodo.utils) (in module MolecularDiffusion.modules.models.oareactdiff.graph_tools) (in module MolecularDiffusion.utils.geom_utils) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM static method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion static method) assert_partial_mean_zero_with_mask() (in module MolecularDiffusion.modules.models.difflinker.utils) assert_rot_equiv() (in module MolecularDiffusion.modules.models.oareactdiff.leftnet) assets_root() (in module MolecularDiffusion.assets) assign_batch_stats() (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) atol (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTSGenerator attribute) Atom (class in MolecularDiffusion.data.component.pointcloud) atom_and_pharmacophore_mask (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates property) atom_center_identification() (in module MolecularDiffusion.data.component.feature) atom_cgr_embedding (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet attribute) (MolecularDiffusion.modules.models.goflow.ops.NodeInit attribute) ATOM_COLOR_MAP (in module MolecularDiffusion.modules.models.tabasco.chem.constants) atom_coords (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates property) atom_count_histogram (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask property) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask property) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask property) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask property) atom_decoder (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.diffsbdd.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) atom_default() (in module MolecularDiffusion.data.component.feature) ATOM_DICT (in module MolecularDiffusion.data.component.diffpharma_prep) atom_dim (MolecularDiffusion.modules.models.syncogen.models.layers.HierarchicalPositionalEmbedding attribute) (MolecularDiffusion.modules.models.tabasco_egnn.egnn_backbone.EGNNBackbone attribute) (MolecularDiffusion.modules.models.tabasco_equiformer.equiformer_backbone.EquiformerV2TabascoBackbone attribute) (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone attribute) atom_embedder (MolecularDiffusion.modules.models.loqi.fn_model.MegaFNV3Conf attribute) atom_embedding (MolecularDiffusion.modules.models.goflow.ops.AtomCGREmbedding attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.HierarchicalPositionalEmbedding attribute) atom_encoder (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.diffsbdd.dynamics.EGNNDynamics attribute) atom_explicit_property_prediction() (in module MolecularDiffusion.data.component.feature) atom_feat_embedding (MolecularDiffusion.modules.models.goflow.ops.AtomCGREmbedding attribute) atom_geom() (in module MolecularDiffusion.data.component.feature) atom_geom_compact() (in module MolecularDiffusion.data.component.feature) atom_geom_opt() (in module MolecularDiffusion.data.component.feature) atom_geom_v2() (in module MolecularDiffusion.data.component.feature) atom_graph (MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly.FragmentInstance attribute) (MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly.RDKitMoleculeAssembly attribute) ATOM_MAPPING (in module MolecularDiffusion.data.component.oareactdiff_data) atom_mask (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates attribute) atom_mode (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolTaskFactory attribute) ATOM_NAMES (in module MolecularDiffusion.modules.models.tabasco.chem.constants) atom_names (MolecularDiffusion.modules.models.tabasco.utils.metrics.AtomTypeDistribution attribute) atom_nf (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM attribute) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion attribute) atom_pos_to_pair_dist() (in module MolecularDiffusion.modules.layers.gfmdiff.blocks) atom_pretrain() (in module MolecularDiffusion.data.component.feature) atom_property_prediction() (in module MolecularDiffusion.data.component.feature) atom_symbol (MolecularDiffusion.modules.models.tabasco.utils.metrics.AtomFractionMetric attribute) atom_symbol() (in module MolecularDiffusion.data.component.feature) atom_synthon_completion() (in module MolecularDiffusion.data.component.feature) atom_to_feature_vector() (in module MolecularDiffusion.modules.models.etflow.features) atom_topological() (in module MolecularDiffusion.data.component.feature) atom_type_counts (MolecularDiffusion.data.component.graph3d_dataset.Graph3DStats attribute) atom_type_dict (MolecularDiffusion.modules.models.tabasco.utils.metrics.AtomTypeDistribution attribute) atom_type_embed (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) atom_type_embedder (MolecularDiffusion.modules.models.ldm.encoders.transformer.TransformerEncoder attribute) atom_type_embedding (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) atom_type_marginal() (MolecularDiffusion.data.component.graph3d_dataset.Graph3DStats method) ATOM_TYPES (in module MolecularDiffusion.modules.models.syncogen.constants.constants) atom_types() (MolecularDiffusion.data.component.dataset.GraphDataset method) (MolecularDiffusion.data.component.dataset.LazyChunkedDataset method) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset method) (MolecularDiffusion.data.component.dataset.PointCloudDataset method) (MolecularDiffusion.data.component.graph3d_dataset.Graph3DDataset method) atom_types_for() (in module MolecularDiffusion.modules.models.nextmol.featurize) atom_types_head (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.decoders.transformer.TransformerDecoder attribute) atom_types_x1 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) atom_vocab (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataModule attribute) (MolecularDiffusion.data.component.dataset.LazyChunkedDataset attribute) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset attribute) (MolecularDiffusion.data.component.diffdec_data.DiffDecDataModule attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataModule attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataModule attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataModule attribute) (MolecularDiffusion.data.component.feature.NodeFeaturizer attribute) (MolecularDiffusion.data.component.goflow_data.GoFlowDataModule attribute) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataModule attribute) (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataModule attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.syncogen.datamodule.SyncogenDataModule property) (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_apo2mol.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.PointCloudToDiffLinkerBatch attribute) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTask attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask attribute) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTask attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.IPDiffDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.KGDiffDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.Graph3DToLoQIAdapter attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.TabascoEGNNDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.TabascoEquiformerDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.TabascoGVPDiffusionTask attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) (MolecularDiffusion.runmodes.analyze.featurize.SSL3DFeaturizer attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_equiformer.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gcdm.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gfmdiff.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_painn.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_transformer.ModelTaskFactory attribute) atom_vocab_size (MolecularDiffusion.modules.tasks.ssl3d.MaskedAtomTypeObjective attribute) AtomCGREmbedding (class in MolecularDiffusion.modules.models.goflow.ops) AtomDiffusion (class in MolecularDiffusion.modules.models.chefnmr.diffusion) AtomFractionMetric (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) ATOMIC_LEVEL_GROUPS (in module MolecularDiffusion.runmodes.analyze.xtb_electronic) ATOMIC_NUMBERS (in module MolecularDiffusion.modules.tasks.diffusion_pmdm) atomic_numbers (MolecularDiffusion.modules.layers.atomic_data.AtomicData attribute) (MolecularDiffusion.modules.models.ditmc.graphs.LatentGraph attribute) atomic_numbers() (in module MolecularDiffusion.modules.models.en_diffusion) atomic_numbers_full (MolecularDiffusion.modules.layers.graph_module.GraphData attribute) ATOMIC_TYPES (in module MolecularDiffusion.modules.models.ditmc.graph_features) atomic_valence (in module MolecularDiffusion.utils.xyz2mol.converter) atomic_valence_electrons (in module MolecularDiffusion.utils.xyz2mol.converter) AtomicData (class in MolecularDiffusion.modules.layers.atomic_data) atomicdata_list_to_batch() (in module MolecularDiffusion.modules.layers.atomic_data) atomics_interpolant (MolecularDiffusion.modules.models.tabasco.flow_model.FlowMatchingModel attribute) atomics_interpolant_config (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.ModelTaskFactory attribute) atoms_to_batch() (in module MolecularDiffusion.runmodes.analyze.ssl3d_embed) AtomTypeDistribution (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) Atomwise3DOut (class in MolecularDiffusion.modules.models.goflow.outputs) att_mlp (MolecularDiffusion.modules.models.oareactdiff.leftnet.GCLMessage attribute) att_num_parity (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) attach_bonds() (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates method) attach_pharmacophores() (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates method) attempt_sanitize() (in module MolecularDiffusion.modules.models.tabasco.chem.utils) atten_layer (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) Attention (class in MolecularDiffusion.modules.layers.tabasco.attention) (class in MolecularDiffusion.modules.models.chefnmr.embedders) (class in MolecularDiffusion.modules.models.chefnmr.layers) attention (MolecularDiffusion.modules.layers.conv.GCL attribute) (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) (MolecularDiffusion.modules.layers.tabasco.attention.AttentionBlock attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.GCL attribute) (MolecularDiffusion.modules.models.difflinker.egnn.GCL attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.GCL attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.GCL attribute) (MolecularDiffusion.modules.models.ditmc.dit.DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.geoldm.egnn.GCL attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.GCL attribute) (MolecularDiffusion.modules.models.ligandiff.conv_layer.GVPMessagePassing attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) attention() (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer method) attention_layers (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) AttentionBlock (class in MolecularDiffusion.modules.layers.tabasco.attention) AttentionLayerO2TwoUpdateNodeGeneral (class in MolecularDiffusion.modules.models.apo2mol.uni_transformer) (class in MolecularDiffusion.modules.models.diffsmol.uni_transformer) (class in MolecularDiffusion.modules.models.kgdiff.uni_transformer) attn (MolecularDiffusion.modules.models.chefnmr.embedders.Attention attribute) (MolecularDiffusion.modules.models.chefnmr.embedders.AttnPoolToken attribute) (MolecularDiffusion.modules.models.chefnmr.layers.DiTBlock attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiTBlock attribute) attn1 (MolecularDiffusion.modules.models.pmdm.encoders.CrossAttentionBlock attribute) attn2 (MolecularDiffusion.modules.models.pmdm.encoders.CrossAttentionBlock attribute) attn2p (MolecularDiffusion.modules.models.pmdm.encoders.CrossAttentionBlock attribute) attn_activation (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) attn_alpha_channels (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) attn_block (MolecularDiffusion.modules.layers.tabasco.transformer.TransformerBlock attribute) attn_drop (MolecularDiffusion.modules.models.chefnmr.layers.Attention attribute) attn_dropout (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer attribute) attn_hidden_channels (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) attn_mpnn (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) attn_p (MolecularDiffusion.modules.models.pmdm.encoders.CrossAttentionBlock attribute) attn_proj (MolecularDiffusion.modules.models.syncogen.models.semla.CoordAttention attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EquivariantMLP attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.CoordAttention attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquivariantMLP attribute) attn_update() (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer method) attn_value_channels (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) AttnHeads2Vec (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) AttnPoolToken (class in MolecularDiffusion.modules.models.chefnmr.embedders) aug_rotation (MolecularDiffusion.modules.tasks.diffusion_nextmol.Graph3DBatchToNextMolAdapter attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) augment() (in module MolecularDiffusion.cli.data) augment_charge() (in module MolecularDiffusion.runmodes.data.augmentation) augment_distortion() (in module MolecularDiffusion.runmodes.data.augmentation) augment_noise (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) augment_rotation (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) augment_size() (in module MolecularDiffusion.runmodes.data.augmentation) augmentation_bool (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTaskFactory attribute) augmentations (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) autoencoder (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask attribute) autoencoder_ckpt (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTaskFactory attribute) av (in module MolecularDiffusion.utils.xyz2mol.converter) available_features() (MolecularDiffusion.data.component.feature.NodeFeaturizer class method) available_shapes() (in module MolecularDiffusion.utils.shape_measure) avg (MolecularDiffusion.modules.models.diffspectra.specformer_layers.moving_avg attribute) avg_aggregate_num (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.ScaledScatter attribute) avg_num_nodes (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2SymmetricTensorHead attribute) axis_angle_to_quaternion() (in module MolecularDiffusion.modules.models.apo2mol.residue_ops) axis_angle_to_rotation_matrix() (in module MolecularDiffusion.modules.models.apo2mol.residue_ops) B b (MolecularDiffusion.modules.layers.esen.nn.radial.PolynomialEnvelope attribute) (MolecularDiffusion.modules.models.ditmc.layers.GaussianRandomFourierFeatures attribute) b_sigma() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) backbone (MolecularDiffusion.modules.models.diffspectra.specformer.SpecFormer attribute) (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) backbone_kwargs (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) BACKBONE_NAMES (in module MolecularDiffusion.data.component.pmdm_data) BackboneInterface (class in MolecularDiffusion.modules.layers.esen.nn.utils) (class in MolecularDiffusion.modules.layers.graph_module) BAPNet (class in MolecularDiffusion.modules.models.apo2mol.pminet) (class in MolecularDiffusion.modules.models.ipdiff.bapnet) BASE_ATOM_VOCAB (in module MolecularDiffusion.data.component.dataset) base_block (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) BaseDynamics (class in MolecularDiffusion.modules.models.oareactdiff.dynamics) BaseFeaturizer (class in MolecularDiffusion.runmodes.analyze.featurize) BaseGVPAttLayer (class in MolecularDiffusion.modules.models.diffsmol.uni_transformer) BaseH2XAttLayer (class in MolecularDiffusion.modules.models.apo2mol.uni_transformer) (class in MolecularDiffusion.modules.models.kgdiff.uni_transformer) BaseModel (class in MolecularDiffusion.modules.models.shepherd_arch.ocp_compat) BaseNoiseSchedule (class in MolecularDiffusion.modules.models.tabasco.sample.noise_schedule) BaseSelfConditioningModule (class in MolecularDiffusion.modules.models.loqi.self_conditioning) BaseTimeFactor (class in MolecularDiffusion.modules.models.tabasco.flow.time_factor) BaseX2HAttLayer (class in MolecularDiffusion.modules.models.apo2mol.uni_transformer) (class in MolecularDiffusion.modules.models.kgdiff.uni_transformer) basic_fourier() (in module MolecularDiffusion.modules.layers.e3x.radial) basis() (in module MolecularDiffusion.modules.layers.e3x.radial) batch_full (MolecularDiffusion.modules.layers.graph_module.GraphData attribute) batch_hybrid_edge_connection() (in module MolecularDiffusion.modules.models.apo2mol.common) batch_id (MolecularDiffusion.core.meter.Meter attribute) batch_segments (MolecularDiffusion.modules.models.ditmc.graphs.LatentGraph attribute) batch_size (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.core.lightning_callbacks.generative_eval_callback.GenerativeEvalCallback attribute) (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataModule attribute) (MolecularDiffusion.data.component.diffdec_data.DiffDecDataModule attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataModule attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataModule attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataModule attribute) (MolecularDiffusion.data.component.goflow_data.GoFlowDataModule attribute) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataModule attribute) (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataModule attribute) (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule attribute) (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) (MolecularDiffusion.modules.models.syncogen.core.Diffusion property) (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) (MolecularDiffusion.modules.models.syncogen.datamodule.SyncogenDataModule attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecScaffoldGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenSizePrior attribute) (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.pocket_generator.PocketGenerator attribute) (MolecularDiffusion.runmodes.analyze.featurize.SSL3DFeaturizer attribute) (MolecularDiffusion.runmodes.generate.tasks_conformer.ConformerFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize.GCDMOptimizeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) batch_to_atomicdata_list() (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) batch_to_list() (in module MolecularDiffusion.modules.models.tabasco.data.utils) batch_xtb_electronic() (in module MolecularDiffusion.runmodes.analyze.xtb_electronic) batchwise_l2_loss() (in module MolecularDiffusion.modules.models.etflow.flow) bb_indices (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) bb_indices_to_onehot() (in module MolecularDiffusion.modules.models.syncogen.api.ops.graph_ops) bb_onehot (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) bb_onehot_dim (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) bb_onehot_to_indices() (in module MolecularDiffusion.modules.models.syncogen.api.ops.graph_ops) bb_pad (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph attribute) BBRxnGraph (class in MolecularDiffusion.modules.models.syncogen.api.graph.graph) BesselRBFLayer (class in MolecularDiffusion.modules.models.painn_backbone) beta (MolecularDiffusion.callbacks.train_helper.EMA attribute) (MolecularDiffusion.modules.models.apo2mol.common.Swish attribute) beta_0 (MolecularDiffusion.modules.models.jodo.noise_schedule.NoiseScheduleVP attribute) (MolecularDiffusion.modules.models.nextmol.scheduler.NoiseScheduleVPV2 attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) beta_1 (MolecularDiffusion.modules.models.jodo.noise_schedule.NoiseScheduleVP attribute) (MolecularDiffusion.modules.models.nextmol.scheduler.NoiseScheduleVPV2 attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) beta_max (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) beta_min (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory attribute) betas (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) (MolecularDiffusion.modules.models.reactot.schedule.SBSchedule attribute), [1] (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) bias (MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf.GaussianRadialBasisLayer attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_LinearV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf.GaussianRadialBasisLayer attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_LinearV2 attribute) (MolecularDiffusion.modules.layers.esen.nn.so3_layers.SO3_Linear attribute) bias_init (MolecularDiffusion.modules.models.goflow.ops.Dense attribute) (MolecularDiffusion.modules.models.goflow.outputs.SNNDense attribute) (MolecularDiffusion.modules.models.ligandiff.egnn.DenseLayer attribute) biases (MolecularDiffusion.modules.models.syncogen.models.layers.GraphNorm attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.SetNorm attribute) bin_peaks() (in module MolecularDiffusion.modules.models.chefnmr.unknown) bin_width (MolecularDiffusion.modules.models.tabasco.flow.utils.HistogramTimeDistribution attribute) bin_window (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeNodeDistribution attribute) binary (MolecularDiffusion.modules.models.chefnmr.unknown.Channel attribute), [1] bins (MolecularDiffusion.utils.geom_analyzer.Histogram_cont attribute) (MolecularDiffusion.utils.geom_analyzer.Histogram_discrete attribute) block (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2SymmetricTensorHead attribute) block_calc (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) blocks (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.chefnmr.score_models.DiffusionModuleTransformer attribute) (MolecularDiffusion.modules.models.diffsmol.shape_ae.DecoderInner attribute) (MolecularDiffusion.modules.models.diffsmol.shape_ae.VNDGCNNEncoder attribute) (MolecularDiffusion.modules.models.diffsmol.shape_ae.VNResnetEncoder attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) BO2mol() (in module MolecularDiffusion.utils.xyz2mol.converter) BO_is_OK() (in module MolecularDiffusion.utils.xyz2mol.converter) BOHR_DEBYE (in module MolecularDiffusion.runmodes.analyze.xtb_electronic) BOND_CLASSES (in module MolecularDiffusion.modules.models.nextmol.featurize) bond_collate (MolecularDiffusion.runmodes.train.data.DataModule attribute) bond_default() (in module MolecularDiffusion.data.component.feature) bond_dict (in module MolecularDiffusion.utils.geom_analyzer) (in module MolecularDiffusion.utils.smilify) bond_emb (MolecularDiffusion.modules.models.goflow.ops.EdgeCGREmbedding attribute) bond_feat_dim (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.BaseModel attribute) bond_index (MolecularDiffusion.data.component.reaction_data.ReactionSide attribute), [1] bond_length() (in module MolecularDiffusion.data.component.feature) BOND_MARGINS (in module MolecularDiffusion.modules.models.diffsmol.uni_transformer) bond_matrix (MolecularDiffusion.utils.smilify.Molecule attribute) BOND_ORDER_TO_CLASS (in module MolecularDiffusion.data.component.graph3d_dataset) bond_pretrain() (in module MolecularDiffusion.data.component.feature) bond_property_prediction() (in module MolecularDiffusion.data.component.feature) bond_refine (MolecularDiffusion.modules.models.syncogen.models.semla.EquiInvDynamics attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiInvDynamics attribute) BOND_TOLERANCE (in module MolecularDiffusion.modules.tasks.diffusion_pmdm) bond_type (MolecularDiffusion.data.component.reaction_data.ReactionSide attribute), [1] bond_type_counts (MolecularDiffusion.data.component.graph3d_dataset.Graph3DStats attribute) BOND_TYPE_MAP (in module MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly) bond_type_marginal() (MolecularDiffusion.data.component.graph3d_dataset.Graph3DStats method) bond_type_to_symbol() (in module MolecularDiffusion.utils.geom_stability) BOND_TYPES (in module MolecularDiffusion.modules.models.goflow.cgr_graph_utils) bond_types_x1 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) BOND_VOCAB (in module MolecularDiffusion.data.component.graph3d_dataset) BondLengthLoss (class in MolecularDiffusion.modules.models.syncogen.diffusion.loss.bond_length) BondRefine (class in MolecularDiffusion.modules.models.syncogen.models.semla) (class in MolecularDiffusion.modules.models.syncogen.models.semla_pharm) bonds (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates attribute) bonds1 (in module MolecularDiffusion.utils.geom_analyzer) bonds2 (in module MolecularDiffusion.utils.geom_analyzer) bonds3 (in module MolecularDiffusion.utils.geom_analyzer) BONDS_AROMATIC (in module MolecularDiffusion.modules.models.diffsmol.bond_tables) BONDS_DOUBLE (in module MolecularDiffusion.modules.models.diffsmol.bond_tables) bonds_mask (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates attribute) BONDS_SINGLE (in module MolecularDiffusion.modules.models.diffsmol.bond_tables) BONDS_TRIPLE (in module MolecularDiffusion.modules.models.diffsmol.bond_tables) bottleneck (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) BOX_BUFFER (in module MolecularDiffusion.runmodes.analyze.docking) box_for() (in module MolecularDiffusion.runmodes.analyze.docking) broadcast_equivariant_multiplication() (in module MolecularDiffusion.modules.layers.e3x.features) BrownianBridgeNoise (class in MolecularDiffusion.modules.models.syncogen.diffusion.noise.brownian) build() (MolecularDiffusion.modules.tasks.diffusion_apo2mol.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_ditmc.Graph3DBatchToDiTMCAdapter method) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_etflow.Graph3DBatchToETFlowAdapter method) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_goflow.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_pmdm.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative method) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory method) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory method) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory method) (MolecularDiffusion.runmodes.train.tasks_equiformer.ModelTaskFactory method) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory method) (MolecularDiffusion.runmodes.train.tasks_gcdm.ModelTaskFactory method) (MolecularDiffusion.runmodes.train.tasks_gfmdiff.ModelTaskFactory method) (MolecularDiffusion.runmodes.train.tasks_painn.ModelTaskFactory method) (MolecularDiffusion.runmodes.train.tasks_transformer.ModelTaskFactory method) build_bond_length_tensors() (in module MolecularDiffusion.modules.models.diffsmol.uni_transformer) build_cat_temp_schedule() (MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field.CTMCVectorField static method) build_cond_embeddings() (in module MolecularDiffusion.modules.models.ditmc.embedding) build_continuous_inv_temp_func() (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField static method) build_default_noise_schedule() (in module MolecularDiffusion.data.component.pharmacophore) build_diffsmol_bond_tensors() (in module MolecularDiffusion.modules.models.diffsmol.uni_transformer) build_edge_idxs() (in module MolecularDiffusion.modules.models.flowmol.graph_utils) build_edges() (MolecularDiffusion.modules.tasks.diffusion_loqi.Graph3DToLoQIAdapter method) build_encoders_decoders() (MolecularDiffusion.modules.models.oareactdiff.dynamics.BaseDynamics method) build_extra_node_template() (in module MolecularDiffusion.utils.geom_constraint) build_head() (MolecularDiffusion.modules.tasks.ssl3d.CoordDenoiseObjective method) (MolecularDiffusion.modules.tasks.ssl3d.MaskedAtomTypeObjective method) (MolecularDiffusion.modules.tasks.ssl3d.PairwiseDistObjective method) (MolecularDiffusion.modules.tasks.ssl3d.SSL3DObjective method) build_interpolant() (in module MolecularDiffusion.modules.models.loqi.interpolant) build_molecule() (in module MolecularDiffusion.modules.models.syncogen.utils.rdkit) (in module MolecularDiffusion.utils.geom_analyzer) build_molecules_from_graphs() (in module MolecularDiffusion.modules.models.syncogen.utils.rdkit) build_prior() (in module MolecularDiffusion.modules.models.ditmc.priors) build_rdkit() (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph method) build_rdkit_mol() (in module MolecularDiffusion.data.component.graph3d_dataset) build_scheduler() (in module MolecularDiffusion.modules.models.loqi.interpolant) build_variant() (in module MolecularDiffusion.modules.models.ditmc.build) build_xae_molecule() (in module MolecularDiffusion.utils.geom_analyzer) BUILDING_BLOCKS (in module MolecularDiffusion.modules.models.syncogen.constants.constants) building_blocks (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) BUILDING_BLOCKS_IDX_TO_SMI (in module MolecularDiffusion.modules.models.syncogen.constants.constants) BUILDING_BLOCKS_SMI_TO_IDX (in module MolecularDiffusion.modules.models.syncogen.constants.constants) BuildingBlock (class in MolecularDiffusion.modules.models.syncogen.api.graph.building_block) bundle_cmd() (in module MolecularDiffusion.cli.zoo) C c (MolecularDiffusion.modules.layers.esen.nn.radial.PolynomialEnvelope attribute) c_in() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) c_sigma() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) c_to_e (MolecularDiffusion.modules.models.syncogen.models.layers.CtoX attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.Ctoy attribute) c_tokenizer (MolecularDiffusion.modules.models.chefnmr.embedders.NMRSpectraEmbedder attribute) ca_pocket() (in module MolecularDiffusion.data.component.diffint_prep) cache (MolecularDiffusion.modules.tasks.diffusion_ditmc.Graph3DBatchToDiTMCAdapter attribute) (MolecularDiffusion.modules.tasks.diffusion_etflow.Graph3DBatchToETFlowAdapter attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.Graph3DBatchToNextMolAdapter attribute) cache_size (MolecularDiffusion.modules.models.etflow.flow.HarmonicSampler attribute) calc_distances() (in module MolecularDiffusion.modules.models.syncogen.models.semla_utils) calc_energy() (in module MolecularDiffusion.modules.models.syncogen.utils.rdkit) CalcSpherePoints() (in module MolecularDiffusion.modules.models.shepherd_arch.ocp_compat) calculate_bonds() (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph method) calculate_fan_in() (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.TensorProductRescale method) calculate_props() (in module MolecularDiffusion.runmodes.data.preparation) calculate_quat_loss() (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D method) calculate_sa_score() (in module MolecularDiffusion.runmodes.data.preparation) calculate_score() (MolecularDiffusion.modules.models.tabasco.flow.interpolate.SDEMetricInterpolant method) calculate_tm_score() (in module MolecularDiffusion.modules.models.apo2mol.score_model) calculateScore() (in module MolecularDiffusion.utils.sascore) call (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) campbell_step() (MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field.CTMCVectorField static method) Candidate (class in MolecularDiffusion.modules.tasks.elucidation_generator) CANONICAL_FEAT_ORDER (in module MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d) canonical_feat_order (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) canonical_smiles() (in module MolecularDiffusion.modules.tasks.diffusion_chefnmr) capture_rdkit_log() (in module MolecularDiffusion.utils.io) CaptureStdIO (class in MolecularDiffusion.utils.io) cartesian_permutation() (in module MolecularDiffusion.modules.layers.e3x.so3) cartesian_permutation_for_degree() (in module MolecularDiffusion.modules.layers.e3x.so3) cat() (in module MolecularDiffusion.utils.comm) (in module MolecularDiffusion.utils.torch) cat_temp_decay_a (MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field.CTMCVectorField attribute) cat_temp_decay_max (MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field.CTMCVectorField attribute) cat_temp_func (MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field.CTMCVectorField attribute) cat_temperature_schedule (MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field.CTMCVectorField attribute) categorical (MolecularDiffusion.modules.models.tabasco.flow.utils.HistogramTimeDistribution attribute) categorical_kl() (in module MolecularDiffusion.modules.models.apo2mol.score_model) (in module MolecularDiffusion.modules.models.diffsmol.score_model) (in module MolecularDiffusion.modules.models.kgdiff.score_model) ccosine_schedule() (in module MolecularDiffusion.modules.models.oareactdiff.schedule) cdf_standard_gaussian() (in module MolecularDiffusion.modules.models.en_diffusion) (in module MolecularDiffusion.modules.models.oareactdiff.graph_tools) (MolecularDiffusion.modules.models.difflinker.edm.EDM static method) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM static method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion static method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM static method) ce_loss (MolecularDiffusion.modules.models.tabasco.flow.interpolate.DiscreteInterpolant attribute) cell (MolecularDiffusion.modules.layers.atomic_data.AtomicData attribute) cell_offsets (MolecularDiffusion.modules.layers.atomic_data.AtomicData attribute) (MolecularDiffusion.modules.layers.graph_module.GraphData attribute) center (MolecularDiffusion.data.component.diffint_data.DiffIntDataModule attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataset attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataModule attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataset attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataModule attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataset attribute) (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffTS1xDataset attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataModule attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataset attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.RBF_Emb attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDPocketGenerator attribute) center() (in module MolecularDiffusion.modules.models.etflow.torchmd) (in module MolecularDiffusion.modules.models.syncogen.api.ops.coordinates_ops) (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates method) center_coords (MolecularDiffusion.runmodes.train.data.DataModule attribute) center_data() (in module MolecularDiffusion.modules.models.ditmc.flow_matching) center_of_mass (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) center_of_mass() (in module MolecularDiffusion.modules.models.etflow.flow) center_pos() (in module MolecularDiffusion.modules.models.apo2mol.score_model) (in module MolecularDiffusion.modules.models.kgdiff.score_model) center_pos_lp() (in module MolecularDiffusion.modules.models.pmdm.common) center_pos_mode (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) center_pos_pl() (in module MolecularDiffusion.modules.models.pmdm.common) center_random_augmentation() (in module MolecularDiffusion.modules.models.chefnmr.utils) centered (MolecularDiffusion.modules.models.tabasco.flow.interpolate.CenteredMetricInterpolant attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) centered_normal_prior_batched_graph() (in module MolecularDiffusion.modules.models.flowmol.priors) (in module MolecularDiffusion.modules.models.flowmol_graph3d.priors) CenteredMetricInterpolant (class in MolecularDiffusion.modules.models.tabasco.flow.interpolate) centering (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.models.difflinker.egnn.Dynamics attribute) centers (MolecularDiffusion.modules.layers.gfmdiff.blocks.RBF attribute) centralize() (in module MolecularDiffusion.modules.models.gcdm.gcp_utils) CFConvS2V (class in MolecularDiffusion.modules.models.oareactdiff.leftnet) cfg_file (MolecularDiffusion.modules.models.tabasco.callbacks.posebusters.PoseBustersCallback attribute) cg_change_mat() (in module MolecularDiffusion.modules.layers.esen.nn.utils) change_mat (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2DecompositionEdgeBlock attribute) change_max_degree_or_type() (in module MolecularDiffusion.modules.layers.e3x.features) Channel (class in MolecularDiffusion.modules.models.chefnmr.unknown) charge (MolecularDiffusion.modules.layers.atomic_data.AtomicData attribute) charge_cmd() (in module MolecularDiffusion.cli.data) charge_counts (MolecularDiffusion.data.component.graph3d_dataset.Graph3DStats attribute) charge_is_OK() (in module MolecularDiffusion.utils.xyz2mol.converter) CHARGE_OFFSET (in module MolecularDiffusion.modules.tasks.diffusion_loqi) charge_offset (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.Graph3DToDGLAdapter attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) charge_range (MolecularDiffusion.data.component.graph3d_dataset.Graph3DStats property) charge_types_x1 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) charges (MolecularDiffusion.modules.models.midi.placeholder.Dims attribute) (MolecularDiffusion.modules.models.midi.placeholder.PlaceHolder attribute) charges_classes (MolecularDiffusion.modules.models.midi.noise_model.DiscreteUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.MarginalUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) charges_marginals (MolecularDiffusion.modules.models.midi.noise_model.DiscreteUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.MarginalUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) check_accessibility (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) check_chem_validity() (in module MolecularDiffusion.utils.geom_metrics) check_connected() (in module MolecularDiffusion.utils.geom_analyzer) (in module MolecularDiffusion.utils.smilify) check_consistency_bond_dictionaries() (in module MolecularDiffusion.utils.geom_analyzer) check_issues_norm_values() (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.oareactdiff.schedule.DiffSchedule method) check_mask_correct() (in module MolecularDiffusion.modules.models.jodo.utils) (in module MolecularDiffusion.utils.geom_utils) check_neutrality() (in module MolecularDiffusion.runmodes.analyze.xtb_optimization) (in module MolecularDiffusion.utils.geom_metrics) check_quality() (in module MolecularDiffusion.utils.geom_analyzer) check_sanity_xh() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) check_sorted() (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.ConcatIrrepsTensor method) check_stability() (in module MolecularDiffusion.utils.geom_analyzer), [1] check_symmetric() (in module MolecularDiffusion.utils.geom_analyzer) (in module MolecularDiffusion.utils.smilify) check_validity_v0() (in module MolecularDiffusion.utils.geom_metrics) check_validity_v1() (in module MolecularDiffusion.utils.geom_metrics) check_vdw_radii() (in module MolecularDiffusion.modules.models.diffsmol.shape_utils) check_xyz() (in module MolecularDiffusion.runmodes.analyze.xtb_optimization) checkpoint_path (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) CHEFNMR_ATOM_DECODER (in module MolecularDiffusion.modules.tasks.diffusion_chefnmr) ChefNMRElucidationGenerator (class in MolecularDiffusion.modules.tasks.diffusion_chefnmr) ChefNMRElucidationTask (class in MolecularDiffusion.modules.tasks.diffusion_chefnmr) ChefNMRRecord (class in MolecularDiffusion.modules.tasks.diffusion_chefnmr) ChefNMRSidecar (class in MolecularDiffusion.modules.models.chefnmr.sidecar) ChefNMRTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_chefnmr) Chem (in module MolecularDiffusion.data.component.dataset) (in module MolecularDiffusion.data.component.graph3d_dataset) (in module MolecularDiffusion.data.component.pharmacophore) (in module MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d) (in module MolecularDiffusion.modules.tasks.diffusion_jodo) (in module MolecularDiffusion.modules.tasks.diffusion_midi) (in module MolecularDiffusion.runmodes.data.ase_ops) (in module MolecularDiffusion.runmodes.data.featurization) (in module MolecularDiffusion.runmodes.data.preparation) (in module MolecularDiffusion.utils.geom_metrics) chemical_validity() (in module MolecularDiffusion.modules.tasks.metrics) ChgSpinDatasetEmbedding (class in MolecularDiffusion.modules.layers.esen.nn.embedding) CHI_BOND_DICTS (in module MolecularDiffusion.modules.models.apo2mol.residue_ops) CHI_BONDS (in module MolecularDiffusion.modules.models.loqi.graph_utils) CHI_ORDER (in module MolecularDiffusion.modules.models.apo2mol.residue_ops) chiral_stereo_check() (in module MolecularDiffusion.utils.xyz2mol.converter) chirality_sign() (in module MolecularDiffusion.modules.models.etflow.features) chkpt_path (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_equiformer.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gcdm.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gfmdiff.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_painn.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_transformer.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) chunk_dir (MolecularDiffusion.data.component.dataset.LazyChunkedDataset attribute) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) chunk_paths (MolecularDiffusion.data.component.dataset.LazyChunkedDataset attribute) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset attribute) chunk_size (MolecularDiffusion.runmodes.train.data.DataModule attribute) chunk_sizes (MolecularDiffusion.data.component.dataset.LazyChunkedDataset attribute) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset attribute) clamp_t (MolecularDiffusion.modules.models.flowmol.interpolant_scheduler.InterpolantScheduler attribute) clamps (MolecularDiffusion.modules.models.loqi.self_conditioning.BaseSelfConditioningModule attribute) CLASS_AC (in module MolecularDiffusion.data.component.diffint_prep) CLASS_DD (in module MolecularDiffusion.data.component.diffint_prep) clean_charges() (in module MolecularDiffusion.utils.xyz2mol.converter) clean_condition_tensor (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) clean_prediction() (MolecularDiffusion.modules.models.ditmc.flow_matching.FlowMatching method) clear() (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator method) clebsch_gordan() (in module MolecularDiffusion.modules.layers.e3x.so3) cli() (in module MolecularDiffusion.cli.main) clip (MolecularDiffusion.modules.models.loqi.interpolant.CosineSchedule attribute) clip_denoise (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask attribute) clip_during_norm (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) clip_noise_schedule() (in module MolecularDiffusion.modules.models.difflinker.noise) (in module MolecularDiffusion.modules.models.diffpharma.conditional_ddpm) (in module MolecularDiffusion.modules.models.diffsbdd.en_diffusion) (in module MolecularDiffusion.modules.models.en_diffusion) (in module MolecularDiffusion.modules.models.ligandiff.noise) (in module MolecularDiffusion.modules.models.noisemodel) (in module MolecularDiffusion.modules.models.oareactdiff.schedule) clip_norm() (in module MolecularDiffusion.modules.models.pmdm.common) clip_t (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant attribute) clip_value (MolecularDiffusion.core.engine.Engine attribute) clipped_policy_gradient_objective() (in module MolecularDiffusion.modules.layers.functional) clipping_gradient (MolecularDiffusion.core.engine.Engine attribute) clone() (in module MolecularDiffusion.utils.torch) (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Embedding method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Embedding method) (MolecularDiffusion.modules.models.gcdm.gcp_utils.ScalarVector method) (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates method) (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph method) cls (MolecularDiffusion.modules.models.chefnmr.embedders.AttnPoolToken attribute) CN_OCT (in module MolecularDiffusion.modules.models.ligandiff_multi.utils) Cnflows (class in MolecularDiffusion.modules.models.equifm.cnflows) cnflows (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTask attribute) cnmr_dim (MolecularDiffusion.modules.models.chefnmr.embedders.NMRSpectraEmbedder attribute) coef (MolecularDiffusion.modules.models.syncogen.diffusion.loss.base.LossBase attribute) coeff (MolecularDiffusion.modules.layers.esen.nn.radial.GaussianSmearing attribute) (MolecularDiffusion.modules.models.apo2mol.common.GaussianSmearing attribute) (MolecularDiffusion.modules.models.diffsmol.common.GaussianSmearing attribute) (MolecularDiffusion.modules.models.kgdiff.common.GaussianSmearing attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.GaussianSmearing attribute) (MolecularDiffusion.modules.models.pmdm.common.GaussianSmearing attribute) (MolecularDiffusion.modules.models.shepherd_arch.egnn.GaussianSmearing attribute) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.GaussianSmearing attribute) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.LinearSigmoidSmearing attribute) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.SigmoidSmearing attribute) coefficient_idx() (MolecularDiffusion.modules.layers.equiformer_v2.so3.CoefficientMappingModule method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.CoefficientMappingModule method) (MolecularDiffusion.modules.layers.esen.common.so3.CoefficientMapping method) CoefficientMapping (class in MolecularDiffusion.modules.layers.esen.common.so3) CoefficientMappingModule (class in MolecularDiffusion.modules.layers.equiformer_v2.so3) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.so3) collapse() (MolecularDiffusion.modules.models.midi.placeholder.PlaceHolder method) collate() (MolecularDiffusion.modules.tasks.diffusion_nextmol.Graph3DBatchToNextMolAdapter method) collate_fn (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataModule attribute) (MolecularDiffusion.data.component.diffdec_data.DiffDecDataModule attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataModule attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataModule attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataModule attribute) (MolecularDiffusion.data.component.goflow_data.GoFlowDataModule attribute) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataModule attribute) (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataModule attribute) (MolecularDiffusion.modules.models.syncogen.datamodule.SyncogenDataModule property) collected_params (MolecularDiffusion.modules.models.syncogen.models.ema.ExponentialMovingAverage attribute) color_pcd_with_electrostatics() (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) CoM (MolecularDiffusion.modules.models.diffspectra.dmt.DMT attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.Cond_DGT_concat attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.DGT_concat attribute) com (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) com() (in module MolecularDiffusion.modules.models.oareactdiff.leftnet) com_free (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousDiffusionInterpolant attribute) (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant attribute) comb_input_dim (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) combine (MolecularDiffusion.modules.models.etflow.torchmd.NeighborEmbedding attribute) (MolecularDiffusion.modules.models.goflow.ops.NodeInit attribute) compact (MolecularDiffusion.runmodes.train.data.DataModule attribute) compare() (in module MolecularDiffusion.runmodes.analyze.similarity3d) compare_graph_topology() (in module MolecularDiffusion.utils.geom_metrics) compare_stereo() (in module MolecularDiffusion.runmodes.analyze.conformer_metrics) COMPATIBILITY (in module MolecularDiffusion.modules.models.syncogen.constants.constants) compatibility_masks (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) compile_cmd() (in module MolecularDiffusion.cli.data) compile_to_asedb() (in module MolecularDiffusion.runmodes.data.preparation) complex_from_files() (in module MolecularDiffusion.data.component.diffint_prep) (in module MolecularDiffusion.data.component.diffpharma_prep) complex_idx() (MolecularDiffusion.modules.layers.equiformer_v2.so3.CoefficientMappingModule method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.CoefficientMappingModule method) (MolecularDiffusion.modules.layers.esen.common.so3.CoefficientMapping method) complex_index (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecScaffoldGenerator attribute) ComplexesGraph (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet attribute) compose_context() (in module MolecularDiffusion.modules.models.apo2mol.common) (in module MolecularDiffusion.modules.models.kgdiff.common) compute() (in module MolecularDiffusion.runmodes.analyze.druglike) (MolecularDiffusion.modules.models.tabasco.utils.metrics.AtomFractionMetric method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.AtomTypeDistribution method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularConnectivity method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularDiversity method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularLipinski method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularLogP method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularNovelty method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularQEDValue method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularUniqueness method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularValidity method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.PoseBustersValidity method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.PoseCheckStrainEnergy method) compute_all_metrics() (in module MolecularDiffusion.runmodes.analyze.compare_to_optimized) compute_alphas() (MolecularDiffusion.modules.models.loqi.interpolant.CosineSchedule method) (MolecularDiffusion.modules.models.loqi.interpolant.LinearSchedule method) compute_atom_type_accuracy() (in module MolecularDiffusion.utils.geom_utils) compute_batched_over0_posterior_distribution() (in module MolecularDiffusion.modules.models.midi.diffusion_utils) compute_bond_angles_diff() (in module MolecularDiffusion.utils.geom_stability) compute_bond_lengths_diff() (in module MolecularDiffusion.utils.geom_stability) compute_compatibility_masks() (in module MolecularDiffusion.modules.models.syncogen.api.ops.graph_ops) compute_conformer_metrics() (in module MolecularDiffusion.runmodes.analyze.conformer_metrics) compute_coord_rmsd() (in module MolecularDiffusion.runmodes.analyze.compare_to_optimized) compute_coords() (MolecularDiffusion.modules.models.syncogen.diffusion.loss.base.LossList method) compute_dataset_stats() (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory method) compute_differences() (in module MolecularDiffusion.utils.geom_stability) compute_drug_likeness() (in module MolecularDiffusion.utils.geom_metrics) compute_error() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) compute_error_pyG() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) compute_esp_similarity() (in module MolecularDiffusion.utils.geom_metrics) compute_every (MolecularDiffusion.modules.models.tabasco.callbacks.molecule_metrics.MoleculeMetricsCallback attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.posebusters.PoseBustersCallback attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.save_molecules.SaveGeneratedMolsCallback attribute) compute_frag_index() (MolecularDiffusion.modules.models.oareactdiff.dynamics.EGNNDynamics static method) compute_gaussian_product_coef() (in module MolecularDiffusion.modules.models.reactot.schedule) compute_geom() (MolecularDiffusion.data.component.feature.NodeFeaturizer method) compute_graph() (MolecularDiffusion.modules.models.syncogen.diffusion.loss.base.LossList method) compute_label() (MolecularDiffusion.modules.models.reactot.en_sb.EnSB method) compute_loss() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.bond_length.BondLengthLoss method) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.mse.MSELoss method) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.pairwise_distance.PairwiseDistanceLoss method) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.smooth_lddt.SmoothLDDTLoss method) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.CenteredMetricInterpolant method) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.DiscreteInterpolant method) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.Interpolant method) (MolecularDiffusion.modules.tasks.ssl3d.CoordDenoiseObjective method) (MolecularDiffusion.modules.tasks.ssl3d.MaskedAtomTypeObjective method) (MolecularDiffusion.modules.tasks.ssl3d.PairwiseDistObjective method) (MolecularDiffusion.modules.tasks.ssl3d.SSL3DObjective method) compute_loss_distillation() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) compute_loss_per_graph() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) compute_loss_pyG() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) compute_md5() (in module MolecularDiffusion.utils.file) compute_mean_mad_from_dataloader() (in module MolecularDiffusion.utils.diffusion_utils) compute_mmff_energy_drop() (in module MolecularDiffusion.utils.geom_stability) compute_mol_esp_values() (in module MolecularDiffusion.utils.geom_metrics) compute_mol_pharmacophores() (in module MolecularDiffusion.utils.geom_metrics) compute_mol_surface_pts() (in module MolecularDiffusion.utils.geom_metrics) compute_molecules_stability() (in module MolecularDiffusion.utils.geom_stability) compute_molecules_stability_from_graph() (in module MolecularDiffusion.utils.geom_stability) compute_moment_of_inertia() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca) compute_moment_of_inertia_np() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca_np) compute_neighbors() (in module MolecularDiffusion.modules.layers.graph_module) compute_ohe() (MolecularDiffusion.data.component.feature.NodeFeaturizer method) compute_pharm_similarity() (in module MolecularDiffusion.utils.geom_metrics) compute_pred_x0() (MolecularDiffusion.modules.models.reactot.en_sb.EnSB method) compute_principal_moments_of_interia() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca) compute_principal_moments_of_interia_np() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca_np) compute_reconstruction_error() (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE method) compute_rmsd() (in module MolecularDiffusion.utils.geom_stability) (in module MolecularDiffusion.utils.geom_utils) compute_scaled_err() (in module MolecularDiffusion.modules.models.reactot.en_sb) compute_shape_similarity() (in module MolecularDiffusion.utils.geom_metrics) compute_statistics() (in module MolecularDiffusion.utils.geom_stability) compute_tensor_fans_and_mask() (in module MolecularDiffusion.modules.layers.e3x.initializers) compute_torsion_angles_diff() (in module MolecularDiffusion.utils.geom_stability) compute_v_Lt() (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D method) compute_velocity() (MolecularDiffusion.modules.models.syncogen.diffusion.sampling.integrators.euler.EulerIntegrator method) compute_x1 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) compute_x2 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) compute_x3 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) compute_x4 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) compute_x_pred() (MolecularDiffusion.modules.models.difflinker.edm.EDM method) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion method) compute_xtb_electronic() (in module MolecularDiffusion.runmodes.analyze.xtb_electronic) concat() (MolecularDiffusion.modules.models.gcdm.gcp_utils.ScalarVector method) concat_combine_input (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) concat_indices (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer attribute) (MolecularDiffusion.modules.models.tabasco_egnn.egnn_backbone.EGNNBackbone attribute) (MolecularDiffusion.modules.models.tabasco_equiformer.equiformer_backbone.EquiformerV2TabascoBackbone attribute) (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone attribute) ConcatIrrepsTensor (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) cond (MolecularDiffusion.modules.models.chefnmr.sidecar.ChefNMRSidecar attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRRecord attribute) Cond_DGT_concat (class in MolecularDiffusion.modules.models.jodo.mol_gnn) cond_dim (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.chefnmr.sidecar.ChefNMRSidecar property) (MolecularDiffusion.modules.models.ipdiff.score_model.IPDiffScorePosNet3D attribute) (MolecularDiffusion.modules.tasks.diffusion_apo2mol.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.ModelTaskFactory attribute) cond_encoder (MolecularDiffusion.modules.models.diffspectra.dmt.DMT attribute) cond_flag (MolecularDiffusion.modules.models.apo2mol.attn.RetAugmentationLinearAttention attribute) cond_lin (MolecularDiffusion.modules.models.diffspectra.dmt.DMT attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.Cond_DGT_concat attribute) cond_mask_prob (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) cond_mlp (MolecularDiffusion.modules.models.jodo.mol_gnn.Cond_DGT_concat attribute) cond_norm (MolecularDiffusion.modules.models.ditmc.dit.DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.readout.EquivariantReadout attribute) cond_path (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) cond_scaling_edges (MolecularDiffusion.modules.models.ditmc.graphs.LatentGraph attribute) cond_scaling_nodes (MolecularDiffusion.modules.models.ditmc.graphs.LatentGraph attribute) cond_time (MolecularDiffusion.modules.models.diffspectra.dmt.DMT attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) CondCoorsNorm (class in MolecularDiffusion.modules.models.jodo.layers) CondEquiUpdate (class in MolecularDiffusion.modules.models.jodo.mol_gnn) CondGaussianLayer (class in MolecularDiffusion.modules.models.jodo.layers) CondGraph (class in MolecularDiffusion.modules.models.ditmc.graphs) condition (MolecularDiffusion.modules.models.chefnmr.score_models.DiffusionModuleTransformer attribute) (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.TabascoEGNNDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.TabascoEquiformerDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.TabascoGVPDiffusionTask attribute) condition_adapters (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer attribute) condition_configs (MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize.GCDMOptimizeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) condition_names (MolecularDiffusion.modules.tasks.diffusion_apo2mol.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_equiformer.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gcdm.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gfmdiff.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_painn.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_transformer.ModelTaskFactory attribute) condition_nf (MolecularDiffusion.modules.models.oareactdiff.dynamics.BaseDynamics attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) condition_on_context (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) condition_on_time (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) condition_tensor (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) condition_time (MolecularDiffusion.modules.models.difflinker.egnn.Dynamics attribute) (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.diffsbdd.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.egt.EGT_dynamics attribute) (MolecularDiffusion.modules.models.equiformer_v2_dynamics.EquiformerV2_dynamics attribute) (MolecularDiffusion.modules.models.esen.eSEN_dynamics attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_dynamics_QM9 attribute) (MolecularDiffusion.modules.models.oareactdiff.dynamics.BaseDynamics attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) condition_type (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) conditional_generation() (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory method) conditional_grad() (in module MolecularDiffusion.modules.models.shepherd_arch.ocp_compat) ConditionalDDPM (class in MolecularDiffusion.modules.models.diffpharma.conditional_ddpm) (class in MolecularDiffusion.modules.models.diffsbdd.en_diffusion) conditioner (MolecularDiffusion.modules.models.ditmc.dit.GenerativeModel attribute) conditioning_bool (MolecularDiffusion.modules.models.ditmc.dit.GenerativeModel attribute) (MolecularDiffusion.modules.models.ditmc.flow_matching.FlowMatching attribute) conditioning_pool() (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask method) conf (MolecularDiffusion.modules.models.chefnmr.sidecar.ChefNMRSidecar attribute) conf_path (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) CONFIG (in module MolecularDiffusion.modules.models.kgdiff.atom_num_config) config (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) config_cmd() (in module MolecularDiffusion.cli.zoo) config_dict (MolecularDiffusion.runmodes.train.data.DatasetConfigDict attribute) Configurable (class in MolecularDiffusion.core.core) configure_gradient_clipping() (MolecularDiffusion.core.engine_lightning.EngineLightning method) configure_optimizers() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) ConformerFactory (class in MolecularDiffusion.runmodes.generate.tasks_conformer) conformers_path (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataset attribute) conformers_per_molecule (MolecularDiffusion.runmodes.generate.tasks_conformer.ConformerFactory attribute) CONNECTORS_KEY (in module MolecularDiffusion.utils.geom_constraint) constrain_edge_sampling (MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.base.DiscreteStrategyBase attribute) context_dim (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) context_mask_rate (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.TabascoEGNNDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.TabascoEquiformerDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.TabascoGVPDiffusionTask attribute) context_node_nf (MolecularDiffusion.modules.models.difflinker.egnn.Dynamics attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.egt.EGT_dynamics attribute) (MolecularDiffusion.modules.models.equiformer_v2_dynamics.EquiformerV2_dynamics attribute) (MolecularDiffusion.modules.models.esen.eSEN_dynamics attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_decoder_QM9 attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_dynamics_QM9 attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_encoder_QM9 attribute) (MolecularDiffusion.modules.models.gfmdiff.dynamics.GFMDiffDynamics attribute) (MolecularDiffusion.modules.models.painn_dynamics.PaiNNDynamics attribute) (MolecularDiffusion.modules.models.transformer_dynamics.TransformerDynamics attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_equiformer.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gcdm.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gfmdiff.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_painn.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_transformer.ModelTaskFactory attribute) CONTEXT_SETTINGS (in module MolecularDiffusion.cli.analyze) (in module MolecularDiffusion.cli.main) contiguous() (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) continuous_beta_0 (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) continuous_beta_1 (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) continuous_inv_temp_func (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) continuous_inv_temp_max (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) continuous_inv_temp_schedule (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) ContinuousDiffusionInterpolant (class in MolecularDiffusion.modules.models.loqi.interpolant) ContinuousFlowMatchingInterpolant (class in MolecularDiffusion.modules.models.loqi.interpolant) conv1 (MolecularDiffusion.modules.models.apo2mol.uni_transformer.SAGPoolNet attribute) conv_blocks (MolecularDiffusion.modules.models.chefnmr.embedders.SpectraTokenizerConv1D attribute) conv_c (MolecularDiffusion.modules.models.diffsmol.shape_ae.VNDGCNNEncoder attribute) conv_cfg (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPMessagePassing attribute) conv_layers (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone attribute) conv_pos (MolecularDiffusion.modules.models.diffsmol.shape_ae.VNDGCNNEncoder attribute) (MolecularDiffusion.modules.models.diffsmol.shape_ae.VNResnetEncoder attribute) convert_e3nn_to_equiformerv2() (in module MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) convert_equiformerv2_to_e3nn() (in module MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) convert_props_to_float() (in module MolecularDiffusion.runmodes.data.preparation) convs (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) convs_per_update (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone attribute) coor_update_clamp_value (MolecularDiffusion.modules.models.loqi.fn_model.XEGNNK attribute) Coord1dPosEncoding() (in module MolecularDiffusion.modules.models.diffspectra.specformer_layers) coord2cosine() (in module MolecularDiffusion.utils.geom_utils) coord2cross() (in module MolecularDiffusion.modules.models.diffpharma.egnn) (in module MolecularDiffusion.modules.models.diffsbdd.egnn) coord2diff() (in module MolecularDiffusion.modules.models.apo2mol.pminet) (in module MolecularDiffusion.modules.models.difflinker.egnn) (in module MolecularDiffusion.modules.models.diffpharma.egnn) (in module MolecularDiffusion.modules.models.diffsbdd.egnn) (in module MolecularDiffusion.modules.models.geoldm.egnn) (in module MolecularDiffusion.modules.models.ipdiff.bapnet) (in module MolecularDiffusion.modules.models.jodo.utils) (in module MolecularDiffusion.utils.geom_utils) coord2diff_adj() (in module MolecularDiffusion.modules.models.jodo.utils) coord2dist() (in module MolecularDiffusion.modules.models.jodo.utils) (in module MolecularDiffusion.modules.models.nextmol.dgt) coord2distfn() (in module MolecularDiffusion.modules.models.loqi.fn_model) Coord2dPosEncoding() (in module MolecularDiffusion.modules.models.diffspectra.specformer_layers) coord_attn (MolecularDiffusion.modules.models.syncogen.models.semla.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiMessagePassingLayer attribute) coord_emb (MolecularDiffusion.modules.models.loqi.fn_model.MegaFNV3Conf attribute) coord_file (MolecularDiffusion.runmodes.train.data.DataModule attribute) coord_head (MolecularDiffusion.modules.models.syncogen.models.semla.EquiInvDynamics attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiInvDynamics attribute) (MolecularDiffusion.modules.tasks.ssl3d.CoordDenoiseObjective attribute) coord_mask_value (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataset attribute) coord_mlp (MolecularDiffusion.modules.layers.conv.EquivariantUpdate attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.PosUpdate attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.CondEquiUpdate attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.MultiCondEquiUpdate attribute) coord_model() (MolecularDiffusion.modules.layers.conv.EquivariantUpdate method) (MolecularDiffusion.modules.models.apo2mol.pminet.EquivariantUpdate method) (MolecularDiffusion.modules.models.difflinker.egnn.EquivariantUpdate method) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantUpdate method) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantUpdate method) coord_norm (MolecularDiffusion.modules.models.jodo.mol_gnn.CondEquiUpdate attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.MultiCondEquiUpdate attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.BondRefine attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.CoordAttention attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EdgeMessages attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EquiInvDynamics attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.NodeFeedForward attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.BondRefine attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.CoordAttention attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EdgeMessages attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiInvDynamics attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.NodeFeedForward attribute) coord_pred (MolecularDiffusion.modules.models.loqi.fn_model.MegaFNV3Conf attribute) coord_proj (MolecularDiffusion.modules.models.syncogen.models.semla.CoordAttention attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EquiInvDynamics attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EquivariantMLP attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.CoordAttention attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiInvDynamics attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquivariantMLP attribute) coord_projection (MolecularDiffusion.modules.models.loqi.fn_model.XEGNNK attribute) coord_range (MolecularDiffusion.modules.layers.gfmdiff.blocks.PosUpdate attribute) coord_sites_from_geometry() (in module MolecularDiffusion.modules.models.ligandiff_multi.utils) CoordAttention (class in MolecularDiffusion.modules.models.syncogen.models.semla) (class in MolecularDiffusion.modules.models.syncogen.models.semla_pharm) CoordDenoiseObjective (class in MolecularDiffusion.modules.tasks.ssl3d) coordinate_mlp (MolecularDiffusion.modules.models.shepherd_arch.egnn.EGNN attribute) coordinate_transformation_when_training (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion attribute) Coordinates (class in MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates) CoordNorm (class in MolecularDiffusion.modules.models.syncogen.models.semla) (class in MolecularDiffusion.modules.models.syncogen.models.semla_pharm) coords (MolecularDiffusion.modules.tasks.elucidation_generator.Candidate attribute), [1] coords_interpolant (MolecularDiffusion.modules.models.tabasco.flow_model.FlowMatchingModel attribute) coords_interpolant_config (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.ModelTaskFactory attribute) coords_range (MolecularDiffusion.modules.layers.conv.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.EquivariantUpdate attribute) coords_range_layer (MolecularDiffusion.modules.layers.conv.EquivariantBlock attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.EquivariantBlock attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EGNN attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EGNN attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EGNN attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.EquivariantBlock attribute) COORDS_STD (in module MolecularDiffusion.modules.models.syncogen.constants.constants) coors_mlp (MolecularDiffusion.modules.models.pmdm.encoders.EGNNSparseLayer attribute) coors_norm (MolecularDiffusion.modules.models.pmdm.encoders.EGNNSparseLayer attribute) CoorsNorm (class in MolecularDiffusion.modules.models.jodo.layers) copy() (MolecularDiffusion.modules.models.midi.placeholder.PlaceHolder method) (MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly.RDKitMoleculeAssembly method) copy_to() (MolecularDiffusion.modules.models.syncogen.models.ema.ExponentialMovingAverage method) core (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask attribute) correct_edges() (in module MolecularDiffusion.runmodes.data.augmentation) (in module MolecularDiffusion.utils.geom_analyzer) (in module MolecularDiffusion.utils.geom_utils) (in module MolecularDiffusion.utils.molgraph_utils) corrupt (MolecularDiffusion.modules.tasks.diffusion_ldm.FlowMatchingInterpolant attribute) corrupt() (MolecularDiffusion.modules.tasks.ssl3d.CoordDenoiseObjective method) (MolecularDiffusion.modules.tasks.ssl3d.MaskedAtomTypeObjective method) (MolecularDiffusion.modules.tasks.ssl3d.PairwiseDistObjective method) (MolecularDiffusion.modules.tasks.ssl3d.SSL3DObjective method) corrupt_batch() (MolecularDiffusion.modules.tasks.diffusion_ldm.FlowMatchingInterpolant method) cosine_alpha_t() (MolecularDiffusion.modules.models.flowmol.interpolant_scheduler.InterpolantScheduler method) cosine_alpha_t_prime() (MolecularDiffusion.modules.models.flowmol.interpolant_scheduler.InterpolantScheduler method) cosine_beta_schedule() (in module MolecularDiffusion.modules.models.apo2mol.score_model) (in module MolecularDiffusion.modules.models.difflinker.noise) (in module MolecularDiffusion.modules.models.diffpharma.conditional_ddpm) (in module MolecularDiffusion.modules.models.diffsbdd.en_diffusion) (in module MolecularDiffusion.modules.models.diffsmol.score_model) (in module MolecularDiffusion.modules.models.en_diffusion) (in module MolecularDiffusion.modules.models.kgdiff.score_model) (in module MolecularDiffusion.modules.models.ligandiff.noise) (in module MolecularDiffusion.modules.models.oareactdiff.schedule) cosine_beta_schedule_discrete() (in module MolecularDiffusion.modules.models.midi.diffusion_utils) cosine_log_alpha_0 (MolecularDiffusion.modules.models.jodo.noise_schedule.NoiseScheduleVP attribute) (MolecularDiffusion.modules.models.nextmol.scheduler.NoiseScheduleVPV2 attribute) cosine_params (MolecularDiffusion.modules.models.flowmol.interpolant_scheduler.InterpolantScheduler attribute) cosine_s (MolecularDiffusion.modules.models.jodo.noise_schedule.NoiseScheduleVP attribute) (MolecularDiffusion.modules.models.nextmol.scheduler.NoiseScheduleVPV2 attribute) cosine_schedule() (in module MolecularDiffusion.modules.models.noisemodel) CosineCutoff (class in MolecularDiffusion.modules.models.etflow.torchmd) (class in MolecularDiffusion.modules.models.goflow.ops) CosineNoise (class in MolecularDiffusion.modules.models.syncogen.diffusion.noise.cosine) CosineSchedule (class in MolecularDiffusion.modules.models.loqi.interpolant) CosineSqrNoise (class in MolecularDiffusion.modules.models.syncogen.diffusion.noise.cosine) COULOMB_SCALING (in module MolecularDiffusion.utils.geom_metrics) (in module MolecularDiffusion.utils.shepherd_score.score.constants) (in module MolecularDiffusion.utils.shepherd_utils) count_atoms_from_xyz() (in module MolecularDiffusion.cli.predict) counter (MolecularDiffusion.modules.models.syncogen.data.dataloader.FaultTolerantDistributedSampler attribute) (MolecularDiffusion.modules.models.syncogen.data.dataloader.RandomFaultTolerantSampler attribute) cov_radius() (in module MolecularDiffusion.utils.smilify) covalent_radii (in module MolecularDiffusion.utils.geom_metrics) cpu() (in module MolecularDiffusion.utils.torch) (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) cpu_group (in module MolecularDiffusion.utils.comm) cpu_offload (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA attribute) create_mask() (in module MolecularDiffusion.modules.layers.gfmdiff.blocks) create_masked_graph() (in module MolecularDiffusion.modules.models.syncogen.api.ops.graph_ops) create_path() (MolecularDiffusion.modules.models.tabasco.flow.interpolate.CenteredMetricInterpolant method) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.DiscreteInterpolant method) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.Interpolant method) create_pyg_graph() (in module MolecularDiffusion.runmodes.data.augmentation) (in module MolecularDiffusion.utils.geom_analyzer) (in module MolecularDiffusion.utils.geom_utils) (in module MolecularDiffusion.utils.molgraph_utils) create_template() (in module MolecularDiffusion.data.component.diffdec_data) create_templates_for_rgroup_generation_single() (in module MolecularDiffusion.data.component.diffdec_data) create_zero_vector() (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCP method) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCP2 method) criterion (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) cross_attention (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) cross_product_mlp (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EquivariantUpdate attribute) CrossAdaLNAttention (class in MolecularDiffusion.modules.layers.tabasco.attention) CrossAttentionBlock (class in MolecularDiffusion.modules.models.pmdm.encoders) csd_embedding() (MolecularDiffusion.modules.models.esen.eSEN_Backbone method) CSV_FIELDS (in module MolecularDiffusion.runmodes.data.augmentation) ctmc_masked_edge_prior() (in module MolecularDiffusion.modules.models.flowmol_graph3d.priors) ctmc_masked_prior() (in module MolecularDiffusion.modules.models.flowmol_graph3d.priors) CTMCVectorField (class in MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field) CtoE (class in MolecularDiffusion.modules.models.syncogen.models.layers) CtoX (class in MolecularDiffusion.modules.models.syncogen.models.layers) Ctoy (class in MolecularDiffusion.modules.models.syncogen.models.layers) cuda() (in module MolecularDiffusion.utils.torch) (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) current_step (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) custom_noise (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) custom_weight_init (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) cut (MolecularDiffusion.modules.models.loqi.interpolant.CosineSchedule attribute) CUTOFF (in module MolecularDiffusion.runmodes.data.augmentation) cutoff (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf.GaussianRadialBasisLayer attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf.GaussianRadialBasisLayer attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) (MolecularDiffusion.modules.models.etflow.torchmd.NeighborEmbedding attribute) (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet attribute) (MolecularDiffusion.modules.models.goflow.ops.CosineCutoff attribute) (MolecularDiffusion.modules.models.goflow.ops.ExpNormalSmearing attribute) (MolecularDiffusion.modules.models.goflow.ops.NodeInit attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) (MolecularDiffusion.modules.models.painn_dynamics.PaiNNDynamics attribute) (MolecularDiffusion.modules.models.pmdm.encoders.SchNetProteinEncoder attribute) (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.smooth_lddt.SmoothLDDTLoss attribute) (MolecularDiffusion.modules.models.tabasco.sample.noise_schedule.BaseNoiseSchedule attribute) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) cutoff_fn (MolecularDiffusion.modules.models.etflow.torchmd.ExpNormalSmearing attribute) (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet attribute) (MolecularDiffusion.modules.models.goflow.ops.ExpNormalSmearing attribute) cutoff_lower (MolecularDiffusion.modules.models.etflow.torchmd.CosineCutoff attribute) (MolecularDiffusion.modules.models.etflow.torchmd.ExpNormalSmearing attribute) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) cutoff_mode (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) cutoff_upper (MolecularDiffusion.modules.models.etflow.torchmd.CosineCutoff attribute) (MolecularDiffusion.modules.models.etflow.torchmd.ExpNormalSmearing attribute) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) D d_attn (MolecularDiffusion.modules.models.syncogen.models.semla.NodeAttention attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.NodeAttention attribute) d_coord_message (MolecularDiffusion.modules.models.syncogen.models.semla.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiMessagePassingLayer attribute) d_edge (MolecularDiffusion.modules.models.syncogen.models.semla.EdgeMessages attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EquiInvDynamics attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EdgeMessages attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiInvDynamics attribute) d_edge_in (MolecularDiffusion.modules.models.syncogen.models.semla.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiMessagePassingLayer attribute) d_edge_out (MolecularDiffusion.modules.models.syncogen.models.semla.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiMessagePassingLayer attribute) d_head (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.NodeAttention attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.NodeAttention attribute) d_message (MolecularDiffusion.modules.models.syncogen.models.semla.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiMessagePassingLayer attribute) d_message_hidden (MolecularDiffusion.modules.models.syncogen.models.semla.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiMessagePassingLayer attribute) d_model (MolecularDiffusion.modules.models.equiformer_v2_backbone.EquiformerV2Backbone attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.decoders.transformer.TransformerDecoder attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.transformer.TransformerEncoder attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.HierarchicalPositionalEmbedding attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.SinusoidalPositionalEmbedding attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EquiInvDynamics attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.NodeAttention attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiInvDynamics attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.NodeAttention attribute) d_sigma() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) d_x (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT attribute) Data (in module MolecularDiffusion.utils.geom_metrics) data (MolecularDiffusion.data.component.diffdec_data.DiffDecDataset attribute) data() (in module MolecularDiffusion.cli.data) DATA_ATTRS_TO_ADD_LAST_DIM (in module MolecularDiffusion.data.component.diffdec_data) DATA_ATTRS_TO_PAD (in module MolecularDiffusion.data.component.diffdec_data) data_augmentation (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) data_efficient_collator (MolecularDiffusion.runmodes.train.data.DataModule attribute) data_file (MolecularDiffusion.data.component.goflow_data.GoFlowDataModule attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecScaffoldGenerator attribute) data_fraction (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) data_list (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataset attribute) data_list() (MolecularDiffusion.modules.tasks.diffusion_nextmol.Graph3DBatchToNextMolAdapter method) DATA_LIST_ATTRS (in module MolecularDiffusion.data.component.diffdec_data) data_manager (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) data_module (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule attribute) data_name (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) data_to_atom_array() (MolecularDiffusion.modules.models.tabasco.chem.convert.MoleculeConverter method) data_type (MolecularDiffusion.runmodes.train.data.DataModule attribute) DataLoader (class in MolecularDiffusion.data.dataloader) DataModule (class in MolecularDiffusion.runmodes.train.data) dataset (MolecularDiffusion.modules.models.ditmc.graph_features.MoleculeFeatureCache attribute) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ditmc.Graph3DBatchToDiTMCAdapter attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.Graph3DBatchToNextMolAdapter attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.MoleculeFeatureCache attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) dataset_embedder (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT attribute) dataset_name (MolecularDiffusion.data.component.graph3d_dataset.Graph3DDataset attribute) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) dataset_normalizer (MolecularDiffusion.modules.models.tabasco.chem.convert.MoleculeConverter attribute) dataset_stats (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.ModelTaskFactory attribute) DatasetConfigDict (class in MolecularDiffusion.runmodes.train.data) DatasetStatsCallback (class in MolecularDiffusion.modules.models.tabasco.callbacks.dataset_stats) db_path (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataset attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataset attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataset attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataset attribute) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataset attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataset attribute) db_required_msg (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTSGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.KGDiffPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTSGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMConstrainedGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTSGenerator attribute) (MolecularDiffusion.modules.tasks.pocket_generator.PocketGenerator attribute) (MolecularDiffusion.modules.tasks.ts_generator.TSGenerator attribute) ddpm (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask attribute) ddpm_kwargs (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.ModelTaskFactory attribute) DDPM_MODES (in module MolecularDiffusion.modules.models.diffsbdd) ddpm_sampling() (MolecularDiffusion.modules.models.reactot.en_sb.EnSB method) de (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) debug (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) decay (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback attribute) (MolecularDiffusion.modules.models.syncogen.models.ema.ExponentialMovingAverage attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) decode() (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE method) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask method) decoder (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) decoder_config (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) decoder_joint_heterogeneous_graph_encoder (MolecularDiffusion.modules.models.shepherd_arch.model.Model attribute) DecoderInner (class in MolecularDiffusion.modules.models.diffsmol.shape_ae) decompose (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2SymmetricTensorHead attribute) decorate() (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask method) default() (in module MolecularDiffusion.modules.models.chefnmr.utils) default_bottleneck (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) DEFAULT_CONFIG (in module MolecularDiffusion.modules.models.diffsmol.score_model) DEFAULT_IPNET_CKPT (in module MolecularDiffusion.modules.tasks.diffusion_ipdiff) default_n_timesteps (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) default_num_steps (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolTaskFactory attribute) DEFAULT_PMINET_CKPT (in module MolecularDiffusion.modules.tasks.diffusion_apo2mol) DEFAULT_POCKET_EXTENT (in module MolecularDiffusion.modules.tasks.diffusion_kgdiff) DEFAULT_SHAPE_AE_CHECKPOINT (in module MolecularDiffusion.modules.models.diffsmol.shape_ae) DEFAULT_SOAP_SPECIES (in module MolecularDiffusion.runmodes.analyze.featurize) DEFAULT_UMA_CHECKPOINT (in module MolecularDiffusion.runmodes.analyze.uma_embeddings) default_vector_residual (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) degree_angles_ref (in module MolecularDiffusion.utils.geom_constant) delete_raw() (in module MolecularDiffusion.runmodes.data.graph3d_import) delta_log_px() (MolecularDiffusion.modules.models.difflinker.edm.EDM method) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion method) denoise_graph() (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField method) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField method) denoiser (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask attribute) denoiser_config (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTaskFactory attribute) denoising_noise_scale (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) Dense (class in MolecularDiffusion.modules.layers.e3x.modules) (class in MolecularDiffusion.modules.models.goflow.ops) dense (MolecularDiffusion.modules.layers.e3x.modules.Dense attribute) dense_edge_mask() (in module MolecularDiffusion.modules.tasks.diffusion_difflinker) dense_layers (MolecularDiffusion.modules.models.goflow.ops.MLP attribute) DenseLayer (class in MolecularDiffusion.modules.models.ligandiff.egnn) density_estimation() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETask method) denticity_split (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) DepthwiseTensorProduct() (in module MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) derive_connectors_from_scaffold() (in module MolecularDiffusion.utils.geom_constraint) derive_stereo_edges() (in module MolecularDiffusion.modules.models.loqi.graph_utils) derive_x_update() (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPInteractions method) desc (MolecularDiffusion.runmodes.analyze.featurize.SOAPFeaturizer attribute) detach() (in module MolecularDiffusion.utils.torch) detect_layout() (in module MolecularDiffusion.runmodes.analyze.conformer_metrics) device (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.CoefficientMappingModule attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Embedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.CoefficientMappingModule attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Embedding attribute) (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion property) (MolecularDiffusion.modules.models.difflinker.egnn.EGNN attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.difflinker.egnn.GNN attribute) (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EGNN attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EGNN attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.geoldm.egnn.GNN attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_decoder_QM9 attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_dynamics_QM9 attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_encoder_QM9 attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.ligandiff.egnn.Dynamics attribute) (MolecularDiffusion.modules.models.oareactdiff.dynamics.BaseDynamics attribute) (MolecularDiffusion.modules.models.pharmacophore_dynamics.PharmacophoreEnVariationalDiff attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) (MolecularDiffusion.modules.models.shepherd_arch.model.Model attribute) (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates property) (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) (MolecularDiffusion.modules.models.syncogen.core.Diffusion property) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction property) (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask property) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecScaffoldGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask property) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask property) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTask property) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDTask property) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask property) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTask property) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTask property) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask property) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask property) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask property) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTask property) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.IPDiffDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.KGDiffDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_ldm.FlowMatchingInterpolant attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask property) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask property) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask property) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask property) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask property) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask property) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask property) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask property) (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.pocket_generator.PocketGenerator attribute) (MolecularDiffusion.modules.tasks.ssl3d.SSL3D property) (MolecularDiffusion.runmodes.analyze.featurize.SSL3DFeaturizer attribute) (MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize.GCDMOptimizeFactory attribute) (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator attribute) device_as() (MolecularDiffusion.modules.models.midi.placeholder.PlaceHolder method) df (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) dfm_type (MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field.CTMCVectorField attribute) DGLToPointCloudAdapter (class in MolecularDiffusion.modules.tasks.diffusion_flowmol) DGT_concat (class in MolecularDiffusion.modules.models.jodo.mol_gnn) DGTDiffusion (class in MolecularDiffusion.modules.models.nextmol.dgt) DiagonalGaussianDistribution (class in MolecularDiffusion.modules.tasks.diffusion_ldm) diagonalize() (MolecularDiffusion.modules.models.etflow.flow.HarmonicSampler method) DIFFDEC_ATOM_VOCAB (in module MolecularDiffusion.data.component.diffdec_data) DIFFDEC_CHARGES (in module MolecularDiffusion.data.component.diffdec_data) diffdec_collate() (in module MolecularDiffusion.data.component.diffdec_data) DiffDecDataModule (class in MolecularDiffusion.data.component.diffdec_data) DiffDecDataset (class in MolecularDiffusion.data.component.diffdec_data) DiffDecScaffoldGenerator (class in MolecularDiffusion.modules.tasks.diffusion_diffdec) DiffDecTask (class in MolecularDiffusion.modules.tasks.diffusion_diffdec) DiffDecTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_diffdec) diffint_collate() (in module MolecularDiffusion.data.component.diffint_data) DIFFINT_POCKET_VOCAB (in module MolecularDiffusion.data.component.diffint_prep) DiffIntDataModule (class in MolecularDiffusion.data.component.diffint_data) DiffIntDataset (class in MolecularDiffusion.data.component.diffint_data) DiffIntPocketGenerator (class in MolecularDiffusion.modules.tasks.diffusion_diffint) DIFFLINKER_ROW_DATA_COLUMNS (in module MolecularDiffusion.modules.tasks.diffusion_difflinker) DiffLinkerTask (class in MolecularDiffusion.modules.tasks.diffusion_difflinker) DiffLinkerTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_difflinker) DIFFPHARMA_ATOM_VOCAB (in module MolecularDiffusion.modules.tasks.diffusion_diffpharma) diffpharma_collate() (in module MolecularDiffusion.data.component.diffpharma_data) DiffPharmaDataModule (class in MolecularDiffusion.data.component.diffpharma_data) DiffPharmaDataset (class in MolecularDiffusion.data.component.diffpharma_data) DiffPharmaPocketGenerator (class in MolecularDiffusion.modules.tasks.diffusion_diffpharma) DiffPharmaTask (class in MolecularDiffusion.modules.tasks.diffusion_diffpharma) DiffPharmaTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_diffpharma) DIFFSBDD_ATOM_VOCAB (in module MolecularDiffusion.data.component.diffsbdd_data) diffsbdd_collate() (in module MolecularDiffusion.data.component.diffsbdd_data) DIFFSBDD_ELEMENTS (in module MolecularDiffusion.data.component.diffsbdd_data) DiffSBDDDataModule (class in MolecularDiffusion.data.component.diffsbdd_data) DiffSBDDDataset (class in MolecularDiffusion.data.component.diffsbdd_data) DiffSBDDPocketGenerator (class in MolecularDiffusion.modules.tasks.diffusion_diffsbdd) DiffSBDDTask (class in MolecularDiffusion.modules.tasks.diffusion_diffsbdd) DiffSchedule (class in MolecularDiffusion.modules.models.oareactdiff.schedule) DIFFSMOL_AROMATIC_FLAGS (in module MolecularDiffusion.modules.tasks.diffusion_diffsmol) DIFFSMOL_AROMATIC_VOCAB (in module MolecularDiffusion.modules.tasks.diffusion_diffsmol) DIFFSMOL_ATOM_VOCAB (in module MolecularDiffusion.modules.tasks.diffusion_diffsmol) DIFFSMOL_BOND_TABLES (in module MolecularDiffusion.modules.models.diffsmol.bond_tables) DiffSMolDiffusionTask (class in MolecularDiffusion.modules.tasks.diffusion_diffsmol) DiffSMolShapeGenerator (class in MolecularDiffusion.modules.tasks.diffusion_diffsmol) DiffSMolShapeNodeDistribution (class in MolecularDiffusion.modules.tasks.diffusion_diffsmol) DiffSMolTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_diffsmol) DiffSpectraElucidationGenerator (class in MolecularDiffusion.modules.tasks.diffusion_diffspectra) DiffSpectraElucidationTask (class in MolecularDiffusion.modules.tasks.diffusion_diffspectra) DiffSpectraRecord (class in MolecularDiffusion.modules.tasks.diffusion_diffspectra) DiffSpectraTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_diffspectra) Diffusion (class in MolecularDiffusion.modules.models.syncogen.core) diffusion_loss_args (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) diffusion_loss_type (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) diffusion_multiplicity (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) diffusion_noise_precision (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) diffusion_noise_schedule (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) diffusion_process_args (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) diffusion_steps (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) diffusion_type (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousDiffusionInterpolant attribute) DiffusionModuleTransformer (class in MolecularDiffusion.modules.models.chefnmr.score_models) dim (MolecularDiffusion.modules.layers.common.SinusoidsEmbeddingNew attribute) (MolecularDiffusion.modules.layers.tabasco.attention.AdaLNAttention attribute) (MolecularDiffusion.modules.layers.tabasco.attention.CrossAdaLNAttention attribute) (MolecularDiffusion.modules.layers.vn.vn_layers.VNBatchNorm attribute) (MolecularDiffusion.modules.layers.vn.vn_layers.VNLinearLeakyReLU attribute) (MolecularDiffusion.modules.layers.vn.vn_layers.VNStdFeature attribute) (MolecularDiffusion.modules.models.apo2mol.score_model.SinusoidalPosEmb attribute) (MolecularDiffusion.modules.models.difflinker.egnn.SinusoidsEmbeddingNew attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.SinusoidsEmbeddingNew attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.SinusoidsEmbeddingNew attribute) (MolecularDiffusion.modules.models.diffsmol.common.SinusoidalPosEmb attribute) (MolecularDiffusion.modules.models.en_diffusion.SinusoidalPosEmb attribute) (MolecularDiffusion.modules.models.geoldm.egnn.SinusoidsEmbeddingNew attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.SinusoidsEmbeddingNew attribute) dim_feats_in (MolecularDiffusion.modules.layers.gvp.gvp.GVP attribute) dim_head (MolecularDiffusion.modules.models.chefnmr.embedders.Attention attribute) dim_vectors_in (MolecularDiffusion.modules.layers.gvp.gvp.GVP attribute) dim_vectors_out (MolecularDiffusion.modules.layers.gvp.gvp.GVP attribute) dimensionality() (MolecularDiffusion.modules.models.difflinker.edm.EDM method) (MolecularDiffusion.modules.models.difflinker.edm.InpaintingEDM method) Dims (class in MolecularDiffusion.modules.models.midi.placeholder) dims (MolecularDiffusion.modules.layers.common.MLP attribute) (MolecularDiffusion.modules.models.pmdm.common.MultiLayerPerceptron attribute) dir_proj (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiMessage attribute) dir_wandb (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.runmodes.train.logger.Logger attribute) direct_forces (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) DIRECTIONAL_PTYPES (in module MolecularDiffusion.utils.shepherd_score.score.constants) disable_com (MolecularDiffusion.modules.models.nextmol.dgt.DGTDiffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.Graph3DBatchToNextMolAdapter attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) discrete_mode (MolecularDiffusion.modules.models.nextmol.scheduler.NoiseScheduleVPV2 attribute) discrete_noise (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.base.DiscreteStrategyBase attribute) discrete_path (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory attribute) DISCRETE_PATHS (in module MolecularDiffusion.modules.models.equifm.cnflows) discrete_schedule (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) discrete_strategy (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) DiscreteInterpolant (class in MolecularDiffusion.modules.models.tabasco.flow.interpolate) DiscreteStrategyBase (class in MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.base) DiscreteUniformTransition (class in MolecularDiffusion.modules.models.midi.noise_model) display (MolecularDiffusion.utils.pretty.PrettyPrinter attribute) display_dict() (in module MolecularDiffusion.modules.models.shepherd_arch.model) dist_add_e (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) dist_cutoff (MolecularDiffusion.modules.tasks.diffusion_diffint.DiffIntPocketGenerator attribute) (MolecularDiffusion.modules.tasks.ssl3d.PairwiseDistObjective attribute) dist_decoder (MolecularDiffusion.modules.layers.gfmdiff.blocks.PosUpdate attribute) dist_dim (MolecularDiffusion.modules.models.diffspectra.dmt.DMT attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.Cond_DGT_concat attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.DGT_concat attribute) (MolecularDiffusion.modules.models.oareactdiff.dynamics.BaseDynamics attribute) dist_gbf (MolecularDiffusion.modules.models.diffspectra.dmt.DMT attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) (MolecularDiffusion.modules.models.nextmol.dgt.DGTDiffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) dist_head (MolecularDiffusion.modules.tasks.ssl3d.PairwiseDistObjective attribute) dist_mul_e (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) dist_projection (MolecularDiffusion.modules.models.loqi.fn_model.MegaFNV3Conf attribute) DIST_RELAX_BOND (in module MolecularDiffusion.runmodes.train.eval) DIST_THRESHOLD (in module MolecularDiffusion.runmodes.train.eval) distance_expansion (MolecularDiffusion.modules.models.apo2mol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.pmdm.encoders.SchNetProteinEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.egnn.EGNN attribute) distance_function (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) distance_influence (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) distance_proj (MolecularDiffusion.modules.models.etflow.torchmd.NeighborEmbedding attribute) (MolecularDiffusion.modules.models.goflow.ops.NodeInit attribute) distance_threshold (MolecularDiffusion.modules.layers.tabasco.losses.InterDistancesLoss attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.pairwise_distance.PairwiseDistanceLoss attribute) DistEncoder (class in MolecularDiffusion.modules.layers.gfmdiff.blocks) distort_p (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) distort_t (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) distortion_cmd() (in module MolecularDiffusion.cli.data) distribute_atoms() (in module MolecularDiffusion.modules.models.ligandiff_multi.utils) DISTRIBUTED_DEFAULT_TIMEOUT_SEC (in module MolecularDiffusion.runmodes.train.eval) distribution_similarity() (MolecularDiffusion.modules.models.tabasco.utils.metrics.AtomTypeDistribution method) DistributionNodes (class in MolecularDiffusion.modules.models.difflinker.linker_size) (class in MolecularDiffusion.modules.models.diffpharma.distributions) (class in MolecularDiffusion.modules.models.diffsbdd.en_diffusion) (class in MolecularDiffusion.modules.models.en_diffusion) DistributionProperty (class in MolecularDiffusion.modules.models.en_diffusion) distributions (MolecularDiffusion.modules.models.en_diffusion.DistributionProperty attribute) DiT (class in MolecularDiffusion.modules.models.ldm.denoisers.dit) dit_layers (MolecularDiffusion.modules.models.loqi.fn_model.MegaFNV3Conf attribute) DiTBlock (class in MolecularDiffusion.modules.models.chefnmr.layers) (class in MolecularDiffusion.modules.models.ldm.denoisers.dit) DiTeBlock (class in MolecularDiffusion.modules.models.loqi.fn_model) DiTEdgeEmbed (class in MolecularDiffusion.modules.models.ditmc.embedding) DiTLayer (class in MolecularDiffusion.modules.models.ditmc.dit) DiTMCTask (class in MolecularDiffusion.modules.tasks.diffusion_ditmc) DiTMCTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_ditmc) DiTNodeEmbed (class in MolecularDiffusion.modules.models.ditmc.embedding) dk_proj (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) DMT (class in MolecularDiffusion.modules.models.diffspectra.dmt) DOCK_MODES (in module MolecularDiffusion.runmodes.analyze.docking) down_proj (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) download() (in module MolecularDiffusion.utils.file) drop (MolecularDiffusion.modules.layers.equiformer_v2.drop.EquivariantDropout attribute) (MolecularDiffusion.modules.layers.equiformer_v2.drop.EquivariantDropoutArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.EquivariantDropout attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.EquivariantDropoutArraySphericalHarmonics attribute) drop1 (MolecularDiffusion.modules.models.chefnmr.layers.Mlp attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.Mlp attribute) drop2 (MolecularDiffusion.modules.models.chefnmr.layers.Mlp attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.Mlp attribute) drop_channels (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) drop_graph (MolecularDiffusion.modules.layers.equiformer_v2.drop.EquivariantDropoutArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.EquivariantDropoutArraySphericalHarmonics attribute) drop_path (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.TransBlockV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.TransBlockV2 attribute) drop_path() (in module MolecularDiffusion.modules.layers.equiformer_v2.drop) (in module MolecularDiffusion.modules.layers.equiformer_v2_s.drop) drop_path_rate (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) drop_prob (MolecularDiffusion.modules.layers.equiformer_v2.drop.DropPath attribute) (MolecularDiffusion.modules.layers.equiformer_v2.drop.EquivariantDropout attribute) (MolecularDiffusion.modules.layers.equiformer_v2.drop.EquivariantDropoutArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2.drop.EquivariantScalarsDropout attribute) (MolecularDiffusion.modules.layers.equiformer_v2.drop.GraphDropPath attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.DropPath attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.EquivariantDropout attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.EquivariantDropoutArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.EquivariantScalarsDropout attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.GraphDropPath attribute) drop_rate (MolecularDiffusion.modules.models.gcdm.gcp_utils.VectorDropout attribute) (MolecularDiffusion.modules.models.ligandiff.conv_layer.GVPConvLayer attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) drop_transform (MolecularDiffusion.modules.models.chefnmr.score_models.DiffusionModuleTransformer attribute) dropout (MolecularDiffusion.modules.layers.conv.GCL attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer attribute) (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) (MolecularDiffusion.modules.layers.tabasco.transition.Transition attribute) (MolecularDiffusion.modules.models.chefnmr.embedders.NMRSpectraEmbedder attribute) (MolecularDiffusion.modules.models.diffspectra.specformer.TSTiEncoder attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPLayerConfig attribute) (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) (MolecularDiffusion.modules.models.jodo.layers.EdgeGateTransLayer attribute) (MolecularDiffusion.modules.models.jodo.layers.Trans_Layer attribute) (MolecularDiffusion.modules.models.jodo.layers.TransMixLayer attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) (MolecularDiffusion.modules.models.ligandiff.conv_layer.GVPConvLayer attribute) (MolecularDiffusion.modules.models.pmdm.common.MultiLayerPerceptron attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_transformer.ModelTaskFactory attribute) dropout_attn (MolecularDiffusion.modules.models.diffspectra.specformer.TSTEncoderLayer attribute) dropout_features (MolecularDiffusion.modules.models.ligandiff.dropout.GVPDropout attribute) dropout_ffn (MolecularDiffusion.modules.models.diffspectra.specformer.TSTEncoderLayer attribute) dropout_prob (MolecularDiffusion.modules.models.ldm.denoisers.dit.LabelEmbedder attribute) dropout_rate (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) dropout_vector (MolecularDiffusion.modules.models.ligandiff.dropout.GVPDropout attribute) dropoutE1 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) dropoutE2 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) dropoutE3 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) dropoutX1 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) dropoutX2 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) dropoutX3 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) DropPath (class in MolecularDiffusion.modules.layers.equiformer_v2.drop) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.drop) drugs_types (in module MolecularDiffusion.modules.models.nextmol.featurize) dtp (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.SeparableFCTP attribute) dtp_rad (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.SeparableFCTP attribute) dtype (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Embedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Embedding attribute) (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates property) (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) dummy_param (MolecularDiffusion.modules.models.diffsmol.common.GVP attribute) duplication_indices_for_max_degree() (in module MolecularDiffusion.modules.layers.e3x.modules) dv_proj (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) dx (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) dx_t (MolecularDiffusion.modules.models.tabasco.flow.path.FlowPath attribute) dy (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) Dynamics (class in MolecularDiffusion.modules.models.difflinker.egnn) (class in MolecularDiffusion.modules.models.ligandiff.egnn) dynamics (MolecularDiffusion.modules.models.difflinker.edm.EDM attribute) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM attribute) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.ligandiff.edm.EDM attribute) (MolecularDiffusion.modules.models.ligandiff.egnn.Dynamics attribute) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.pharmacophore_dynamics.PharmacophoreEnVariationalDiff attribute) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute), [1] (MolecularDiffusion.modules.models.syncogen.models.semla.SemlaGenerator attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory attribute) dynamics_in_node_nf (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) dynamics_kwargs (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.ModelTaskFactory attribute) dynamics_teacher (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) DynamicsWithPockets (class in MolecularDiffusion.modules.models.difflinker.egnn) E E (MolecularDiffusion.modules.models.midi.placeholder.Dims attribute) (MolecularDiffusion.modules.models.midi.placeholder.PlaceHolder attribute) E3MLP (class in MolecularDiffusion.modules.models.ditmc.layers) E3Norm (class in MolecularDiffusion.modules.models.loqi.fn_model) E_atomtofrag_out (MolecularDiffusion.modules.models.syncogen.models.semla.SemlaGenerator attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator attribute) e_att_mul (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) E_classes (MolecularDiffusion.modules.models.midi.noise_model.DiscreteUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.MarginalUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) E_marginals (MolecularDiffusion.modules.models.midi.noise_model.DiscreteUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.MarginalUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) e_out (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) e_pos1 (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) e_pos2 (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) e_to_x (MolecularDiffusion.modules.models.syncogen.models.layers.CtoX attribute) e_to_y (MolecularDiffusion.modules.models.syncogen.models.layers.Ctoy attribute) e_x_mul (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) early_stopped (MolecularDiffusion.runmodes.generate.sweep.RunResult attribute) ECFP (in module MolecularDiffusion.data.component.feature) edge_attr (MolecularDiffusion.modules.models.ditmc.graphs.CondGraph attribute) (MolecularDiffusion.modules.models.ditmc.graphs.PriorGraph attribute) edge_attr_dim (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) edge_attr_embedding (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) edge_attr_input_channels (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) edge_cache (MolecularDiffusion.modules.models.difflinker.egnn.Dynamics attribute) edge_cat (MolecularDiffusion.modules.models.goflow.ops.EdgeCGREmbedding attribute) edge_cgr_embedding (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet attribute) (MolecularDiffusion.modules.models.goflow.ops.EdgeInit attribute) (MolecularDiffusion.modules.models.goflow.ops.NodeInit attribute) edge_ch (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) edge_channels (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) edge_channels_list (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.esen.esen_block.Edgewise attribute) (MolecularDiffusion.modules.layers.esen.nn.embedding.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Linear attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) edge_classifier_head (MolecularDiffusion.modules.models.syncogen.models.semla.SemlaGenerator attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator attribute) edge_cutoff (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.oareactdiff.dynamics.BaseDynamics attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) edge_cutoff_i (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.diffsbdd.dynamics.EGNNDynamics attribute) edge_cutoff_l (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.diffsbdd.dynamics.EGNNDynamics attribute) edge_cutoff_p (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.diffsbdd.dynamics.EGNNDynamics attribute) edge_degree_embedding (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) edge_dim (MolecularDiffusion.modules.models.jodo.layers.EdgeGateTransLayer attribute) (MolecularDiffusion.modules.models.jodo.layers.Trans_Layer attribute) (MolecularDiffusion.modules.models.jodo.layers.TransMixLayer attribute) edge_dims (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) edge_distance (MolecularDiffusion.modules.layers.graph_module.GraphData attribute) edge_distance_vec (MolecularDiffusion.modules.layers.graph_module.GraphData attribute) edge_distances() (MolecularDiffusion.modules.models.flowmol_graph3d.self_conditioning.SelfConditioningResidualLayer method) edge_emb (MolecularDiffusion.modules.models.diffspectra.dmt.DMT attribute) (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.Cond_DGT_concat attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.DGT_concat attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) (MolecularDiffusion.modules.models.nextmol.dgt.DGTDiffusion attribute) edge_embed_dim (MolecularDiffusion.modules.models.oareactdiff.dynamics.BaseDynamics attribute) edge_embedder (MolecularDiffusion.modules.models.loqi.fn_model.MegaFNV3Conf attribute) edge_embedding (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.diffsbdd.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.ditmc.dit.GenerativeModel attribute) (MolecularDiffusion.modules.models.ditmc.meshgraphnet.MeshGraphNetEncoder attribute) (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPEmbedding attribute) (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet attribute) (MolecularDiffusion.modules.models.ligandiff.gvp_model.GVPNetwork attribute) (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone attribute) edge_encoder_global (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) edge_encoder_local (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) edge_exist_mlp (MolecularDiffusion.modules.models.diffspectra.dmt.DMT attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.Cond_DGT_concat attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.DGT_concat attribute) edge_feat_dim (MolecularDiffusion.modules.models.apo2mol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) edge_feat_size (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) edge_features() (in module MolecularDiffusion.modules.models.gcdm.gcp_utils) edge_featurizers (MolecularDiffusion.modules.models.painn_backbone.EquivNet attribute) edge_gvps (MolecularDiffusion.modules.models.ligandiff.conv_layer.GVPMessagePassing attribute) edge_hidden_size (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) edge_in_proj (MolecularDiffusion.modules.models.syncogen.models.semla.SemlaGenerator attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator attribute) edge_index (MolecularDiffusion.modules.layers.atomic_data.AtomicData attribute) (MolecularDiffusion.modules.layers.graph_module.GraphData attribute) edge_input_dims (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) edge_level (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2Block attribute) (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2DecompositionEdgeBlock attribute) edge_mask_index() (MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.base.DiscreteStrategyBase static method) edge_message (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) edge_message() (MolecularDiffusion.modules.models.oareactdiff.leftnet.GCLMessage method) edge_mlp (MolecularDiffusion.modules.layers.conv.GCL attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.GCL attribute) (MolecularDiffusion.modules.models.difflinker.egnn.GCL attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.GCL attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.GCL attribute) (MolecularDiffusion.modules.models.ditmc.meshgraphnet.MeshGraphNetLayer attribute) (MolecularDiffusion.modules.models.geoldm.egnn.GCL attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.GCL attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.GCLMessage attribute) (MolecularDiffusion.modules.models.pmdm.encoders.EGNNSparseLayer attribute) edge_mlp_dim (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) edge_model() (MolecularDiffusion.modules.layers.conv.GCL method) (MolecularDiffusion.modules.models.apo2mol.pminet.GCL method) (MolecularDiffusion.modules.models.difflinker.egnn.GCL method) (MolecularDiffusion.modules.models.diffpharma.egnn.GCL method) (MolecularDiffusion.modules.models.geoldm.egnn.GCL method) edge_nf (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.diffsbdd.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.oareactdiff.dynamics.BaseDynamics attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) edge_no_edge_index() (MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.base.DiscreteStrategyBase static method) edge_norm (MolecularDiffusion.modules.layers.gvp.gvp.EdgeUpdate attribute) (MolecularDiffusion.modules.models.ditmc.meshgraphnet.MeshGraphNetLayer attribute) (MolecularDiffusion.modules.models.flowmol.vector_field.EdgeUpdate attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.BondRefine attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EdgeMessages attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.BondRefine attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EdgeMessages attribute) edge_order (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet attribute) (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) edge_out_trans (MolecularDiffusion.modules.models.oareactdiff.leftnet.GCLMessage attribute) edge_quan_th (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) edge_radius (MolecularDiffusion.runmodes.analyze.featurize.SSL3DFeaturizer attribute) edge_residual_mlp (MolecularDiffusion.modules.models.flowmol_graph3d.self_conditioning.SelfConditioningResidualLayer attribute) edge_size (MolecularDiffusion.modules.models.painn_backbone.EquivNetHParams attribute) edge_th (MolecularDiffusion.modules.models.diffspectra.dmt.DMT attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.Cond_DGT_concat attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.DGT_concat attribute) EDGE_THRESHOLD (in module MolecularDiffusion.runmodes.analyze.compute_metrics) (in module MolecularDiffusion.utils.geom_analyzer) (in module MolecularDiffusion.utils.geom_constraint) (in module MolecularDiffusion.utils.geom_metrics) edge_time_embedding (MolecularDiffusion.modules.models.loqi.fn_model.MegaFNV3Conf attribute) edge_time_mlp (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) edge_type (MolecularDiffusion.runmodes.train.data.DataModule attribute) edge_type_mlp (MolecularDiffusion.modules.models.diffspectra.dmt.DMT attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.Cond_DGT_concat attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.DGT_concat attribute) edge_up (MolecularDiffusion.modules.models.goflow.ops.EdgeInit attribute) edge_update() (MolecularDiffusion.modules.models.goflow.gotennet.GATA method) edge_update_fn (MolecularDiffusion.modules.layers.gvp.gvp.EdgeUpdate attribute) (MolecularDiffusion.modules.models.flowmol.vector_field.EdgeUpdate attribute) edge_updater (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone attribute) edge_updaters (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) edge_updates (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) edge_vec_dim (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) edge_weight (MolecularDiffusion.modules.models.pmdm.encoders.EGNNSparseLayer attribute) edge_wise (MolecularDiffusion.modules.layers.esen.esen_block.eSEN_Block attribute) EdgeAttributeEmbedding (class in MolecularDiffusion.modules.models.ditmc.embedding) EdgeCGREmbedding (class in MolecularDiffusion.modules.models.goflow.ops) EdgeDegreeEmbedding (class in MolecularDiffusion.modules.layers.equiformer_v2.input_block) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.input_block) (class in MolecularDiffusion.modules.layers.esen.nn.embedding) (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder) EdgeGateTransLayer (class in MolecularDiffusion.modules.models.jodo.layers) EdgeInit (class in MolecularDiffusion.modules.models.goflow.ops) EdgeMessages (class in MolecularDiffusion.modules.models.syncogen.models.semla) (class in MolecularDiffusion.modules.models.syncogen.models.semla_pharm) edges_from_adj() (in module MolecularDiffusion.modules.models.syncogen.models.semla_utils) edges_from_nodes() (in module MolecularDiffusion.modules.models.syncogen.models.semla_utils) EdgeUpdate (class in MolecularDiffusion.modules.layers.gvp.gvp) (class in MolecularDiffusion.modules.models.flowmol.vector_field) Edgewise (class in MolecularDiffusion.modules.layers.esen.esen_block) EDM (class in MolecularDiffusion.modules.models.difflinker.edm) (class in MolecularDiffusion.modules.models.ligandiff.edm) edm (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask attribute) edm_args (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion attribute) EGNN (class in MolecularDiffusion.modules.models.difflinker.egnn) (class in MolecularDiffusion.modules.models.diffpharma.egnn) (class in MolecularDiffusion.modules.models.diffsbdd.egnn) (class in MolecularDiffusion.modules.models.egcl) (class in MolecularDiffusion.modules.models.geoldm.egnn) (class in MolecularDiffusion.modules.models.shepherd_arch.egnn) egnn (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.diffsbdd.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.egt.EGT_dynamics attribute) (MolecularDiffusion.modules.models.esen.eSEN_dynamics attribute) (MolecularDiffusion.modules.models.tabasco_egnn.egnn_backbone.EGNNBackbone attribute) egnn_config (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.ModelTaskFactory attribute) EGNN_decoder_QM9 (class in MolecularDiffusion.modules.models.geoldm.networks) EGNN_dynamics (class in MolecularDiffusion.modules.models.egcl) EGNN_dynamics_QM9 (class in MolecularDiffusion.modules.models.geoldm.networks) EGNN_encoder_QM9 (class in MolecularDiffusion.modules.models.geoldm.networks) egnn_kwargs (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTaskFactory attribute) egnn_layers (MolecularDiffusion.modules.models.loqi.fn_model.MegaFNV3Conf attribute) EGNNBackbone (class in MolecularDiffusion.modules.models.tabasco_egnn.egnn_backbone) EGNNDynamics (class in MolecularDiffusion.modules.models.diffpharma.dynamics) (class in MolecularDiffusion.modules.models.diffsbdd.dynamics) (class in MolecularDiffusion.modules.models.oareactdiff.dynamics) EGNNSparseLayer (class in MolecularDiffusion.modules.models.pmdm.encoders) EGNNSparseNetwork (class in MolecularDiffusion.modules.models.pmdm.encoders) EGT_dynamics (class in MolecularDiffusion.modules.models.egt) eig_cache (MolecularDiffusion.modules.models.etflow.flow.HarmonicSampler attribute) ElectroNegativityPauling (MolecularDiffusion.utils.xyz2mol.elements.ElementData attribute) elemdatabase (in module MolecularDiffusion.utils.xyz2mol.converter) element (MolecularDiffusion.data.component.pointcloud.Atom attribute) elementblock (MolecularDiffusion.utils.xyz2mol.elements.ElementData attribute) ElementData (class in MolecularDiffusion.utils.xyz2mol.elements) elementgroup (MolecularDiffusion.utils.xyz2mol.elements.ElementData attribute) elementnr (MolecularDiffusion.utils.xyz2mol.elements.ElementData attribute) elementperiod (MolecularDiffusion.utils.xyz2mol.elements.ElementData attribute) elementsym (MolecularDiffusion.utils.xyz2mol.elements.ElementData attribute) Ellipsis (class in MolecularDiffusion.utils.pretty) ellipsis (in module MolecularDiffusion.utils.pretty) elucidate() (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask method) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask method) ElucidationGenerator (class in MolecularDiffusion.modules.tasks.elucidation_generator) EMA (class in MolecularDiffusion.callbacks.train_helper) (class in MolecularDiffusion.modules.models.tabasco.callbacks.ema) ema (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback attribute) (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) ema_decay (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) ema_model (MolecularDiffusion.core.engine_lightning.EngineLightning property) (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback attribute) ema_optimizer (MolecularDiffusion.modules.models.tabasco.sample.guided_sampling.GuidedSampling attribute) ema_params (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) ema_update() (in module MolecularDiffusion.modules.models.tabasco.callbacks.ema) EMACallback (class in MolecularDiffusion.core.lightning_callbacks.ema_callback) EMAOptimizer (class in MolecularDiffusion.modules.models.tabasco.callbacks.ema) emb_dim (MolecularDiffusion.modules.layers.gfmdiff.blocks.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.Low2High attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.SimLow2High attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer attribute) (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) emb_mlp (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.ipdiff.score_model.IPDiffScorePosNet3D attribute) emb_mlp_aug (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) emb_size (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2Block attribute) (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2DecompositionEdgeBlock attribute) embed (MolecularDiffusion.modules.models.ditmc.embedding.DiTNodeEmbed attribute) embed_dim (MolecularDiffusion.modules.models.oareactdiff.dynamics.BaseDynamics attribute) embed_distances_bool (MolecularDiffusion.modules.models.ditmc.embedding.DiTEdgeEmbed attribute) embed_fusion (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet attribute) embed_ligand_shape() (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer method) embed_message_att_weight() (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer method) embed_shortest_hops_bool (MolecularDiffusion.modules.models.ditmc.embedding.DiTEdgeEmbed attribute) (MolecularDiffusion.modules.models.ditmc.embedding.RadialSphericalEdgeEmbedding attribute) embedding (MolecularDiffusion.modules.models.difflinker.egnn.EGNN attribute) (MolecularDiffusion.modules.models.difflinker.egnn.GNN attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EGNN attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EGNN attribute) (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.etflow.torchmd.NeighborEmbedding attribute) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EGNN attribute) (MolecularDiffusion.modules.models.geoldm.egnn.GNN attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.NeighborEmb attribute) (MolecularDiffusion.modules.models.painn_dynamics.PaiNNDynamics attribute) embedding2 (MolecularDiffusion.modules.models.diffpharma.egnn.EGNN attribute) embedding2_out (MolecularDiffusion.modules.models.diffpharma.egnn.EGNN attribute) embedding3 (MolecularDiffusion.modules.models.diffpharma.egnn.EGNN attribute) embedding3_out (MolecularDiffusion.modules.models.diffpharma.egnn.EGNN attribute) embedding_dim (MolecularDiffusion.modules.models.goflow.gotennet.TimestepEmbedding attribute) embedding_in (MolecularDiffusion.modules.models.difflinker.size_gnn.SizeGNN attribute) (MolecularDiffusion.modules.models.ligandiff.gvp_model.GVPNetwork attribute) embedding_out (MolecularDiffusion.modules.models.difflinker.egnn.EGNN attribute) (MolecularDiffusion.modules.models.difflinker.egnn.GNN attribute) (MolecularDiffusion.modules.models.difflinker.size_gnn.SizeGNN attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EGNN attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EGNN attribute) (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.esen.eSEN_dynamics attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EGNN attribute) (MolecularDiffusion.modules.models.geoldm.egnn.GNN attribute) (MolecularDiffusion.modules.models.ligandiff.gvp_model.GVPNetwork attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) embedding_table (MolecularDiffusion.modules.models.ldm.denoisers.dit.LabelEmbedder attribute) embedding_target (MolecularDiffusion.modules.layers.esen.nn.embedding.ChgSpinDatasetEmbedding attribute) embedding_type (MolecularDiffusion.modules.layers.esen.nn.embedding.ChgSpinDatasetEmbedding attribute) emblin (MolecularDiffusion.modules.models.pmdm.encoders.SchNetProteinEncoder attribute) encode() (MolecularDiffusion.modules.models.diffsmol.shape_ae.PointCloudAE method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE method) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask method) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask method) encode_no_edge() (in module MolecularDiffusion.modules.models.syncogen.data.utils) encoder (MolecularDiffusion.modules.models.diffsmol.shape_ae.PointCloudAE attribute) (MolecularDiffusion.modules.models.diffspectra.specformer.TSTiEncoder attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) encoder_config (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) encoder_global (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) encoder_local (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) EndpointVectorField (class in MolecularDiffusion.modules.models.flowmol.vector_field) (class in MolecularDiffusion.modules.models.flowmol_graph3d.vector_field) energy_block (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.esen.MLP_EFS_Head attribute) (MolecularDiffusion.modules.models.esen.MLP_Energy_Head attribute) enforce_max_neighbors_strictly (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) enforce_min_nodes_per_connector() (in module MolecularDiffusion.utils.geom_constraint) Engine (class in MolecularDiffusion.core.engine) engine_wrapper() (in module MolecularDiffusion.cli.eval_predict) (in module MolecularDiffusion.cli.train) EngineLightning (class in MolecularDiffusion.core.engine_lightning) EnHierarchicalVAE (class in MolecularDiffusion.modules.models.geoldm.diffusion) EnLatentDiffusion (class in MolecularDiffusion.modules.models.geoldm.diffusion) EnSB (class in MolecularDiffusion.modules.models.reactot.en_sb) ensure_intact() (in module MolecularDiffusion.utils.geom_constraint) ensure_qm9_splits() (in module MolecularDiffusion.runmodes.data.graph3d_import) ensure_train_lengths_loaded() (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager method) ensure_vocabulary() (in module MolecularDiffusion.modules.models.syncogen.vocab) entries (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataset attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataset attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataset attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataset attribute) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataset attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataset attribute) entry() (in module MolecularDiffusion.assets) EnVariationalDiffusion (class in MolecularDiffusion.modules.models.diffsbdd.en_diffusion) (class in MolecularDiffusion.modules.models.en_diffusion) (class in MolecularDiffusion.modules.models.geoldm.diffusion) (class in MolecularDiffusion.modules.models.oareactdiff.en_diffusion) envelop_layer (MolecularDiffusion.modules.models.painn_backbone.EquivNet attribute) envelope (MolecularDiffusion.modules.layers.esen.nn.radial.EnvelopedBesselBasis attribute) EnvelopedBesselBasis (class in MolecularDiffusion.modules.layers.esen.nn.radial) EnvelopLayer (class in MolecularDiffusion.modules.models.painn_backbone) eot_max_iters (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory attribute) epoch (MolecularDiffusion.core.engine.Engine property) epoch2batch (MolecularDiffusion.core.meter.Meter attribute) epoch_id (MolecularDiffusion.core.meter.Meter attribute) EPS (in module MolecularDiffusion.modules.models.diffsmol.shape_ae) (in module MolecularDiffusion.modules.models.diffsmol.uni_transformer) (in module MolecularDiffusion.modules.models.equifm.paths) (in module MolecularDiffusion.modules.models.oareactdiff.leftnet) eps (MolecularDiffusion.modules.layers.conv.PositionsMLP attribute) (MolecularDiffusion.modules.layers.conv.SE3Norm attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantLayerNormArray attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantLayerNormArray attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantRMSNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantLayerNormArray attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.layers.gvp.gvp.GVPLayerNorm attribute) (MolecularDiffusion.modules.models.gcdm.gcp_utils.GCPLayerNorm attribute) (MolecularDiffusion.modules.models.goflow.ops.VecLayerNorm attribute) (MolecularDiffusion.modules.models.jodo.layers.CondCoorsNorm attribute) (MolecularDiffusion.modules.models.jodo.layers.CoorsNorm attribute) (MolecularDiffusion.modules.models.ligandiff.gvp.GVP attribute) (MolecularDiffusion.modules.models.ligandiff.gvp_model.GVPNetwork attribute) (MolecularDiffusion.modules.models.ligandiff.layer_norm.GVPLayerNorm attribute) (MolecularDiffusion.modules.models.loqi.fn_model.E3Norm attribute) (MolecularDiffusion.modules.models.midi.layers.PositionsMLP attribute) (MolecularDiffusion.modules.models.midi.layers.SE3Norm attribute) (MolecularDiffusion.modules.models.painn_backbone.GraphLayerNorm attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNorm attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNormV2 attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.brownian.BrownianBridgeNoise attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.cosine.CosineNoise attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.cosine.CosineSqrNoise attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.loglinear.LogLinearNoise attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.CtoE attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.PositionsMLP attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.SE3Norm attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.CoordAttention attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.CoordNorm attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EdgeMessages attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.CoordAttention attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.CoordNorm attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EdgeMessages attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.tabasco.flow.time_factor.BaseTimeFactor attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) epsilon (MolecularDiffusion.modules.models.ditmc.layers.EquivariantLayerNorm attribute) (MolecularDiffusion.modules.models.goflow.gotennet.EQFF attribute) (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) eq_transform() (in module MolecularDiffusion.modules.models.pmdm.common) EQFF (class in MolecularDiffusion.modules.models.goflow.gotennet) eqff (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet attribute) equi_update (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) EquiFMTask (class in MolecularDiffusion.modules.tasks.diffusion_equifm) EquiFMTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_equifm) equiformer (MolecularDiffusion.modules.models.equiformer_v2_backbone.EquiformerV2Backbone attribute) (MolecularDiffusion.modules.models.equiformer_v2_dynamics.EquiformerV2_dynamics attribute) (MolecularDiffusion.modules.models.tabasco_equiformer.equiformer_backbone.EquiformerV2TabascoBackbone attribute) equiformer_config (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.ModelTaskFactory attribute) EquiformerEncoder (class in MolecularDiffusion.modules.models.ldm.encoders.equiformer) EquiformerV2 (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder) EquiformerV2_dynamics (class in MolecularDiffusion.modules.models.equiformer_v2_dynamics) EquiformerV2_OC20 (class in MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20) EquiformerV2Backbone (class in MolecularDiffusion.modules.models.equiformer_v2_backbone) EquiformerV2TabascoBackbone (class in MolecularDiffusion.modules.models.tabasco_equiformer.equiformer_backbone) EquiGNN (class in MolecularDiffusion.modules.models.gfmdiff.equignn) equignn (MolecularDiffusion.modules.models.gfmdiff.dynamics.GFMDiffDynamics attribute) EquiInvDynamics (class in MolecularDiffusion.modules.models.syncogen.models.semla) (class in MolecularDiffusion.modules.models.syncogen.models.semla_pharm) EquiMessage (class in MolecularDiffusion.modules.models.oareactdiff.leftnet) EquiMessagePassingLayer (class in MolecularDiffusion.modules.models.syncogen.models.semla) (class in MolecularDiffusion.modules.models.syncogen.models.semla_pharm) EquiOutput (class in MolecularDiffusion.modules.models.oareactdiff.leftnet) EquiUpdate (class in MolecularDiffusion.modules.models.oareactdiff.leftnet) equivariant_mlp (MolecularDiffusion.modules.models.syncogen.models.semla.NodeFeedForward attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.NodeFeedForward attribute) equivariant_ot_prior() (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant method) EquivariantBlock (class in MolecularDiffusion.modules.layers.conv) (class in MolecularDiffusion.modules.models.apo2mol.pminet) (class in MolecularDiffusion.modules.models.difflinker.egnn) (class in MolecularDiffusion.modules.models.diffpharma.egnn) (class in MolecularDiffusion.modules.models.diffsbdd.egnn) (class in MolecularDiffusion.modules.models.geoldm.egnn) (class in MolecularDiffusion.modules.models.ipdiff.bapnet) (class in MolecularDiffusion.modules.models.jodo.mol_gnn) EquivariantDegreeLayerScale (class in MolecularDiffusion.modules.layers.equiformer_v2.layer_norm) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm) (class in MolecularDiffusion.modules.layers.esen.nn.layer_norm) EquivariantDropout (class in MolecularDiffusion.modules.layers.equiformer_v2.drop) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.drop) EquivariantDropoutArraySphericalHarmonics (class in MolecularDiffusion.modules.layers.equiformer_v2.drop) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.drop) EquivariantGraphNorm (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) EquivariantGraphNormV2 (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) EquivariantLayerNorm (class in MolecularDiffusion.modules.models.ditmc.layers) EquivariantLayerNormArray (class in MolecularDiffusion.modules.layers.equiformer_v2.layer_norm) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm) (class in MolecularDiffusion.modules.layers.esen.nn.layer_norm) EquivariantLayerNormArraySphericalHarmonics (class in MolecularDiffusion.modules.layers.equiformer_v2.layer_norm) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm) (class in MolecularDiffusion.modules.layers.esen.nn.layer_norm) EquivariantMixBlock (class in MolecularDiffusion.modules.models.jodo.mol_gnn) EquivariantMLP (class in MolecularDiffusion.modules.models.syncogen.models.semla) (class in MolecularDiffusion.modules.models.syncogen.models.semla_pharm) EquivariantMultiHeadAttention (class in MolecularDiffusion.modules.models.etflow.torchmd) EquivariantReadout (class in MolecularDiffusion.modules.models.ditmc.readout) EquivariantRMSNormArraySphericalHarmonics (class in MolecularDiffusion.modules.layers.equiformer_v2.layer_norm) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm) EquivariantRMSNormArraySphericalHarmonicsV2 (class in MolecularDiffusion.modules.layers.equiformer_v2.layer_norm) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm) (class in MolecularDiffusion.modules.layers.esen.nn.layer_norm) EquivariantScalarsDropout (class in MolecularDiffusion.modules.layers.equiformer_v2.drop) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.drop) EquivariantUpdate (class in MolecularDiffusion.modules.layers.conv) (class in MolecularDiffusion.modules.models.apo2mol.pminet) (class in MolecularDiffusion.modules.models.difflinker.egnn) (class in MolecularDiffusion.modules.models.diffpharma.egnn) (class in MolecularDiffusion.modules.models.diffsbdd.egnn) (class in MolecularDiffusion.modules.models.geoldm.egnn) (class in MolecularDiffusion.modules.models.ipdiff.bapnet) EquivariantVectorOutput (class in MolecularDiffusion.modules.models.etflow.torchmd) EquivNet (class in MolecularDiffusion.modules.models.painn_backbone) equivnet (MolecularDiffusion.modules.models.painn_dynamics.PaiNNDynamics attribute) EquivNetHParams (class in MolecularDiffusion.modules.models.painn_backbone) eSEN_Backbone (class in MolecularDiffusion.modules.models.esen) eSEN_Block (class in MolecularDiffusion.modules.layers.esen.esen_block) eSEN_dynamics (class in MolecularDiffusion.modules.models.esen) eSEN_Encoder (class in MolecularDiffusion.modules.models.esen) eSEN_VelocityFFN (class in MolecularDiffusion.modules.models.esen) esp_combo_score() (in module MolecularDiffusion.utils.shepherd_score.score.electrostatic_scoring) esp_combo_score_np() (in module MolecularDiffusion.utils.shepherd_score.score.electrostatic_scoring_np) ESP_LAMBDA (in module MolecularDiffusion.runmodes.analyze.similarity3d) estimate_batch_size() (in module MolecularDiffusion.data.dataloader) eta (MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field.CTMCVectorField attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.p2.PathPlanning attribute) ETFlowFeatureCache (class in MolecularDiffusion.modules.models.etflow.features) ETFlowTask (class in MolecularDiffusion.modules.tasks.diffusion_etflow) ETFlowTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_etflow) EtoC (class in MolecularDiffusion.modules.models.syncogen.models.layers) EtoX (class in MolecularDiffusion.modules.layers.conv) (class in MolecularDiffusion.modules.models.midi.layers) (class in MolecularDiffusion.modules.models.syncogen.models.layers) Etoy (class in MolecularDiffusion.modules.layers.conv) (class in MolecularDiffusion.modules.models.midi.layers) (class in MolecularDiffusion.modules.models.syncogen.models.layers) euler_integrate() (in module MolecularDiffusion.modules.models.goflow.flow) EulerIntegrator (class in MolecularDiffusion.modules.models.syncogen.diffusion.sampling.integrators.euler) eval_batch_size (MolecularDiffusion.modules.models.syncogen.core.Diffusion property) (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenSizePrior attribute) eval_mode (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) eval_predict() (in module MolecularDiffusion.cli.main) (MolecularDiffusion.molcraftdiff.MolCraftDiff method) eval_predict_main() (in module MolecularDiffusion.cli.eval_predict) eval_reconstruction (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) evaluate() (in module MolecularDiffusion.runmodes.train.eval) (MolecularDiffusion.core.engine.Engine method) (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask method) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask method) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask method) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTask method) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDTask method) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask method) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTask method) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTask method) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask method) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask method) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask method) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTask method) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.IPDiffDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.KGDiffDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask method) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask method) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask method) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask method) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask method) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask method) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask method) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask method) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask method) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative method) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction method) (MolecularDiffusion.modules.tasks.ssl3d.SSL3D method) (MolecularDiffusion.modules.tasks.task.Task method) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETask method) evaluate_and_save() (in module MolecularDiffusion.cli.train), [1] every_n_steps (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) ew_net_type (MolecularDiffusion.modules.models.apo2mol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) exclude_variables_from_decoder_heterogeneous_graph (MolecularDiffusion.modules.models.shepherd_arch.model.Model attribute) exists() (in module MolecularDiffusion.modules.layers.gvp.gvp) (in module MolecularDiffusion.modules.models.chefnmr.utils) expand_dims() (in module MolecularDiffusion.modules.tasks.diffusion_jodo) expand_edge() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Embedding method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Embedding method) expand_edge_indices_to_matrix() (in module MolecularDiffusion.modules.models.syncogen.data.dataloader) expert_pred (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) explicit_diffusion_variables (MolecularDiffusion.modules.models.shepherd_arch.model.Model attribute) expm1() (in module MolecularDiffusion.modules.models.en_diffusion) (MolecularDiffusion.modules.models.difflinker.edm.EDM static method) ExpNormalSmearing (class in MolecularDiffusion.modules.models.etflow.torchmd) (class in MolecularDiffusion.modules.models.goflow.ops) ExponentialMovingAverage (class in MolecularDiffusion.modules.models.syncogen.models.ema) extend_bond_index() (in module MolecularDiffusion.modules.models.etflow.flow) extend_graph_order_radius() (in module MolecularDiffusion.modules.models.pmdm.common) extend_ts_graph_order_radius() (in module MolecularDiffusion.modules.models.goflow.cgr_graph_utils) ExtendedConnectivityFingerprint() (in module MolecularDiffusion.data.component.feature) extensive (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2Block attribute) (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2DecompositionEdgeBlock attribute) extra_heads (MolecularDiffusion.modules.models.jodo.layers.TransMixLayer attribute) extra_m0_output_channels (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Convolution attribute) extra_norm_values (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) extra_repr() (MolecularDiffusion.modules.layers.conv.SE3Norm method) (MolecularDiffusion.modules.layers.equiformer_v2.activation.ScaledSiLU method) (MolecularDiffusion.modules.layers.equiformer_v2.activation.ScaledSmoothLeakyReLU method) (MolecularDiffusion.modules.layers.equiformer_v2.activation.SmoothLeakyReLU method) (MolecularDiffusion.modules.layers.equiformer_v2.drop.DropPath method) (MolecularDiffusion.modules.layers.equiformer_v2.drop.EquivariantDropoutArraySphericalHarmonics method) (MolecularDiffusion.modules.layers.equiformer_v2.drop.EquivariantScalarsDropout method) (MolecularDiffusion.modules.layers.equiformer_v2.drop.GraphDropPath method) (MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf.GaussianRadialBasisLayer method) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.ScaledSiLU method) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.ScaledSmoothLeakyReLU method) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.SmoothLeakyReLU method) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.DropPath method) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.EquivariantDropoutArraySphericalHarmonics method) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.EquivariantScalarsDropout method) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.GraphDropPath method) (MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf.GaussianRadialBasisLayer method) (MolecularDiffusion.modules.models.midi.layers.SE3Norm method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Activation method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.ScaledScatter method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.SmoothLeakyReLU method) (MolecularDiffusion.modules.models.syncogen.models.layers.SE3Norm method) extract() (in module MolecularDiffusion.modules.models.apo2mol.score_model) (in module MolecularDiffusion.modules.models.diffsmol.score_model) (in module MolecularDiffusion.modules.models.kgdiff.score_model) (in module MolecularDiffusion.utils.file) extract_features() (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet method) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet method) extract_max_degree() (in module MolecularDiffusion.modules.layers.e3x.features) extract_profiles() (in module MolecularDiffusion.runmodes.analyze.similarity3d) extract_scaffold_and_fingerprints() (in module MolecularDiffusion.runmodes.analyze.xyz2mol) F f1_max() (in module MolecularDiffusion.modules.tasks.metrics) FACTOR (MolecularDiffusion.callbacks.train_helper.gradient_clipping attribute) FAKE_ATOM_INDEX (in module MolecularDiffusion.data.component.diffdec_data) fake_atom_index (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.Graph3DToDGLAdapter attribute) fake_atom_p (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.Graph3DToDGLAdapter attribute) fake_atom_std (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.Graph3DToDGLAdapter attribute) fake_atoms (MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field.CTMCVectorField attribute) fast_forward_batches (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) fast_forward_epochs (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) FaultTolerantDistributedSampler (class in MolecularDiffusion.modules.models.syncogen.data.dataloader) fc (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_m_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_m_Convolution attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_m_Conv attribute) fc1 (MolecularDiffusion.modules.models.chefnmr.layers.Mlp attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.Mlp attribute) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.SiLUSmearing attribute) fc2 (MolecularDiffusion.modules.models.chefnmr.layers.Mlp attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.Mlp attribute) fc_0 (MolecularDiffusion.modules.layers.vn.vn_layers.ResnetBlockFC attribute) (MolecularDiffusion.modules.layers.vn.vn_layers.VNResnetBlockFC attribute) fc_1 (MolecularDiffusion.modules.layers.vn.vn_layers.ResnetBlockFC attribute) (MolecularDiffusion.modules.layers.vn.vn_layers.VNResnetBlockFC attribute) fc_c (MolecularDiffusion.modules.models.diffsmol.shape_ae.VNResnetEncoder attribute) fc_in (MolecularDiffusion.modules.models.diffsmol.shape_ae.DecoderInner attribute) fc_m0 (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Linear attribute) fc_out (MolecularDiffusion.modules.models.diffsmol.shape_ae.DecoderInner attribute) fc_pos (MolecularDiffusion.modules.models.diffsmol.shape_ae.VNResnetEncoder attribute) fctp_1 (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.FeedForwardNetwork_equiformer attribute) fctp_2 (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.FeedForwardNetwork_equiformer attribute) feat (MolecularDiffusion.data.component.reaction_data.ReactionSide attribute), [1] feat_dict_file (MolecularDiffusion.data.component.goflow_data.GoFlowDataModule attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTSGenerator attribute) feat_dropout (MolecularDiffusion.modules.layers.gvp.gvp.GVPDropout attribute) feat_embed (MolecularDiffusion.modules.models.transformer_dynamics.TransformerDynamics attribute) feat_norm (MolecularDiffusion.modules.layers.gvp.gvp.GVPLayerNorm attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.NodeAttention attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.NodeAttention attribute) feat_proj (MolecularDiffusion.modules.models.syncogen.models.semla.SemlaGenerator attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator attribute) feats (MolecularDiffusion.modules.models.flowmol.interpolant_scheduler.InterpolantScheduler attribute) feats_dim (MolecularDiffusion.modules.models.pmdm.encoders.EGNNSparseLayer attribute) (MolecularDiffusion.modules.models.pmdm.encoders.EGNNSparseNetwork attribute) feature_colors (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmacophore) feature_embedder (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) feature_layer_norm (MolecularDiffusion.modules.models.ligandiff.layer_norm.GVPLayerNorm attribute) FEATURE_MAPPING (in module MolecularDiffusion.modules.models.oareactdiff.normalizer) features (MolecularDiffusion.modules.layers.e3x.modules.Tensor attribute) featurize() (in module MolecularDiffusion.cli.analyze) (in module MolecularDiffusion.runmodes.data.featurization) (MolecularDiffusion.data.component.feature.NodeFeaturizer method) (MolecularDiffusion.runmodes.analyze.featurize.BaseFeaturizer method) (MolecularDiffusion.runmodes.analyze.featurize.SOAPFeaturizer method) (MolecularDiffusion.runmodes.analyze.featurize.SSL3DFeaturizer method) (MolecularDiffusion.runmodes.analyze.featurize.UMAFeaturizer method) featurize_all() (MolecularDiffusion.data.component.feature.NodeFeaturizer method) featurize_cmd() (in module MolecularDiffusion.cli.data) featurize_mol() (in module MolecularDiffusion.modules.models.nextmol.featurize) FeedForward (class in MolecularDiffusion.modules.layers.tabasco.transition) (class in MolecularDiffusion.modules.models.chefnmr.embedders) feedforward_network (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPInteractions attribute) FeedForwardDecoder (class in MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward) FeedForwardNetwork (class in MolecularDiffusion.modules.layers.equiformer_v2.transformer_block) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block) (class in MolecularDiffusion.modules.layers.gfmdiff.blocks) FeedForwardNetwork_equiformer (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) fetch() (in module MolecularDiffusion.assets) fetch_cmd() (in module MolecularDiffusion.cli.zoo) ff (MolecularDiffusion.modules.models.diffspectra.specformer.TSTEncoderLayer attribute) (MolecularDiffusion.modules.models.ditmc.embedding.TimeEmbedding attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) (MolecularDiffusion.modules.models.pmdm.encoders.CrossAttentionBlock attribute) ff_block (MolecularDiffusion.modules.layers.tabasco.transformer.TransformerBlock attribute) ff_func (MolecularDiffusion.modules.models.ligandiff.conv_layer.GVPConvLayer attribute) ff_linear1 (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) ff_linear2 (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) ff_linear3 (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) ff_linear4 (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) ffn (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.TransBlockV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.TransBlockV2 attribute) (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) ffn_activation (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) ffn_dim (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) ffn_edge (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) ffn_emb_dim (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer attribute) ffn_hidden_channels (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) ffn_norm (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) ffn_norm_edge (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) ffp (MolecularDiffusion.modules.models.pmdm.encoders.CrossAttentionBlock attribute) file (MolecularDiffusion.utils.io.CaptureStdIO attribute) filename (MolecularDiffusion.runmodes.train.data.DataModule attribute) final_block_channels (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) final_ff_block (MolecularDiffusion.modules.models.syncogen.models.semla.EquiInvDynamics attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiInvDynamics attribute) final_layer (MolecularDiffusion.modules.models.chefnmr.score_models.DiffusionModuleTransformer attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT attribute) final_linear (MolecularDiffusion.modules.models.nextmol.dgt.DGTDiffusion attribute) final_mlp (MolecularDiffusion.modules.models.geoldm.networks.EGNN_encoder_QM9 attribute) final_norm (MolecularDiffusion.modules.models.chefnmr.embedders.TransformerEncoder attribute) FinalLayer (class in MolecularDiffusion.modules.models.chefnmr.layers) (class in MolecularDiffusion.modules.models.ldm.denoisers.dit) FinalOutput (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet attribute) find_close_points_torch() (in module MolecularDiffusion.utils.geom_constraint) find_close_points_torch_and_push() (in module MolecularDiffusion.utils.geom_constraint) find_close_points_torch_and_push_op() (in module MolecularDiffusion.utils.geom_constraint) find_close_points_torch_and_push_op2() (in module MolecularDiffusion.utils.geom_constraint) find_close_points_torch_and_push_op_v0() (in module MolecularDiffusion.utils.geom_constraint) find_connected_components() (in module MolecularDiffusion.utils.geom_constraint) find_hydrophobes() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmacophore) (in module MolecularDiffusion.utils.shepherd_utils) find_nan_idx() (MolecularDiffusion.modules.models.difflinker.utils.FoundNaNException static method) (MolecularDiffusion.modules.models.ligandiff.utils.FoundNaNException static method) find_project_root() (in module MolecularDiffusion.molcraftdiff) find_rigid_alignment() (in module MolecularDiffusion.modules.models.etflow.flow) find_subgraph_centroids() (in module MolecularDiffusion.utils.geom_constraint) first_iteration (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) fixed (MolecularDiffusion.modules.layers.atomic_data.AtomicData attribute) fixed_atom_indices (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDPocketGenerator attribute) fixed_idx (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) flatten() (MolecularDiffusion.core.core.Tree method) (MolecularDiffusion.modules.models.gcdm.gcp_utils.ScalarVector method) Flatten_Head (class in MolecularDiffusion.modules.models.diffspectra.specformer) flax_dense() (in module MolecularDiffusion.modules.models.ditmc.layers) flax_embedding() (in module MolecularDiffusion.modules.models.ditmc.embedding) flax_layer_norm() (in module MolecularDiffusion.modules.models.ditmc.layers) float_to_tensor() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) FLOAT_TYPE (in module MolecularDiffusion.modules.tasks.diffusion_diffpharma) (in module MolecularDiffusion.modules.tasks.diffusion_diffsbdd) flow_kwargs (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTaskFactory attribute) flow_matching_config (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.ModelTaskFactory attribute) FlowMatching (class in MolecularDiffusion.modules.models.ditmc.flow_matching) FlowMatchingInterpolant (class in MolecularDiffusion.modules.tasks.diffusion_ldm) FlowMatchingModel (class in MolecularDiffusion.modules.models.tabasco.flow_model) FlowMolFlowMatchingTask (class in MolecularDiffusion.modules.tasks.diffusion_flowmol) FlowMolGraph3DTask (class in MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d) FlowMolGraph3DTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d) FlowMolTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_flowmol) FlowPath (class in MolecularDiffusion.modules.models.tabasco.flow.path) fm_num_timesteps (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask property) fn (MolecularDiffusion.modules.models.chefnmr.embedders.PreNorm attribute) for_conf (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) forbidden_atom (MolecularDiffusion.runmodes.train.data.DataModule attribute) forced_n_nodes (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenSizePrior attribute) foreach (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) formal_charge_diffusion (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) format() (in module MolecularDiffusion.utils.pretty) formula_to_symbols() (in module MolecularDiffusion.modules.models.chefnmr.unknown) forward() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.modules.layers.common.MLP method) (MolecularDiffusion.modules.layers.common.SinusoidalPositionEmbedding method) (MolecularDiffusion.modules.layers.common.SinusoidsEmbeddingNew method) (MolecularDiffusion.modules.layers.conv.EquivariantBlock method) (MolecularDiffusion.modules.layers.conv.EquivariantUpdate method) (MolecularDiffusion.modules.layers.conv.EtoX method) (MolecularDiffusion.modules.layers.conv.Etoy method) (MolecularDiffusion.modules.layers.conv.GCL method) (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock method) (MolecularDiffusion.modules.layers.conv.PositionsMLP method) (MolecularDiffusion.modules.layers.conv.SE3Norm method) (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer method) (MolecularDiffusion.modules.layers.conv.Xtoy method) (MolecularDiffusion.modules.layers.e3x.modules.Dense method) (MolecularDiffusion.modules.layers.e3x.modules.SelfAttention method) (MolecularDiffusion.modules.layers.e3x.modules.Tensor method) (MolecularDiffusion.modules.layers.equiformer_v2.activation.GateActivation method) (MolecularDiffusion.modules.layers.equiformer_v2.activation.S2Activation method) (MolecularDiffusion.modules.layers.equiformer_v2.activation.ScaledSigmoid method) (MolecularDiffusion.modules.layers.equiformer_v2.activation.ScaledSiLU method) (MolecularDiffusion.modules.layers.equiformer_v2.activation.ScaledSmoothLeakyReLU method) (MolecularDiffusion.modules.layers.equiformer_v2.activation.ScaledSwiGLU method) (MolecularDiffusion.modules.layers.equiformer_v2.activation.SeparableS2Activation method) (MolecularDiffusion.modules.layers.equiformer_v2.activation.SmoothLeakyReLU method) (MolecularDiffusion.modules.layers.equiformer_v2.activation.SwiGLU method) (MolecularDiffusion.modules.layers.equiformer_v2.drop.DropPath method) (MolecularDiffusion.modules.layers.equiformer_v2.drop.EquivariantDropout method) (MolecularDiffusion.modules.layers.equiformer_v2.drop.EquivariantDropoutArraySphericalHarmonics method) (MolecularDiffusion.modules.layers.equiformer_v2.drop.EquivariantScalarsDropout method) (MolecularDiffusion.modules.layers.equiformer_v2.drop.GraphDropPath method) (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 method) (MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf.GaussianRadialBasisLayer method) (MolecularDiffusion.modules.layers.equiformer_v2.input_block.EdgeDegreeEmbedding method) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantDegreeLayerScale method) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantLayerNormArray method) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantLayerNormArraySphericalHarmonics method) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonics method) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 method) (MolecularDiffusion.modules.layers.equiformer_v2.radial_function.RadialFunction method) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Convolution method) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Linear method) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_m_Convolution method) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Linear method) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_LinearV2 method) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork method) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention method) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.TransBlockV2 method) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.GateActivation method) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.S2Activation method) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.ScaledSigmoid method) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.ScaledSiLU method) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.ScaledSmoothLeakyReLU method) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.ScaledSwiGLU method) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.SeparableS2Activation method) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.SmoothLeakyReLU method) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.SwiGLU method) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.DropPath method) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.EquivariantDropout method) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.EquivariantDropoutArraySphericalHarmonics method) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.EquivariantScalarsDropout method) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.GraphDropPath method) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 method) (MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf.GaussianRadialBasisLayer method) (MolecularDiffusion.modules.layers.equiformer_v2_s.input_block.EdgeDegreeEmbedding method) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantDegreeLayerScale method) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantLayerNormArray method) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantLayerNormArraySphericalHarmonics method) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantRMSNormArraySphericalHarmonics method) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 method) (MolecularDiffusion.modules.layers.equiformer_v2_s.radial_function.RadialFunction method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Convolution method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Linear method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_m_Convolution method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Linear method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_LinearV2 method) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork method) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention method) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.TransBlockV2 method) (MolecularDiffusion.modules.layers.esen.esen_block.Edgewise method) (MolecularDiffusion.modules.layers.esen.esen_block.eSEN_Block method) (MolecularDiffusion.modules.layers.esen.esen_block.GridAtomwise method) (MolecularDiffusion.modules.layers.esen.esen_block.SpectralAtomwise method) (MolecularDiffusion.modules.layers.esen.nn.activation.GateActivation method) (MolecularDiffusion.modules.layers.esen.nn.activation.S2Activation method) (MolecularDiffusion.modules.layers.esen.nn.activation.SeparableS2Activation method) (MolecularDiffusion.modules.layers.esen.nn.embedding.ChgSpinDatasetEmbedding method) (MolecularDiffusion.modules.layers.esen.nn.embedding.EdgeDegreeEmbedding method) (MolecularDiffusion.modules.layers.esen.nn.gaussian_embedding.GaussianFeatureEmbedding method) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantDegreeLayerScale method) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantLayerNormArray method) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantLayerNormArraySphericalHarmonics method) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 method) (MolecularDiffusion.modules.layers.esen.nn.radial.EnvelopedBesselBasis method) (MolecularDiffusion.modules.layers.esen.nn.radial.GaussianSmearing method) (MolecularDiffusion.modules.layers.esen.nn.radial.PolynomialEnvelope method) (MolecularDiffusion.modules.layers.esen.nn.radial.RadialMLP method) (MolecularDiffusion.modules.layers.esen.nn.radial.SphericalBesselBasis method) (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2Block method) (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2DecompositionEdgeBlock method) (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2SymmetricTensorHead method) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Convolution method) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Linear method) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_m_Conv method) (MolecularDiffusion.modules.layers.esen.nn.so3_layers.SO3_Linear method) (MolecularDiffusion.modules.layers.esen.nn.utils.BackboneInterface method) (MolecularDiffusion.modules.layers.esen.nn.utils.HeadInterface method) (MolecularDiffusion.modules.layers.gfmdiff.blocks.DistEncoder method) (MolecularDiffusion.modules.layers.gfmdiff.blocks.FeedForwardNetwork method) (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock method) (MolecularDiffusion.modules.layers.gfmdiff.blocks.Low2High method) (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer method) (MolecularDiffusion.modules.layers.gfmdiff.blocks.PosUpdate method) (MolecularDiffusion.modules.layers.gfmdiff.blocks.RBF method) (MolecularDiffusion.modules.layers.gfmdiff.blocks.RBF_Emb method) (MolecularDiffusion.modules.layers.gfmdiff.blocks.SimLow2High method) (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer method) (MolecularDiffusion.modules.layers.graph_module.BackboneInterface method) (MolecularDiffusion.modules.layers.graph_module.HeadInterface method) (MolecularDiffusion.modules.layers.gvp.gvp.EdgeUpdate method) (MolecularDiffusion.modules.layers.gvp.gvp.GVP method) (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv method) (MolecularDiffusion.modules.layers.gvp.gvp.GVPDropout method) (MolecularDiffusion.modules.layers.gvp.gvp.GVPLayerNorm method) (MolecularDiffusion.modules.layers.gvp.gvp.NodePositionUpdate method) (MolecularDiffusion.modules.layers.tabasco.attention.AdaLNAttention 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(MolecularDiffusion.modules.models.apo2mol.pminet.EquivariantBlock method) (MolecularDiffusion.modules.models.apo2mol.pminet.EquivariantUpdate method) (MolecularDiffusion.modules.models.apo2mol.pminet.GCL method) (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.apo2mol.score_model.SinusoidalPosEmb method) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral method) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseH2XAttLayer method) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseX2HAttLayer method) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.SAGPoolNet method) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral method) (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) (MolecularDiffusion.modules.models.chefnmr.embedders.Attention method) 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(MolecularDiffusion.modules.models.diffsbdd.egnn.SinusoidsEmbeddingNew method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.PredefinedNoiseSchedule method) (MolecularDiffusion.modules.models.diffsmol.common.GaussianSmearing method) (MolecularDiffusion.modules.models.diffsmol.common.GVP method) (MolecularDiffusion.modules.models.diffsmol.common.GVPLayerNorm method) (MolecularDiffusion.modules.models.diffsmol.common.MLP method) (MolecularDiffusion.modules.models.diffsmol.common.ShiftedSoftplus method) (MolecularDiffusion.modules.models.diffsmol.common.SinusoidalPosEmb method) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.diffsmol.shape_ae.DecoderInner method) (MolecularDiffusion.modules.models.diffsmol.shape_ae.PointCloudAE method) (MolecularDiffusion.modules.models.diffsmol.shape_ae.VNDGCNNEncoder method) (MolecularDiffusion.modules.models.diffsmol.shape_ae.VNResnetEncoder method) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral method) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer method) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.InvariantShapeEmbLayer method) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral method) (MolecularDiffusion.modules.models.diffspectra.dmt.DMT method) (MolecularDiffusion.modules.models.diffspectra.specformer.Flatten_Head method) (MolecularDiffusion.modules.models.diffspectra.specformer.SpecFormer method) (MolecularDiffusion.modules.models.diffspectra.specformer.TSTEncoder method) (MolecularDiffusion.modules.models.diffspectra.specformer.TSTEncoderLayer method) (MolecularDiffusion.modules.models.diffspectra.specformer.TSTiEncoder method) (MolecularDiffusion.modules.models.diffspectra.specformer_layers.moving_avg method) (MolecularDiffusion.modules.models.diffspectra.specformer_layers.series_decomp method) (MolecularDiffusion.modules.models.diffspectra.specformer_layers.Transpose method) (MolecularDiffusion.modules.models.ditmc.dit.DiTLayer method) (MolecularDiffusion.modules.models.ditmc.dit.GenerativeModel method) (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer method) (MolecularDiffusion.modules.models.ditmc.embedding.DiTEdgeEmbed method) (MolecularDiffusion.modules.models.ditmc.embedding.DiTNodeEmbed method) (MolecularDiffusion.modules.models.ditmc.embedding.EdgeAttributeEmbedding method) (MolecularDiffusion.modules.models.ditmc.embedding.NodeAttributeEmbedding method) (MolecularDiffusion.modules.models.ditmc.embedding.RadialSphericalEdgeEmbedding method) (MolecularDiffusion.modules.models.ditmc.embedding.TimeEmbedding method) (MolecularDiffusion.modules.models.ditmc.layers.E3MLP method) (MolecularDiffusion.modules.models.ditmc.layers.EquivariantLayerNorm method) (MolecularDiffusion.modules.models.ditmc.layers.GaussianRandomFourierFeatures method) (MolecularDiffusion.modules.models.ditmc.layers.MLP method) (MolecularDiffusion.modules.models.ditmc.meshgraphnet.MeshGraphNetEncoder method) (MolecularDiffusion.modules.models.ditmc.meshgraphnet.MeshGraphNetLayer method) (MolecularDiffusion.modules.models.ditmc.readout.EquivariantReadout method) (MolecularDiffusion.modules.models.ditmc.readout.SimpleReadout method) (MolecularDiffusion.modules.models.egcl.EGNN method) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics method) (MolecularDiffusion.modules.models.egt.EGT_dynamics method) (MolecularDiffusion.modules.models.egt.GraphDiffTransformer method) (MolecularDiffusion.modules.models.egt.GraphTransformer method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.GammaNetwork method) (MolecularDiffusion.modules.models.en_diffusion.PositiveLinear method) (MolecularDiffusion.modules.models.en_diffusion.PredefinedNoiseSchedule method) (MolecularDiffusion.modules.models.en_diffusion.SinusoidalPosEmb method) (MolecularDiffusion.modules.models.equiformer_v2_backbone.EquiformerV2Backbone method) (MolecularDiffusion.modules.models.equiformer_v2_dynamics.EquiformerV2_dynamics method) (MolecularDiffusion.modules.models.esen.eSEN_Backbone method) (MolecularDiffusion.modules.models.esen.eSEN_VelocityFFN method) (MolecularDiffusion.modules.models.esen.GaussianFeatureEmbedding method) (MolecularDiffusion.modules.models.esen.Linear_Force_Head method) (MolecularDiffusion.modules.models.esen.MLP_EFS_Head method) (MolecularDiffusion.modules.models.esen.MLP_Energy_Head method) (MolecularDiffusion.modules.models.etflow.torchmd.CosineCutoff method) (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention method) (MolecularDiffusion.modules.models.etflow.torchmd.ExpNormalSmearing method) (MolecularDiffusion.modules.models.etflow.torchmd.GatedEquivariantBlock method) (MolecularDiffusion.modules.models.etflow.torchmd.NeighborEmbedding method) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics method) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMDDynamics method) (MolecularDiffusion.modules.models.flowmol.vector_field.EdgeUpdate method) (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField method) (MolecularDiffusion.modules.models.flowmol.vector_field.NodePositionUpdate method) (MolecularDiffusion.modules.models.flowmol_graph3d.self_conditioning.SelfConditioningResidualLayer method) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField method) (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics method) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCP method) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCP2 method) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPEmbedding method) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPInteractions method) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPMessagePassing method) (MolecularDiffusion.modules.models.gcdm.gcp_utils.GCPDropout method) (MolecularDiffusion.modules.models.gcdm.gcp_utils.GCPLayerNorm method) (MolecularDiffusion.modules.models.gcdm.gcp_utils.VectorDropout method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnLatentDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.egnn.EGNN method) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantBlock method) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantUpdate method) (MolecularDiffusion.modules.models.geoldm.egnn.GCL method) (MolecularDiffusion.modules.models.geoldm.egnn.GNN method) (MolecularDiffusion.modules.models.geoldm.egnn.SinusoidsEmbeddingNew method) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_decoder_QM9 method) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_dynamics_QM9 method) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_encoder_QM9 method) (MolecularDiffusion.modules.models.gfmdiff.dynamics.GFMDiffDynamics method) (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN method) (MolecularDiffusion.modules.models.goflow.gotennet.EQFF method) (MolecularDiffusion.modules.models.goflow.gotennet.GATA method) (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet method) (MolecularDiffusion.modules.models.goflow.gotennet.TimestepEmbedding method) (MolecularDiffusion.modules.models.goflow.ops.AtomCGREmbedding method) (MolecularDiffusion.modules.models.goflow.ops.CosineCutoff method) (MolecularDiffusion.modules.models.goflow.ops.Dense method) (MolecularDiffusion.modules.models.goflow.ops.EdgeCGREmbedding method) (MolecularDiffusion.modules.models.goflow.ops.EdgeInit method) (MolecularDiffusion.modules.models.goflow.ops.ExpNormalSmearing method) (MolecularDiffusion.modules.models.goflow.ops.MLP method) (MolecularDiffusion.modules.models.goflow.ops.NodeInit method) (MolecularDiffusion.modules.models.goflow.ops.swish method) (MolecularDiffusion.modules.models.goflow.ops.TensorInit method) (MolecularDiffusion.modules.models.goflow.ops.VecLayerNorm method) (MolecularDiffusion.modules.models.goflow.outputs.Atomwise3DOut method) (MolecularDiffusion.modules.models.goflow.outputs.GatedEquivariantBlock method) (MolecularDiffusion.modules.models.goflow.outputs.SNNDense method) (MolecularDiffusion.modules.models.ipdiff.bapnet.EquivariantBlock method) (MolecularDiffusion.modules.models.ipdiff.bapnet.EquivariantUpdate method) (MolecularDiffusion.modules.models.ipdiff.bapnet.GCL method) (MolecularDiffusion.modules.models.ipdiff.bapnet.SinusoidsEmbeddingNew method) (MolecularDiffusion.modules.models.jodo.layers.CondCoorsNorm method) (MolecularDiffusion.modules.models.jodo.layers.CondGaussianLayer method) (MolecularDiffusion.modules.models.jodo.layers.CoorsNorm method) (MolecularDiffusion.modules.models.jodo.layers.EdgeGateTransLayer method) (MolecularDiffusion.modules.models.jodo.layers.GaussianLayer method) (MolecularDiffusion.modules.models.jodo.layers.LearnedSinusodialposEmb method) (MolecularDiffusion.modules.models.jodo.layers.Trans_Layer method) (MolecularDiffusion.modules.models.jodo.layers.TransMixLayer method) (MolecularDiffusion.modules.models.jodo.mol_gnn.Cond_DGT_concat method) (MolecularDiffusion.modules.models.jodo.mol_gnn.CondEquiUpdate method) (MolecularDiffusion.modules.models.jodo.mol_gnn.DGT_concat method) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock method) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock method) (MolecularDiffusion.modules.models.jodo.mol_gnn.MultiCondEquiUpdate method) (MolecularDiffusion.modules.models.kgdiff.common.GaussianSmearing method) (MolecularDiffusion.modules.models.kgdiff.common.MLP method) (MolecularDiffusion.modules.models.kgdiff.common.ShiftedSoftplus method) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral method) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseH2XAttLayer method) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseX2HAttLayer method) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral method) (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder method) (MolecularDiffusion.modules.models.ldm.decoders.transformer.TransformerDecoder method) (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT method) (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiTBlock method) (MolecularDiffusion.modules.models.ldm.denoisers.dit.FinalLayer method) (MolecularDiffusion.modules.models.ldm.denoisers.dit.LabelEmbedder method) (MolecularDiffusion.modules.models.ldm.denoisers.dit.Mlp method) (MolecularDiffusion.modules.models.ldm.denoisers.dit.TimestepEmbedder method) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder method) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.GaussianSmearing method) (MolecularDiffusion.modules.models.ldm.encoders.transformer.TransformerEncoder method) (MolecularDiffusion.modules.models.ligandiff.conv_layer.GVPConvLayer method) (MolecularDiffusion.modules.models.ligandiff.conv_layer.GVPMessagePassing method) (MolecularDiffusion.modules.models.ligandiff.dropout.GVPDropout method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) (MolecularDiffusion.modules.models.ligandiff.egnn.Dynamics method) (MolecularDiffusion.modules.models.ligandiff.egnn.ScaledSiLU method) (MolecularDiffusion.modules.models.ligandiff.gvp.GVP method) (MolecularDiffusion.modules.models.ligandiff.gvp_model.GVPNetwork method) (MolecularDiffusion.modules.models.ligandiff.layer_norm.GVPLayerNorm method) (MolecularDiffusion.modules.models.ligandiff.noise.GammaNetwork method) (MolecularDiffusion.modules.models.ligandiff.noise.PositiveLinear method) (MolecularDiffusion.modules.models.ligandiff.noise.PredefinedNoiseSchedule method) (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock method) (MolecularDiffusion.modules.models.loqi.fn_model.E3Norm method) (MolecularDiffusion.modules.models.loqi.fn_model.MegaFNV3Conf method) (MolecularDiffusion.modules.models.loqi.fn_model.MLP method) (MolecularDiffusion.modules.models.loqi.fn_model.SwiGLU method) (MolecularDiffusion.modules.models.loqi.fn_model.TimestepEmbedder method) (MolecularDiffusion.modules.models.loqi.fn_model.XEGNNK method) (MolecularDiffusion.modules.models.loqi.self_conditioning.BaseSelfConditioningModule method) (MolecularDiffusion.modules.models.midi.layers.EtoX method) (MolecularDiffusion.modules.models.midi.layers.Etoy method) (MolecularDiffusion.modules.models.midi.layers.PositionsMLP method) (MolecularDiffusion.modules.models.midi.layers.SE3Norm method) (MolecularDiffusion.modules.models.midi.layers.Xtoy method) (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer method) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock method) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer method) (MolecularDiffusion.modules.models.nextmol.dgt.DGTDiffusion method) (MolecularDiffusion.modules.models.oareactdiff.dynamics.BaseDynamics method) (MolecularDiffusion.modules.models.oareactdiff.dynamics.EGNNDynamics method) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.CFConvS2V method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiMessage method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiOutput method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiUpdate method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.GatedEquivariantBlock method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.GCLMessage method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.MLP method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.NeighborEmb method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.OneLayerActivation method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.RBFEmb method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.vector method) (MolecularDiffusion.modules.models.oareactdiff.schedule.PredefinedNoiseSchedule method) (MolecularDiffusion.modules.models.painn_backbone.BesselRBFLayer method) (MolecularDiffusion.modules.models.painn_backbone.EnvelopLayer method) (MolecularDiffusion.modules.models.painn_backbone.EquivNet method) (MolecularDiffusion.modules.models.painn_backbone.GaussianLinearRBFLayer method) (MolecularDiffusion.modules.models.painn_backbone.GraphLayerNorm method) (MolecularDiffusion.modules.models.painn_dynamics.FourierTimeFeatures method) (MolecularDiffusion.modules.models.painn_dynamics.PaiNNDynamics method) (MolecularDiffusion.modules.models.pharmacophore_dynamics.PharmacophoreEnVariationalDiff method) (MolecularDiffusion.modules.models.pharmacophore_dynamics.PharmacophoreModelWrapper method) (MolecularDiffusion.modules.models.pmdm.common.GaussianSmearing method) (MolecularDiffusion.modules.models.pmdm.common.MultiLayerPerceptron method) (MolecularDiffusion.modules.models.pmdm.common.ShiftedSoftplus method) (MolecularDiffusion.modules.models.pmdm.encoders.CrossAttentionBlock method) (MolecularDiffusion.modules.models.pmdm.encoders.EGNNSparseLayer method) (MolecularDiffusion.modules.models.pmdm.encoders.EGNNSparseNetwork method) (MolecularDiffusion.modules.models.pmdm.encoders.MLPEdgeEncoder method) (MolecularDiffusion.modules.models.pmdm.encoders.SchNetProteinEncoder method) (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet method) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB method) (MolecularDiffusion.modules.models.shepherd_arch.egnn.EGNN method) (MolecularDiffusion.modules.models.shepherd_arch.egnn.GaussianSmearing method) (MolecularDiffusion.modules.models.shepherd_arch.egnn.MultiLayerPerceptron method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Activation method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.AttnHeads2Vec method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.ConcatIrrepsTensor method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNorm method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNormV2 method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.FeedForwardNetwork_equiformer method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.FullyConnectedTensorProductRescaleNorm method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.FullyConnectedTensorProductRescaleNormSwishGate method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.FullyConnectedTensorProductRescaleSwishGate method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Gate method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.LinearRS method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.ScaledScatter method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.SeparableFCTP method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.SmoothLeakyReLU method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.TensorProductRescale method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Vec2AttnHeads method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EdgeDegreeEmbedding method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 method) (MolecularDiffusion.modules.models.shepherd_arch.model.Model method) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.BaseModel method) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.GaussianSmearing method) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.LinearSigmoidSmearing method) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.SigmoidSmearing method) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.SiLUSmearing method) (MolecularDiffusion.modules.models.syncogen.core.Diffusion method) (MolecularDiffusion.modules.models.syncogen.diffusion.interpolation.base.InterpolatorBase method) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.base.LossBase method) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.bond_length.BondLengthLoss method) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.mse.MSELoss method) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.nll.NLLLoss method) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.pairwise_distance.PairwiseDistanceLoss method) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.smooth_lddt.SmoothLDDTLoss method) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.base.NoiseBase method) (MolecularDiffusion.modules.models.syncogen.models.layers.CtoE method) (MolecularDiffusion.modules.models.syncogen.models.layers.CtoX method) (MolecularDiffusion.modules.models.syncogen.models.layers.Ctoy method) (MolecularDiffusion.modules.models.syncogen.models.layers.EtoC method) (MolecularDiffusion.modules.models.syncogen.models.layers.EtoX method) (MolecularDiffusion.modules.models.syncogen.models.layers.Etoy method) (MolecularDiffusion.modules.models.syncogen.models.layers.GraphNorm method) (MolecularDiffusion.modules.models.syncogen.models.layers.HierarchicalPositionalEmbedding method) (MolecularDiffusion.modules.models.syncogen.models.layers.PositionsMLP method) (MolecularDiffusion.modules.models.syncogen.models.layers.SE3Norm method) (MolecularDiffusion.modules.models.syncogen.models.layers.SetNorm method) (MolecularDiffusion.modules.models.syncogen.models.layers.SimplePositionalEmbedding method) (MolecularDiffusion.modules.models.syncogen.models.layers.SinusoidalPositionalEmbedding method) (MolecularDiffusion.modules.models.syncogen.models.layers.TimestepEmbedding method) (MolecularDiffusion.modules.models.syncogen.models.layers.Xtoy method) (MolecularDiffusion.modules.models.syncogen.models.semla.BondRefine method) (MolecularDiffusion.modules.models.syncogen.models.semla.CoordAttention method) (MolecularDiffusion.modules.models.syncogen.models.semla.CoordNorm method) (MolecularDiffusion.modules.models.syncogen.models.semla.EdgeMessages method) (MolecularDiffusion.modules.models.syncogen.models.semla.EquiInvDynamics method) (MolecularDiffusion.modules.models.syncogen.models.semla.EquiMessagePassingLayer method) (MolecularDiffusion.modules.models.syncogen.models.semla.EquivariantMLP method) (MolecularDiffusion.modules.models.syncogen.models.semla.LengthsMLP method) (MolecularDiffusion.modules.models.syncogen.models.semla.NodeAttention method) (MolecularDiffusion.modules.models.syncogen.models.semla.NodeFeedForward method) (MolecularDiffusion.modules.models.syncogen.models.semla.SemlaGenerator method) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.BondRefine method) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.CoordAttention method) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.CoordNorm method) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EdgeMessages method) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiInvDynamics method) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiMessagePassingLayer method) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquivariantMLP method) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.LengthsMLP method) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.NodeAttention method) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.NodeFeedForward method) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator method) (MolecularDiffusion.modules.models.tabasco.flow.time_factor.BaseTimeFactor method) (MolecularDiffusion.modules.models.tabasco.flow.time_factor.InverseTimeFactor method) (MolecularDiffusion.modules.models.tabasco.flow.time_factor.SignalToNoiseTimeFactor method) (MolecularDiffusion.modules.models.tabasco.flow.time_factor.SquaredSignalToNoiseTimeFactor method) (MolecularDiffusion.modules.models.tabasco.flow.time_factor.SquareTimeFactor method) (MolecularDiffusion.modules.models.tabasco.flow.time_factor.ZeroTimeFactor method) (MolecularDiffusion.modules.models.tabasco.flow_model.FlowMatchingModel method) (MolecularDiffusion.modules.models.tabasco_egnn.egnn_backbone.EGNNBackbone method) (MolecularDiffusion.modules.models.tabasco_equiformer.equiformer_backbone.EquiformerV2TabascoBackbone method) (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone method) (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask method) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask method) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask method) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTask method) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDTask method) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask method) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTask method) (MolecularDiffusion.modules.tasks.diffusion_ditmc.Graph3DBatchToDiTMCAdapter method) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTask method) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask method) (MolecularDiffusion.modules.tasks.diffusion_etflow.Graph3DBatchToETFlowAdapter method) (MolecularDiffusion.modules.tasks.diffusion_flowmol.DGLToPointCloudAdapter method) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask method) (MolecularDiffusion.modules.tasks.diffusion_flowmol.PointCloudToDGLAdapter method) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask method) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.Graph3DToDGLAdapter method) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTask method) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.IPDiffDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.KGDiffDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask method) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask method) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask method) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask method) (MolecularDiffusion.modules.tasks.diffusion_loqi.Graph3DToLoQIAdapter method) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask method) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_nextmol.Graph3DBatchToNextMolAdapter method) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask method) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask method) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask method) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.PointCloudToTensorDictAdapter method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TensorDictToPointCloudAdapter method) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative method) (MolecularDiffusion.modules.tasks.regression.MLPRegressor_padded method) (MolecularDiffusion.modules.tasks.regression.MLPRegressor_pernode method) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction method) (MolecularDiffusion.modules.tasks.ssl3d.SSL3D method) forward_decoder_joint_heterogeneous_graph_encoder() (MolecularDiffusion.modules.models.shepherd_arch.model.Model method) forward_decoder_joint_processing() (MolecularDiffusion.modules.models.shepherd_arch.model.Model method) forward_jump() (in module MolecularDiffusion.modules.models.shepherd_arch.inference.noise) forward_jump_parameters() (in module MolecularDiffusion.modules.models.shepherd_arch.inference.noise) forward_schedule() (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousDiffusionInterpolant method) (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant method) forward_tp_rescale_bias() (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.TensorProductRescale method) forward_trajectory() (in module MolecularDiffusion.modules.models.shepherd_arch.inference.noise) forward_with_cfg() (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT method) forward_x1_decoder_denoiser() (MolecularDiffusion.modules.models.shepherd_arch.model.Model method) forward_x1_decoder_encoder() (MolecularDiffusion.modules.models.shepherd_arch.model.Model method) forward_x2_decoder_denoiser() (MolecularDiffusion.modules.models.shepherd_arch.model.Model method) forward_x2_decoder_encoder() (MolecularDiffusion.modules.models.shepherd_arch.model.Model method) forward_x3_decoder_denoiser() (MolecularDiffusion.modules.models.shepherd_arch.model.Model method) forward_x3_decoder_encoder() (MolecularDiffusion.modules.models.shepherd_arch.model.Model method) forward_x4_decoder_denoiser() (MolecularDiffusion.modules.models.shepherd_arch.model.Model method) forward_x4_decoder_encoder() (MolecularDiffusion.modules.models.shepherd_arch.model.Model method) FoundNaNException, [1] FourierTimeFeatures (class in MolecularDiffusion.modules.models.painn_dynamics) fp_size (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularDiversity attribute) fp_type (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularDiversity attribute) frac_coords_embedder (MolecularDiffusion.modules.models.ldm.encoders.transformer.TransformerEncoder attribute) frac_coords_embedding (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) frac_coords_head (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.decoders.transformer.TransformerDecoder attribute) FRAG_FIXED (in module MolecularDiffusion.modules.tasks.diffusion_oareactdiff) (in module MolecularDiffusion.modules.tasks.diffusion_reactot) frag_idx_to_atom_graph() (MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly.RDKitMoleculeAssembly method) frag_order (MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly.FragmentInstance attribute) FRAGMENT_ATOMADJ (in module MolecularDiffusion.modules.models.syncogen.constants.constants) FRAGMENT_ATOMFEATS (in module MolecularDiffusion.modules.models.syncogen.constants.constants) FRAGMENT_BONDFEATS (in module MolecularDiffusion.modules.models.syncogen.constants.constants) fragment_dim (MolecularDiffusion.modules.models.syncogen.models.layers.HierarchicalPositionalEmbedding attribute) fragment_embedding (MolecularDiffusion.modules.models.syncogen.models.layers.HierarchicalPositionalEmbedding attribute) fragment_graph (MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly.RDKitMoleculeAssembly attribute) FRAGMENT_MACCS (in module MolecularDiffusion.modules.models.syncogen.constants.constants) fragment_names (MolecularDiffusion.modules.models.oareactdiff.dynamics.BaseDynamics attribute) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) FRAGMENT_ORDER (in module MolecularDiffusion.data.component.oareactdiff_data) FragmentInstance (class in MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly) frame_gate (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) free_guidance_bool (MolecularDiffusion.modules.models.ditmc.flow_matching.FlowMatching attribute) free_guidance_prob (MolecularDiffusion.modules.models.ditmc.flow_matching.FlowMatching attribute) freeze() (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet method) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet method) frequencies (MolecularDiffusion.modules.layers.common.SinusoidsEmbeddingNew attribute) (MolecularDiffusion.modules.layers.esen.nn.radial.SphericalBesselBasis attribute) (MolecularDiffusion.modules.models.difflinker.egnn.SinusoidsEmbeddingNew attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.SinusoidsEmbeddingNew attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.SinusoidsEmbeddingNew attribute) (MolecularDiffusion.modules.models.geoldm.egnn.SinusoidsEmbeddingNew attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.SinusoidsEmbeddingNew attribute) frequency_embedding_dim (MolecularDiffusion.modules.models.ldm.denoisers.dit.TimestepEmbedder attribute) frequency_embedding_size (MolecularDiffusion.modules.models.chefnmr.layers.TimestepEmbedder attribute) (MolecularDiffusion.modules.models.loqi.fn_model.TimestepEmbedder attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.TimestepEmbedding attribute) from_arrays() (MolecularDiffusion.data.component.pointcloud.PointCloud_Mol class method) from_ase() (MolecularDiffusion.modules.layers.atomic_data.AtomicData class method) from_batch() (MolecularDiffusion.modules.models.tabasco.chem.convert.MoleculeConverter method) from_checkpoint() (MolecularDiffusion.modules.models.difflinker.size_gnn.LinkerSizePredictor class method) from_dict() (MolecularDiffusion.modules.layers.atomic_data.AtomicData class method) from_grid() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Grid method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Grid method) (MolecularDiffusion.modules.layers.esen.common.so3.SO3_Grid method) from_indices() (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph class method) from_onehot() (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph class method) from_tensor() (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates class method) (MolecularDiffusion.modules.models.tabasco.chem.convert.MoleculeConverter method) from_tuple() (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph class method) from_xyz() (MolecularDiffusion.data.component.pointcloud.PointCloud_Mol class method) FULL_ATOM_ENCODER (in module MolecularDiffusion.modules.tasks.diffusion_loqi) fully_connected_edges() (in module MolecularDiffusion.data.component.pmdm_data) FullyConnectedTensorProductRescale (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) FullyConnectedTensorProductRescaleNorm (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) FullyConnectedTensorProductRescaleNormSwishGate (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) FullyConnectedTensorProductRescaleSwishGate (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) fuse_softmax (MolecularDiffusion.modules.models.loqi.self_conditioning.BaseSelfConditioningModule attribute) fused_attn (MolecularDiffusion.modules.models.chefnmr.layers.Attention attribute) FusionGraph (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet attribute) G g_cutoff (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) ga (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.TransBlockV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.TransBlockV2 attribute) gain (MolecularDiffusion.modules.models.goflow.ops.Dense attribute) gamma (MolecularDiffusion.modules.layers.gfmdiff.blocks.RBF attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.RBF_Emb attribute) (MolecularDiffusion.modules.models.difflinker.noise.PredefinedNoiseSchedule attribute) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM attribute) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.PredefinedNoiseSchedule attribute) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.PredefinedNoiseSchedule attribute) (MolecularDiffusion.modules.models.en_diffusion.PredefinedNoiseSchedule attribute) (MolecularDiffusion.modules.models.ligandiff.noise.PredefinedNoiseSchedule attribute) (MolecularDiffusion.modules.models.oareactdiff.schedule.PredefinedNoiseSchedule attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) gamma_0 (MolecularDiffusion.modules.models.difflinker.noise.GammaNetwork attribute) (MolecularDiffusion.modules.models.en_diffusion.GammaNetwork attribute) (MolecularDiffusion.modules.models.ligandiff.noise.GammaNetwork attribute) gamma_1 (MolecularDiffusion.modules.models.difflinker.noise.GammaNetwork attribute) (MolecularDiffusion.modules.models.en_diffusion.GammaNetwork attribute) (MolecularDiffusion.modules.models.ligandiff.noise.GammaNetwork attribute) gamma_m (MolecularDiffusion.modules.models.goflow.gotennet.EQFF attribute) gamma_min (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion attribute) gamma_module (MolecularDiffusion.modules.models.oareactdiff.schedule.DiffSchedule attribute) gamma_s (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) gamma_tilde() (MolecularDiffusion.modules.models.difflinker.noise.GammaNetwork method) (MolecularDiffusion.modules.models.en_diffusion.GammaNetwork method) (MolecularDiffusion.modules.models.ligandiff.noise.GammaNetwork method) gamma_v (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) GammaNetwork (class in MolecularDiffusion.modules.models.difflinker.noise) (class in MolecularDiffusion.modules.models.en_diffusion) (class in MolecularDiffusion.modules.models.ligandiff.noise) GATA (class in MolecularDiffusion.modules.models.goflow.gotennet) gata (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet attribute) GATCONV_ALIASES (in module MolecularDiffusion.modules.models.ipdiff.bapnet) GATCONV_RENAMES (in module MolecularDiffusion.modules.models.ipdiff.bapnet) Gate (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) gate (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.FullyConnectedTensorProductRescaleNormSwishGate attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.FullyConnectedTensorProductRescaleSwishGate attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.SeparableFCTP attribute) gate_act (MolecularDiffusion.modules.layers.equiformer_v2.activation.GateActivation attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.GateActivation attribute) (MolecularDiffusion.modules.layers.esen.nn.activation.GateActivation attribute) (MolecularDiffusion.modules.models.esen.eSEN_VelocityFFN attribute) GateActivation (class in MolecularDiffusion.modules.layers.equiformer_v2.activation) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.activation) (class in MolecularDiffusion.modules.layers.esen.nn.activation) GatedEquivariantBlock (class in MolecularDiffusion.modules.models.etflow.torchmd) (class in MolecularDiffusion.modules.models.goflow.outputs) (class in MolecularDiffusion.modules.models.oareactdiff.leftnet) gather_dst() (in module MolecularDiffusion.modules.layers.e3x.indexed) gather_src() (in module MolecularDiffusion.modules.layers.e3x.indexed) gating_linear (MolecularDiffusion.modules.models.esen.eSEN_VelocityFFN attribute) gaussian() (in module MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf) (in module MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf) (in module MolecularDiffusion.modules.layers.esen.nn.radial) (in module MolecularDiffusion.modules.models.jodo.layers) gaussian_entropy() (in module MolecularDiffusion.modules.models.en_diffusion) gaussian_KL() (in module MolecularDiffusion.modules.models.en_diffusion) gaussian_kl() (MolecularDiffusion.modules.models.difflinker.edm.EDM static method) gaussian_KL() (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM static method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion static method) gaussian_kl() (MolecularDiffusion.modules.models.ligandiff.edm.EDM static method) gaussian_KL() (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion static method) gaussian_KL_for_dimension() (in module MolecularDiffusion.modules.models.en_diffusion) gaussian_kl_for_dimension() (MolecularDiffusion.modules.models.difflinker.edm.EDM static method) GaussianFeatureEmbedding (class in MolecularDiffusion.modules.layers.esen.nn.gaussian_embedding) (class in MolecularDiffusion.modules.models.esen) GaussianLayer (class in MolecularDiffusion.modules.models.jodo.layers) GaussianLinearRBFLayer (class in MolecularDiffusion.modules.models.painn_backbone) GaussianPrior (class in MolecularDiffusion.modules.models.ditmc.priors) GaussianRadialBasisLayer (class in MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf) GaussianRandomFourierFeatures (class in MolecularDiffusion.modules.models.ditmc.layers) GaussianSmearing (class in MolecularDiffusion.modules.layers.esen.nn.radial) (class in MolecularDiffusion.modules.models.apo2mol.common) (class in MolecularDiffusion.modules.models.diffsmol.common) (class in MolecularDiffusion.modules.models.kgdiff.common) (class in MolecularDiffusion.modules.models.ldm.encoders.equiformer) (class in MolecularDiffusion.modules.models.pmdm.common) (class in MolecularDiffusion.modules.models.shepherd_arch.egnn) (class in MolecularDiffusion.modules.models.shepherd_arch.ocp_compat) gbf_name (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) GCDMDynamics (class in MolecularDiffusion.modules.models.gcdm.dynamics) GCDMOptimizeFactory (class in MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize) GCL (class in MolecularDiffusion.modules.layers.conv) (class in MolecularDiffusion.modules.models.apo2mol.pminet) (class in MolecularDiffusion.modules.models.difflinker.egnn) (class in MolecularDiffusion.modules.models.diffpharma.egnn) (class in MolecularDiffusion.modules.models.diffsbdd.egnn) (class in MolecularDiffusion.modules.models.geoldm.egnn) (class in MolecularDiffusion.modules.models.ipdiff.bapnet) gcl1 (MolecularDiffusion.modules.models.difflinker.size_gnn.SizeGNN attribute) gcl_layers (MolecularDiffusion.modules.models.difflinker.size_gnn.SizeGNN attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) GCLMessage (class in MolecularDiffusion.modules.models.oareactdiff.leftnet) GCP (class in MolecularDiffusion.modules.models.gcdm.gcp_layers) GCP2 (class in MolecularDiffusion.modules.models.gcdm.gcp_layers) gcp_dropout (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPInteractions attribute) gcp_embedding (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) gcp_norm (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPInteractions attribute) gcp_version (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) GCPDropout (class in MolecularDiffusion.modules.models.gcdm.gcp_utils) GCPEmbedding (class in MolecularDiffusion.modules.models.gcdm.gcp_layers) GCPInteractions (class in MolecularDiffusion.modules.models.gcdm.gcp_layers) GCPLayerConfig (class in MolecularDiffusion.modules.models.gcdm.gcp_layers) GCPLayerNorm (class in MolecularDiffusion.modules.models.gcdm.gcp_utils) GCPMessagePassing (class in MolecularDiffusion.modules.models.gcdm.gcp_layers) GCPModuleConfig (class in MolecularDiffusion.modules.models.gcdm.gcp_layers) gelu() (in module MolecularDiffusion.modules.layers.e3x.activations) generate() (in module MolecularDiffusion.cli.generate) (in module MolecularDiffusion.cli.main) (in module MolecularDiffusion.modules.models.shepherd_arch.inference.sampler) (MolecularDiffusion.molcraftdiff.MolCraftDiff method) generate_blocks_cmd() (in module MolecularDiffusion.cli.data) generate_canonical_key() (in module MolecularDiffusion.utils.geom_stability) generate_conformers() (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTask method) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask method) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask method) generate_eval_samples (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) generate_from_intermediate_time() (in module MolecularDiffusion.modules.models.shepherd_arch.inference.sampler) generate_graph() (MolecularDiffusion.modules.layers.graph_module.GraphModelMixin method) (MolecularDiffusion.modules.models.esen.eSEN_Backbone method) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder method) generate_main() (in module MolecularDiffusion.cli.generate) generate_mol_blocks_and_sdf() (in module MolecularDiffusion.runmodes.data.preparation) generate_morgan() (in module MolecularDiffusion.runmodes.data.featurization) generate_soap() (in module MolecularDiffusion.runmodes.data.featurization) generate_surface_marching_cubes() (in module MolecularDiffusion.modules.models.diffsmol.shape_utils) generate_sweep() (in module MolecularDiffusion.cli.main) generation_time_keys (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) GenerativeEvalCallback (class in MolecularDiffusion.core.lightning_callbacks.generative_eval_callback) GenerativeFactory (class in MolecularDiffusion.runmodes.generate.tasks_generate) GenerativeModel (class in MolecularDiffusion.modules.models.ditmc.dit) generator (MolecularDiffusion.modules.models.diffsmol.shape_ae.PointCloudAE attribute) GeoGraph (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) GeoLDMTask (class in MolecularDiffusion.modules.tasks.diffusion_geoldm) GeoLDMTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_geoldm) GeoLDMVAETask (class in MolecularDiffusion.modules.tasks.vae_geoldm) GeoLDMVAETaskFactory (class in MolecularDiffusion.modules.tasks.vae_geoldm) geom_feature (MolecularDiffusion.data.component.feature.NodeFeaturizer attribute) GEOM_FEATURES (MolecularDiffusion.data.component.feature.NodeFeaturizer attribute) geom_predictor() (in module MolecularDiffusion.utils.geom_analyzer) GeometricInterpolator (class in MolecularDiffusion.modules.models.syncogen.diffusion.interpolation.geometric) GeometricNoise (class in MolecularDiffusion.modules.models.syncogen.diffusion.noise.geometric) GeomMolecularGenerative (class in MolecularDiffusion.modules.tasks.diffusion) get() (MolecularDiffusion.core.core.Registry class method) (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) (MolecularDiffusion.modules.models.ditmc.graph_features.MoleculeFeatureCache method) (MolecularDiffusion.modules.models.etflow.features.ETFlowFeatureCache method) (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataset method) (MolecularDiffusion.modules.tasks.diffusion_nextmol.MoleculeFeatureCache method) get_1d_sincos_pos_embed_from_grid() (in module MolecularDiffusion.modules.models.chefnmr.utils) get_activation_fn() (in module MolecularDiffusion.modules.layers.e3x.activations) (in module MolecularDiffusion.modules.models.diffspectra.specformer_layers) get_adj_matrix() (in module MolecularDiffusion.modules.models.pmdm.common) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics method) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_decoder_QM9 method) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_dynamics_QM9 method) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_encoder_QM9 method) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction method) get_align_noise() (in module MolecularDiffusion.modules.models.nextmol.dgt) get_align_position() (in module MolecularDiffusion.modules.tasks.diffusion_jodo) get_alpha_bar() (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel method) (MolecularDiffusion.modules.models.noisemodel.NoiseModel method) get_alpha_pos_ts() (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel method) get_alpha_pos_ts_sq() (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel method) get_alpha_sigma_t() (MolecularDiffusion.modules.models.noisemodel.NoiseModel method) get_angle() (in module MolecularDiffusion.modules.layers.gfmdiff.blocks) get_asset_path() (in module MolecularDiffusion.runmodes.data.preparation) get_atom_coords() (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) get_atom_idx() (MolecularDiffusion.modules.models.syncogen.api.graph.building_block.BuildingBlock method) get_atomic_charge() (in module MolecularDiffusion.utils.xyz2mol.converter) get_atomic_valences() (in module MolecularDiffusion.utils.xyz2mol.converter) get_atomic_vdw_radii() (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) (in module MolecularDiffusion.utils.shepherd_utils) get_backbone() (in module MolecularDiffusion.modules.models.syncogen.core) get_batch_idxs() (in module MolecularDiffusion.modules.models.flowmol_graph3d.graph_utils) get_batch_stats() (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) get_beta() (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel method) get_beta_schedule() (in module MolecularDiffusion.modules.models.apo2mol.score_model) (in module MolecularDiffusion.modules.models.diffsmol.score_model) (in module MolecularDiffusion.modules.models.kgdiff.score_model) (in module MolecularDiffusion.modules.models.pmdm.epsnet) get_BO() (in module MolecularDiffusion.utils.xyz2mol.converter) get_bond_order() (in module MolecularDiffusion.utils.geom_analyzer) get_bonds() (in module MolecularDiffusion.utils.xyz2mol.converter) get_center() (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates method) get_chiral_tensors() (in module MolecularDiffusion.modules.models.etflow.features) get_conformer_keys() (in module MolecularDiffusion.modules.models.syncogen.utils.file_readers) get_coord() (MolecularDiffusion.data.component.pointcloud.Atom method) (MolecularDiffusion.data.component.pointcloud.PointCloud_Mol method) get_coordinates() (in module MolecularDiffusion.modules.models.syncogen.utils.file_readers) get_cpu_count() (in module MolecularDiffusion.utils.comm) get_cutoffs() (in module MolecularDiffusion.utils.geom_analyzer) (in module MolecularDiffusion.utils.smilify) get_dataloaders() (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager method) get_default_valencies() (in module MolecularDiffusion.utils.geom_stability) get_diffusion_loss() (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.ipdiff.score_model.IPDiffScorePosNet3D method) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D method) get_dist_edges() (MolecularDiffusion.modules.models.difflinker.egnn.DynamicsWithPockets method) get_dist_edges_4A() (MolecularDiffusion.modules.models.difflinker.egnn.DynamicsWithPockets static method) get_distance() (in module MolecularDiffusion.modules.models.pmdm.common) get_e3x_activation_fn() (in module MolecularDiffusion.modules.layers.e3x.activations) get_edge_attr() (MolecularDiffusion.modules.models.ligandiff.gvp_model.GVPNetwork method) get_edge_batch_idxs() (in module MolecularDiffusion.modules.models.flowmol_graph3d.graph_utils) get_edges() (in module MolecularDiffusion.modules.models.apo2mol.pminet) (in module MolecularDiffusion.modules.models.ipdiff.bapnet) (in module MolecularDiffusion.modules.models.pmdm.common) (MolecularDiffusion.modules.models.difflinker.egnn.Dynamics method) (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics method) (MolecularDiffusion.modules.models.diffsbdd.dynamics.EGNNDynamics method) get_edges_index() (in module MolecularDiffusion.modules.models.oareactdiff.graph_tools) get_electronegativity() (in module MolecularDiffusion.runmodes.data.augmentation) get_electrostatic_potential() (in module MolecularDiffusion.utils.shepherd_score.extract_profiles) get_electrostatics() (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) get_electrostatics_given_point_charges() (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) (in module MolecularDiffusion.utils.shepherd_utils) get_example() (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) get_extra_state() (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask method) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask method) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask method) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask method) get_from_grid_mat() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Grid method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Grid method) (MolecularDiffusion.modules.layers.esen.common.so3.SO3_Grid method) get_fully_connected_edge_index() (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics static method) get_gamma() (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel method) get_GCP_with_custom_cfg() (in module MolecularDiffusion.modules.models.gcdm.gcp_layers) get_graph_data_splits() (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager method) get_graph_feature_cross() (in module MolecularDiffusion.modules.layers.vn.vn_layers) get_group() (in module MolecularDiffusion.utils.comm) get_index_embedding() (in module MolecularDiffusion.modules.models.ditmc.embedding) (in module MolecularDiffusion.modules.models.ldm.decoders.transformer) (in module MolecularDiffusion.modules.models.ldm.encoders.transformer) get_ir_index() (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.ConcatIrrepsTensor method) get_irreps_dim() (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.ConcatIrrepsTensor method) get_item() (MolecularDiffusion.data.component.dataset.GraphDataset method) (MolecularDiffusion.data.component.dataset.LazyChunkedDataset method) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset method) (MolecularDiffusion.data.component.dataset.PointCloudDataset method) (MolecularDiffusion.data.component.graph3d_dataset.Graph3DDataset method) get_l_to_all_m_expand_index() (in module MolecularDiffusion.modules.layers.equiformer_v2.layer_norm) (in module MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm) (in module MolecularDiffusion.modules.layers.esen.nn.layer_norm) get_lengths_path() (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager method) get_limit_dist() (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel method) get_line_count() (in module MolecularDiffusion.utils.file) get_linear_hard_sphere_overlap() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap) get_linear_hard_sphere_overlap_np() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap_np) get_lipinski_descriptors() (in module MolecularDiffusion.modules.models.syncogen.utils.rdkit) get_loss_weight() (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) get_mask_for_frag() (in module MolecularDiffusion.modules.models.oareactdiff.graph_tools) get_max_degree_from_tensor_e3x() (in module MolecularDiffusion.modules.models.ditmc.layers) get_max_neighbors_mask() (in module MolecularDiffusion.modules.layers.graph_module) get_max_overlap() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap) get_max_overlap_np() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap_np) get_mesh() (in module MolecularDiffusion.modules.models.diffsmol.shape_utils) get_metrics() (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator method) get_mol2_data() (in module MolecularDiffusion.modules.models.syncogen.utils.file_readers) get_molecular_surface() (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) (in module MolecularDiffusion.utils.shepherd_utils) get_molecular_surface_const_density() (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) get_molecular_surface_point_cloud() (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) get_molecular_surface_point_cloud_const_density() (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) get_molecular_volume() (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) get_mul_0() (in module MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) get_n_frag_switch() (in module MolecularDiffusion.modules.models.oareactdiff.graph_tools) get_neighbors_pymatgen() (in module MolecularDiffusion.modules.layers.atomic_data) get_node_attr_from_mol() (in module MolecularDiffusion.modules.models.ditmc.graph_features) get_node_batch_idxs() (in module MolecularDiffusion.modules.models.flowmol.graph_utils) get_nonlinearity() (in module MolecularDiffusion.modules.models.gcdm.gcp_utils) get_norm_layer() (in module MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) get_normalization_layer() (in module MolecularDiffusion.modules.layers.equiformer_v2.layer_norm) (in module MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm) (in module MolecularDiffusion.modules.layers.esen.nn.layer_norm) get_num_embedding() (in module MolecularDiffusion.modules.models.pmdm.common) get_num_graphs() (in module MolecularDiffusion.runmodes.data.augmentation) get_optimizer() (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory method) get_overlap() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap) get_overlap_batch() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap) get_overlap_esp() (in module MolecularDiffusion.utils.shepherd_score.score.electrostatic_scoring) get_overlap_esp_np() (in module MolecularDiffusion.utils.shepherd_score.score.electrostatic_scoring_np) get_overlap_full() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap) get_overlap_np() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap_np) get_overlap_pharm() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring) get_overlap_pharm_np() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring_np) get_partial_atom_features() (in module MolecularDiffusion.modules.models.syncogen.constants.utils) get_partial_bond_features() (in module MolecularDiffusion.modules.models.syncogen.constants.utils) get_partial_maccs_keys() (in module MolecularDiffusion.modules.models.syncogen.constants.utils) get_pbc_distances() (in module MolecularDiffusion.modules.layers.graph_module) get_perturbed_flow_point_and_time() (in module MolecularDiffusion.modules.models.goflow.flow) get_pharm_combo_score() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring) (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring_np) get_pharm_cond() (MolecularDiffusion.modules.models.syncogen.core.Diffusion method) get_pharmacophores() (in module MolecularDiffusion.modules.models.syncogen.utils.file_readers) (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmacophore) (in module MolecularDiffusion.utils.shepherd_utils) get_pharmacophores_dict() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmacophore) get_point_cloud() (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) get_pos_embedding() (in module MolecularDiffusion.modules.models.ldm.denoisers.dit) get_pos_indices() (in module MolecularDiffusion.modules.models.ditmc.embedding) get_property() (MolecularDiffusion.data.component.dataset.GraphDataset method) (MolecularDiffusion.data.component.dataset.LazyChunkedDataset method) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset method) (MolecularDiffusion.data.component.dataset.PointCloudDataset method) (MolecularDiffusion.data.component.graph3d_dataset.Graph3DDataset method) get_proto_mol() (in module MolecularDiffusion.utils.xyz2mol.converter) get_Qt() (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel method) get_Qt_bar() (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel method) get_radial_fn() (in module MolecularDiffusion.modules.layers.e3x.radial) get_rank() (in module MolecularDiffusion.utils.comm) (MolecularDiffusion.utils.io.RankState class method) get_repaint_schedule() (in module MolecularDiffusion.modules.models.oareactdiff.schedule) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion static method) get_rotate_inv_rescale() (MolecularDiffusion.modules.layers.equiformer_v2.so3.CoefficientMappingModule method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.CoefficientMappingModule method) get_rotmat_and_wigner() (MolecularDiffusion.modules.models.esen.eSEN_Backbone method) get_rw_feat() (in module MolecularDiffusion.modules.models.jodo.utils) get_sample_atom_volume() (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) get_scheduler() (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory method) get_scscore_model() (in module MolecularDiffusion.runmodes.data.preparation) get_SE3_transform() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.se3) get_SE3_transform_np() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.se3_np) get_shortest_path_fast_batched_x_1() (in module MolecularDiffusion.modules.models.goflow.flow) get_sigma2_bar() (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel method) get_sigma_bar() (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel method) (MolecularDiffusion.modules.models.noisemodel.NoiseModel method) get_sigma_pos_sq_ratio() (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel method) get_simple_valencies() (in module MolecularDiffusion.utils.geom_stability) get_space_size() (in module MolecularDiffusion.modules.models.kgdiff.atom_num) get_split_cache_dir() (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager method) get_split_path() (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager method) get_std_fwd() (MolecularDiffusion.modules.models.reactot.schedule.SBSchedule method) get_stereochemistry_descriptor() (in module MolecularDiffusion.runmodes.analyze.conformer_metrics) get_subgraph_mask() (in module MolecularDiffusion.modules.models.oareactdiff.graph_tools) get_tabasco_stats() (MolecularDiffusion.data.component.dataset.PointCloudDataset method) get_target_count() (in module MolecularDiffusion.runmodes.data.augmentation) get_time_embedding() (in module MolecularDiffusion.modules.layers.gvp.gvp) get_timestep_embedding() (in module MolecularDiffusion.modules.models.goflow.gotennet) get_to_grid_mat() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Grid method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Grid method) (MolecularDiffusion.modules.layers.esen.common.so3.SO3_Grid method) get_UA() (in module MolecularDiffusion.utils.xyz2mol.converter) get_UA_pairs() (in module MolecularDiffusion.utils.xyz2mol.converter) get_uma_molecule_embeddings() (in module MolecularDiffusion.runmodes.analyze.uma_embeddings) get_upper_edge_mask() (in module MolecularDiffusion.modules.models.flowmol_graph3d.graph_utils) get_vector_volume_overlap_score() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring) get_vector_volume_overlap_score_batch() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring) get_vector_volume_overlap_score_np() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring_np) get_versioned_output_path() (in module MolecularDiffusion.runmodes.train.eval) get_vocab() (in module MolecularDiffusion.modules.models.syncogen.constants.constants) get_volume_overlap_score() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring) get_volume_overlap_score_batch() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring) get_volume_overlap_score_extended_points() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring) get_volume_overlap_score_extended_points_np() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring_np) get_volume_overlap_score_np() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring_np) get_vram_size() (in module MolecularDiffusion.utils.torch) get_weight_init_by_string() (in module MolecularDiffusion.modules.models.goflow.ops) get_world_size() (in module MolecularDiffusion.utils.comm) get_x1_data() (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset method) get_x2_data() (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset method) get_x3_data_electrostatics_only() (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset method) get_x4_data() (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset method) get_x_pos_prefactor() (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel method) get_xtb_energy() (in module MolecularDiffusion.runmodes.analyze.compare_to_optimized) get_xtb_optimized_xyz() (in module MolecularDiffusion.runmodes.analyze.xtb_optimization) GetAcceptor1FeatVects() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec) GetAcceptor1FeatVects_single() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec) GetAcceptor2FeatVects() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec) GetAcceptor2FeatVects_single() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec) GetAcceptor3FeatVects() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec) GetAcceptor3FeatVects_single() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec) GetAcceptorFeatVects() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec) (in module MolecularDiffusion.utils.shepherd_utils) GetAromaticFeatVects() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec) (in module MolecularDiffusion.utils.shepherd_utils) GetDonor1FeatVects_single() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec) GetDonor2FeatVects_single() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec) GetDonor3FeatVects_single() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec) GetDonorFeatVects() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec) (in module MolecularDiffusion.utils.shepherd_utils) GetHalogenFeatVects() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec) (in module MolecularDiffusion.utils.shepherd_utils) GFMDiffDynamics (class in MolecularDiffusion.modules.models.gfmdiff.dynamics) global_attributes (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) global_frag_id (MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly.FragmentInstance attribute) glorot_orthogonal_wrapper_() (in module MolecularDiffusion.modules.models.goflow.ops) GNN (class in MolecularDiffusion.modules.models.difflinker.egnn) (class in MolecularDiffusion.modules.models.geoldm.egnn) gnn (MolecularDiffusion.modules.models.difflinker.size_gnn.LinkerSizePredictor attribute) goflow_collate() (in module MolecularDiffusion.data.component.goflow_data) GoFlowDataModule (class in MolecularDiffusion.data.component.goflow_data) GoFlowRDB7Dataset (class in MolecularDiffusion.data.component.goflow_data) GoFlowTask (class in MolecularDiffusion.modules.tasks.diffusion_goflow) GoFlowTSGenerator (class in MolecularDiffusion.modules.tasks.diffusion_goflow) GotenNet (class in MolecularDiffusion.modules.models.goflow.gotennet) gpu_group (in module MolecularDiffusion.utils.comm) gpus (MolecularDiffusion.core.engine.Engine attribute) gpus_per_node (MolecularDiffusion.core.engine.Engine attribute) grad_clip_value (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) grad_forces (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) grad_global_node_mlp (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) grad_local_node_mlp (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) gradient_clip_algorithm (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) gradient_clip_mode (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) gradient_clipping (class in MolecularDiffusion.callbacks.train_helper) gradient_clipping_0 (class in MolecularDiffusion.callbacks.train_helper) gradient_interval (MolecularDiffusion.core.engine.Engine attribute) gradnorm_queue (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) graph3d_dense_collate() (in module MolecularDiffusion.data.component.graph3d_dataset) graph3d_stats (MolecularDiffusion.runmodes.train.data.DataModule attribute) Graph3DBatchToDiTMCAdapter (class in MolecularDiffusion.modules.tasks.diffusion_ditmc) Graph3DBatchToETFlowAdapter (class in MolecularDiffusion.modules.tasks.diffusion_etflow) Graph3DBatchToNextMolAdapter (class in MolecularDiffusion.modules.tasks.diffusion_nextmol) Graph3DDataset (class in MolecularDiffusion.data.component.graph3d_dataset) Graph3DStats (class in MolecularDiffusion.data.component.graph3d_dataset) Graph3DToDGLAdapter (class in MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d) Graph3DToLoQIAdapter (class in MolecularDiffusion.modules.tasks.diffusion_loqi) graph_collate() (in module MolecularDiffusion.data.dataloader) graph_dim (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet attribute) graph_key() (in module MolecularDiffusion.modules.models.etflow.features) graph_layers (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet attribute) graph_type (MolecularDiffusion.modules.models.difflinker.egnn.Dynamics attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) GraphData (class in MolecularDiffusion.modules.layers.graph_module) GraphDataset (class in MolecularDiffusion.data.component.dataset) GraphDiffTransformer (class in MolecularDiffusion.modules.models.egt) GraphDropPath (class in MolecularDiffusion.modules.layers.equiformer_v2.drop) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.drop) GraphLayerNorm (class in MolecularDiffusion.modules.models.painn_backbone) GraphModelMixin (class in MolecularDiffusion.modules.layers.graph_module) GraphNorm (class in MolecularDiffusion.modules.models.syncogen.models.layers) graphs_path (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) GraphTransformer (class in MolecularDiffusion.modules.models.egt) (class in MolecularDiffusion.modules.models.midi.transformer_model) grid() (in module MolecularDiffusion.modules.models.chefnmr.unknown) grid_mlp (MolecularDiffusion.modules.layers.esen.esen_block.GridAtomwise attribute) grid_resolution (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) GridAtomwise (class in MolecularDiffusion.modules.layers.esen.esen_block) ground_truth_atom_mask (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) GROUPS (in module MolecularDiffusion.data.component.diffpharma_data) gt_arrays_list (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator attribute) guess_bond_matrix() (in module MolecularDiffusion.utils.smilify) guidance_scale (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) GuidanceModelPrediction (class in MolecularDiffusion.modules.tasks.diffusion) GuidanceModelPredictionPointCloud (class in MolecularDiffusion.modules.tasks.diffusion) guide_mode (MolecularDiffusion.modules.tasks.diffusion_kgdiff.KGDiffPocketGenerator attribute) GUIDE_MODES (in module MolecularDiffusion.modules.models.kgdiff.score_model) guide_stren (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolTaskFactory attribute) GuidedSampling (class in MolecularDiffusion.modules.models.tabasco.sample.guided_sampling) GVP (class in MolecularDiffusion.modules.layers.gvp.gvp) (class in MolecularDiffusion.modules.models.diffsmol.common) (class in MolecularDiffusion.modules.models.ligandiff.gvp) gvp_config (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.ModelTaskFactory attribute) gvp_layer (MolecularDiffusion.modules.models.diffsmol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) GVPBackbone (class in MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone) GVPConv (class in MolecularDiffusion.modules.layers.gvp.gvp) GVPConvLayer (class in MolecularDiffusion.modules.models.ligandiff.conv_layer) GVPDropout (class in MolecularDiffusion.modules.layers.gvp.gvp) (class in MolecularDiffusion.modules.models.ligandiff.dropout) GVPLayerNorm (class in MolecularDiffusion.modules.layers.gvp.gvp) (class in MolecularDiffusion.modules.models.diffsmol.common) (class in MolecularDiffusion.modules.models.ligandiff.layer_norm) GVPMessagePassing (class in MolecularDiffusion.modules.models.ligandiff.conv_layer) GVPNetwork (class in MolecularDiffusion.modules.models.ligandiff.gvp_model) gvps (MolecularDiffusion.modules.layers.gvp.gvp.NodePositionUpdate attribute) (MolecularDiffusion.modules.models.flowmol.vector_field.NodePositionUpdate attribute) H h (MolecularDiffusion.modules.models.ligandiff.gvp.GVP attribute) h2x_layers (MolecularDiffusion.modules.models.apo2mol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) h_embedding (MolecularDiffusion.modules.models.ligandiff.egnn.Dynamics attribute) h_embedding_out (MolecularDiffusion.modules.models.ligandiff.egnn.Dynamics attribute) h_norm (MolecularDiffusion.modules.models.loqi.fn_model.XEGNNK attribute) h_projection (MolecularDiffusion.modules.models.loqi.fn_model.XEGNNK attribute) h_tokenizer (MolecularDiffusion.modules.models.chefnmr.embedders.NMRSpectraEmbedder attribute) half_last_channel_dim (MolecularDiffusion.modules.models.goflow.ops.AtomCGREmbedding attribute) hard() (MolecularDiffusion.callbacks.train_helper.SP_regularizer method) hard_relax() (MolecularDiffusion.callbacks.train_helper.SP_regularizer method) harmonic_sampler (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask attribute) HarmonicPrior (class in MolecularDiffusion.modules.models.ditmc.priors) HarmonicSampler (class in MolecularDiffusion.modules.models.etflow.flow) HARTREE_TO_EV (in module MolecularDiffusion.runmodes.analyze.xtb_electronic) HARTREE_TO_KCAL (in module MolecularDiffusion.runmodes.analyze.conformer_metrics) has_bonds (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates attribute) has_connectivity (MolecularDiffusion.data.component.reaction_data.ReactionSide property) has_geometry (MolecularDiffusion.data.component.reaction_data.ReactionSide property) has_mask (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) has_pharmacophores (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates attribute) has_pseudotensors (MolecularDiffusion.modules.models.ditmc.layers.EquivariantLayerNorm attribute) has_ylms (MolecularDiffusion.modules.models.ditmc.layers.EquivariantLayerNorm attribute) hbap_ligand (MolecularDiffusion.modules.models.ipdiff.score_model.IPDiffScorePosNet3D attribute) hbap_protein (MolecularDiffusion.modules.models.ipdiff.score_model.IPDiffScorePosNet3D attribute) hbond_particles() (in module MolecularDiffusion.data.component.diffint_prep) (in module MolecularDiffusion.data.component.diffpharma_prep) hc_thresh (MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field.CTMCVectorField attribute) he_orthogonal_init() (in module MolecularDiffusion.modules.models.goflow.ops) head (MolecularDiffusion.modules.models.diffspectra.specformer.SpecFormer attribute) (MolecularDiffusion.modules.models.ditmc.readout.EquivariantReadout attribute) (MolecularDiffusion.modules.models.ditmc.readout.SimpleReadout attribute) head_atom (MolecularDiffusion.modules.models.tabasco_equiformer.equiformer_backbone.EquiformerV2TabascoBackbone attribute) head_dim (MolecularDiffusion.modules.layers.e3x.modules.SelfAttention attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer attribute) (MolecularDiffusion.modules.models.chefnmr.layers.Attention attribute) (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) head_disp_ffn (MolecularDiffusion.modules.models.tabasco_equiformer.equiformer_backbone.EquiformerV2TabascoBackbone attribute) head_h (MolecularDiffusion.modules.models.equiformer_v2_dynamics.EquiformerV2_dynamics attribute) head_indices (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.AttnHeads2Vec attribute) head_nf (MolecularDiffusion.modules.models.diffspectra.specformer.SpecFormer attribute) head_vel_ffn (MolecularDiffusion.modules.models.equiformer_v2_dynamics.EquiformerV2_dynamics attribute) HeadInterface (class in MolecularDiffusion.modules.layers.esen.nn.utils) (class in MolecularDiffusion.modules.layers.graph_module) heads (MolecularDiffusion.modules.models.chefnmr.embedders.Attention attribute) (MolecularDiffusion.modules.models.jodo.layers.EdgeGateTransLayer attribute) (MolecularDiffusion.modules.models.jodo.layers.Trans_Layer attribute) (MolecularDiffusion.modules.models.jodo.layers.TransMixLayer attribute) hid_dim (MolecularDiffusion.modules.models.oareactdiff.leftnet.CFConvS2V attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.NeighborEmb attribute) hidden_channels (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.esen.esen_block.Edgewise attribute) (MolecularDiffusion.modules.layers.esen.esen_block.eSEN_Block attribute) (MolecularDiffusion.modules.layers.esen.esen_block.GridAtomwise attribute) (MolecularDiffusion.modules.layers.esen.esen_block.SpectralAtomwise attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.esen.MLP_EFS_Head attribute) (MolecularDiffusion.modules.models.esen.MLP_Energy_Head attribute) (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) (MolecularDiffusion.modules.models.goflow.ops.VecLayerNorm attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiMessage attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiOutput attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiUpdate attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) (MolecularDiffusion.modules.models.pmdm.encoders.SchNetProteinEncoder attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) hidden_dim (MolecularDiffusion.modules.layers.gfmdiff.blocks.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.chefnmr.embedders.NMRSpectraEmbedder attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer attribute) (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) (MolecularDiffusion.modules.models.goflow.gotennet.TimestepEmbedding attribute) (MolecularDiffusion.modules.models.goflow.ops.EdgeCGREmbedding attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.pmdm.encoders.MLPEdgeEncoder attribute) (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) (MolecularDiffusion.runmodes.train.tasks_transformer.ModelTaskFactory attribute) hidden_dims (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gcdm.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gfmdiff.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_painn.ModelTaskFactory attribute) hidden_layer (MolecularDiffusion.modules.models.diffsmol.uni_transformer.InvariantShapeEmbLayer attribute) hidden_mlp_dims (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) hidden_nf (MolecularDiffusion.modules.layers.conv.EquivariantBlock attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.EquivariantBlock attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EGNN attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.difflinker.egnn.GNN attribute) (MolecularDiffusion.modules.models.difflinker.size_gnn.SizeGNN attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EGNN attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EGNN attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EGNN attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.geoldm.egnn.GNN attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.EquivariantBlock attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) hidden_scalar (MolecularDiffusion.modules.models.ligandiff.conv_layer.GVPMessagePassing attribute) hidden_size (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) hidden_vector (MolecularDiffusion.modules.models.ligandiff.conv_layer.GVPMessagePassing attribute) HierarchicalPositionalEmbedding (class in MolecularDiffusion.modules.models.syncogen.models.layers) high_confidence_threshold (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) higher_is_better (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularConnectivity attribute) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularDiversity attribute) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularLipinski attribute) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularNovelty attribute) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularQEDValue attribute) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularUniqueness attribute) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularValidity attribute) (MolecularDiffusion.modules.models.tabasco.utils.metrics.PoseBustersValidity attribute) (MolecularDiffusion.modules.models.tabasco.utils.metrics.PoseCheckStrainEnergy attribute) (MolecularDiffusion.runmodes.train.eval.TaskEvalConfig attribute) histogram (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQINodeDistribution attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.LigandSizeDistribution attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoNodeDistribution attribute) Histogram_cont (class in MolecularDiffusion.utils.geom_analyzer) Histogram_discrete (class in MolecularDiffusion.utils.geom_analyzer) HistogramTimeDistribution (class in MolecularDiffusion.modules.models.tabasco.flow.utils) hk_func (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseX2HAttLayer attribute) hnmr_dim (MolecularDiffusion.modules.models.chefnmr.embedders.NMRSpectraEmbedder attribute) hp (MolecularDiffusion.modules.models.painn_backbone.EquivNet attribute) hparams (MolecularDiffusion.modules.models.syncogen.models.semla.EquiInvDynamics property) (MolecularDiffusion.modules.models.syncogen.models.semla.EquiMessagePassingLayer property) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiInvDynamics property) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiMessagePassingLayer property) hq_func (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseX2HAttLayer attribute) hv_func (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseX2HAttLayer attribute) hybiridization_map (in module MolecularDiffusion.data.component.dataset) hybrid_edge_connection() (in module MolecularDiffusion.modules.models.apo2mol.common) hybrid_guidance() (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory method) hydrophobic_particles() (in module MolecularDiffusion.data.component.diffpharma_prep) HYDROPHOBIC_TYPES (in module MolecularDiffusion.data.component.diffpharma_prep) I id_embed (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet attribute) identity() (in module MolecularDiffusion.modules.layers.e3x.activations) ids (MolecularDiffusion.data.component.goflow_data.GoFlowRDB7Dataset attribute) idx (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) idx() (MolecularDiffusion.modules.models.gcdm.gcp_utils.ScalarVector method) idx_to_n_nodes (MolecularDiffusion.modules.models.diffpharma.distributions.DistributionNodes attribute) ignore_zeros (MolecularDiffusion.utils.geom_analyzer.Histogram_cont attribute) implementation (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) import_graph3d_cmd() (in module MolecularDiffusion.cli.data) importance_sampling (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) importance_sampling_transformation() (MolecularDiffusion.modules.models.syncogen.diffusion.noise.linear.LinearNoise method) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.loglinear.LogLinearNoise method) in_channels (MolecularDiffusion.modules.layers.equiformer_v2.activation.ScaledSwiGLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2.activation.SwiGLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.ScaledSwiGLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.SwiGLU attribute) in_condition_size (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) in_E (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) in_edge_nf (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) in_features (MolecularDiffusion.modules.layers.e3x.modules.Dense attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_LinearV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_LinearV2 attribute) (MolecularDiffusion.modules.layers.esen.nn.so3_layers.SO3_Linear attribute) (MolecularDiffusion.modules.models.difflinker.noise.PositiveLinear attribute) (MolecularDiffusion.modules.models.en_diffusion.PositiveLinear attribute) (MolecularDiffusion.modules.models.ligandiff.noise.PositiveLinear attribute) in_max_degree (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.readout.EquivariantReadout attribute) in_node_channels (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) in_node_nf (MolecularDiffusion.modules.models.difflinker.edm.EDM attribute) (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.egt.EGT_dynamics attribute) (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows attribute) (MolecularDiffusion.modules.models.equiformer_v2_dynamics.EquiformerV2_dynamics attribute) (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.ligandiff.edm.EDM attribute) (MolecularDiffusion.modules.models.painn_dynamics.PaiNNDynamics attribute) (MolecularDiffusion.modules.models.transformer_dynamics.TransformerDynamics attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_equiformer.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gcdm.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gfmdiff.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_painn.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_transformer.ModelTaskFactory attribute) in_num_parity (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.readout.EquivariantReadout attribute) in_proj (MolecularDiffusion.modules.models.syncogen.models.semla.NodeAttention attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.NodeAttention attribute) in_saving_ema_model_context (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) in_vector (MolecularDiffusion.modules.models.ligandiff.conv_layer.GVPMessagePassing attribute) include_an (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) include_charge (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) (MolecularDiffusion.modules.tasks.ssl3d.SSL3D attribute) include_charges (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_decoder_QM9 attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_encoder_QM9 attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gcdm.ModelTaskFactory attribute) include_cosine (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) include_de (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) include_fc_charge (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) independent_timesteps_x2 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) independent_timesteps_x3 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) independent_timesteps_x4 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) index (MolecularDiffusion.data.component.pointcloud.Atom attribute) index_select() (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) index_to_log_onehot() (in module MolecularDiffusion.modules.models.apo2mol.score_model) (in module MolecularDiffusion.modules.models.diffsmol.score_model) (in module MolecularDiffusion.modules.models.kgdiff.score_model) indexed_max() (in module MolecularDiffusion.modules.layers.e3x.indexed) indexed_softmax() (in module MolecularDiffusion.modules.layers.e3x.indexed) indexed_sum() (in module MolecularDiffusion.modules.layers.e3x.indexed) IndexType (in module MolecularDiffusion.modules.layers.atomic_data) indices (MolecularDiffusion.runmodes.generate.tasks_conformer.ConformerFactory attribute) individual (MolecularDiffusion.modules.models.diffspectra.specformer.Flatten_Head attribute) inference_annealing (MolecularDiffusion.modules.models.syncogen.diffusion.sampling.integrators.euler.EulerIntegrator attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) inference_noise_sigma (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant attribute) inflate_batch_array() (MolecularDiffusion.modules.models.difflinker.edm.EDM static method) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM static method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion static method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM static method) (MolecularDiffusion.modules.models.oareactdiff.schedule.DiffSchedule static method) (MolecularDiffusion.modules.models.reactot.schedule.SBSchedule static method) info_cmd() (in module MolecularDiffusion.cli.zoo) info_str (MolecularDiffusion.modules.layers.equiformer_v2.module_list.ModuleListInfo attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.module_list.ModuleListInfo attribute) init_edge_rot_mat() (in module MolecularDiffusion.modules.layers.equiformer_v2.edge_rot_mat) (in module MolecularDiffusion.modules.layers.equiformer_v2_s.edge_rot_mat) (in module MolecularDiffusion.modules.layers.esen.common.rotation) init_from_ckpt() (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet method) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet method) init_h_emb_layer (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) init_process_group() (in module MolecularDiffusion.utils.comm) init_rescale_bias() (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.TensorProductRescale method) initialize_extra_nodes() (in module MolecularDiffusion.utils.geom_constraint) initialize_extra_nodes_seed() (in module MolecularDiffusion.utils.geom_constraint) initialize_weights() (MolecularDiffusion.modules.models.chefnmr.score_models.DiffusionModuleTransformer method) (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT method) inpaint() (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion method) inpaint_function (MolecularDiffusion.modules.models.tabasco.sample.guided_sampling.GuidedSampling attribute) inpaint_x1_bonds (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) inpaint_x1_pos (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) inpaint_x1_x (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) inpainting_sample() (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet method) InpaintingEDM (class in MolecularDiffusion.modules.models.difflinker.edm) inplace (MolecularDiffusion.modules.layers.equiformer_v2.activation.ScaledSiLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.ScaledSiLU attribute) input_choice() (in module MolecularDiffusion.utils.io) input_dim (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseX2HAttLayer attribute) input_dims (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) input_lin (MolecularDiffusion.modules.models.jodo.mol_gnn.CondEquiUpdate attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.MultiCondEquiUpdate attribute) input_mols_dir (MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize.GCDMOptimizeFactory attribute) input_proj (MolecularDiffusion.modules.models.equiformer_v2_backbone.EquiformerV2Backbone attribute) (MolecularDiffusion.modules.models.equiformer_v2_dynamics.EquiformerV2_dynamics attribute) (MolecularDiffusion.modules.models.tabasco_equiformer.equiformer_backbone.EquiformerV2TabascoBackbone attribute) input_size (MolecularDiffusion.modules.models.painn_backbone.EquivNetHParams attribute) input_sphere_channels (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) inspect_cmd() (in module MolecularDiffusion.cli.data) inspect_db() (in module MolecularDiffusion.runmodes.data.ase_ops) install_hint() (in module MolecularDiffusion.optional) instantiate_first_stage() (MolecularDiffusion.modules.models.geoldm.diffusion.EnLatentDiffusion method) int_atom() (in module MolecularDiffusion.utils.xyz2mol.converter) INT_TYPE (in module MolecularDiffusion.modules.tasks.diffusion_apo2mol) (in module MolecularDiffusion.modules.tasks.diffusion_diffpharma) (in module MolecularDiffusion.modules.tasks.diffusion_diffsbdd) (in module MolecularDiffusion.modules.tasks.diffusion_ipdiff) (in module MolecularDiffusion.modules.tasks.diffusion_kgdiff) (in module MolecularDiffusion.modules.tasks.diffusion_pmdm) (in module MolecularDiffusion.modules.tasks.pocket_generator) integrate() (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField method) (MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field.CTMCVectorField method) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField method) integrator (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) IntegratorBase (class in MolecularDiffusion.modules.models.syncogen.diffusion.sampling.integrators.base) inter_distances() (MolecularDiffusion.modules.layers.tabasco.losses.InterDistancesLoss method) interaction (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPInteractions attribute) interaction_layers (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) interactions (MolecularDiffusion.modules.models.painn_backbone.EquivNet attribute) (MolecularDiffusion.modules.models.pmdm.encoders.SchNetProteinEncoder attribute) InterBlock (class in MolecularDiffusion.modules.layers.gfmdiff.blocks) interdist_loss (MolecularDiffusion.modules.models.tabasco.flow_model.FlowMatchingModel attribute) InterDistancesLoss (class in MolecularDiffusion.modules.layers.tabasco.losses) interh_decoder (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) interh_encoder (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) interh_nf (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM attribute) interhp_decoder (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) interhp_encoder (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) interhp_nf (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM attribute) internal_weights (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Linear attribute) Interpolant (class in MolecularDiffusion.modules.models.loqi.interpolant) (class in MolecularDiffusion.modules.models.tabasco.flow.interpolate) interpolant (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory attribute) interpolant_config (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTaskFactory attribute) interpolant_scheduler (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) interpolant_scheduler_config (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) interpolant_weights() (MolecularDiffusion.modules.models.flowmol.interpolant_scheduler.InterpolantScheduler method) InterpolantGuidance (class in MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance) InterpolantScheduler (class in MolecularDiffusion.modules.models.flowmol.interpolant_scheduler) interpolate() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousDiffusionInterpolant method) (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant method) (MolecularDiffusion.modules.models.syncogen.diffusion.interpolation.base.InterpolatorBase method) (MolecularDiffusion.modules.models.syncogen.diffusion.interpolation.geometric.GeometricInterpolator method) (MolecularDiffusion.modules.models.syncogen.diffusion.interpolation.linear.LinearInterpolator method) interpolator (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) InterpolatorBase (class in MolecularDiffusion.modules.models.syncogen.diffusion.interpolation.base) inv_cutoff (MolecularDiffusion.modules.layers.esen.nn.radial.EnvelopedBesselBasis attribute) inv_power (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) inv_sqrt_2 (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiUpdate attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) inv_sqrt_3 (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiMessage attribute) inv_sqrt_h (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiMessage attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiUpdate attribute) inv_sublayers (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) invariant_mlp (MolecularDiffusion.modules.models.syncogen.models.semla.NodeFeedForward attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.NodeFeedForward attribute) invariant_shape_layer (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) InvariantShapeEmbLayer (class in MolecularDiffusion.modules.models.diffsmol.uni_transformer) inverse_mapping (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) (MolecularDiffusion.modules.models.noisemodel.NoiseModel attribute) InverseTimeFactor (class in MolecularDiffusion.modules.models.tabasco.flow.time_factor) IPDiffDiffusionTask (class in MolecularDiffusion.modules.tasks.diffusion_ipdiff) IPDiffPocketGenerator (class in MolecularDiffusion.modules.tasks.diffusion_ipdiff) IPDiffScorePosNet3D (class in MolecularDiffusion.modules.models.ipdiff.score_model) ir (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraRecord attribute) ir_mul_list (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.ConcatIrrepsTensor attribute) irrep2_MLP (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2DecompositionEdgeBlock attribute) irreps (MolecularDiffusion.modules.layers.equiformer_v2.drop.EquivariantDropout attribute) (MolecularDiffusion.modules.layers.equiformer_v2.drop.EquivariantScalarsDropout attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.EquivariantDropout attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.EquivariantScalarsDropout attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNorm attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNormV2 attribute) irreps2gate() (in module MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) irreps_1 (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.ConcatIrrepsTensor attribute) irreps_2 (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.ConcatIrrepsTensor attribute) irreps_edge_attr (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.SeparableFCTP attribute) irreps_gated (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Gate attribute) irreps_gates (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Gate attribute) irreps_head (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.AttnHeads2Vec attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Vec2AttnHeads attribute) irreps_in (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Activation attribute) irreps_in() (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Gate method) irreps_in1 (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.TensorProductRescale attribute) irreps_in2 (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.TensorProductRescale attribute) irreps_mid_in (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Vec2AttnHeads attribute) irreps_mlp_mid (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.FeedForwardNetwork_equiformer attribute) irreps_node_attr (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.FeedForwardNetwork_equiformer attribute) irreps_node_input (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.FeedForwardNetwork_equiformer attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.SeparableFCTP attribute) irreps_node_output (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.FeedForwardNetwork_equiformer attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.SeparableFCTP attribute) irreps_out (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Activation attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.ConcatIrrepsTensor attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.TensorProductRescale attribute) irreps_out() (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Gate method) irreps_scalars (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Gate attribute) irreps_sum() (in module MolecularDiffusion.modules.layers.esen.nn.utils) is_batched (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates attribute) (MolecularDiffusion.modules.models.syncogen.api.atomics.pharmacophores.ShepherdPharmacophores attribute) (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) is_centered() (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates method) is_clean() (in module MolecularDiffusion.runmodes.data.ase_ops) is_fully_connected() (in module MolecularDiffusion.utils.geom_analyzer) (in module MolecularDiffusion.utils.geom_metrics) is_identity() (in module MolecularDiffusion.modules.models.gcdm.gcp_utils) is_mask (MolecularDiffusion.modules.models.syncogen.api.graph.building_block.BuildingBlock attribute) is_rank_zero() (in module MolecularDiffusion.cli.eval_predict) (in module MolecularDiffusion.cli.generate) (in module MolecularDiffusion.cli.predict) (in module MolecularDiffusion.cli.train) is_valid() (in module MolecularDiffusion.utils.geom_stability) is_valid_action() (in module MolecularDiffusion.modules.models.syncogen.utils.rdkit) is_valid_smiles() (in module MolecularDiffusion.modules.models.syncogen.utils.rdkit) is_vocab_loaded() (in module MolecularDiffusion.modules.models.syncogen.constants.constants) items (MolecularDiffusion.callbacks.train_helper.Queue attribute) iter_files() (in module MolecularDiffusion.runmodes.data.preparation) iter_geom() (in module MolecularDiffusion.runmodes.data.graph3d_import) iter_qm9() (in module MolecularDiffusion.runmodes.data.graph3d_import) iterations (MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize.GCDMOptimizeFactory attribute) J JodoDiffusionTask (class in MolecularDiffusion.modules.tasks.diffusion_jodo) join() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer method) joint_SO3_grid (MolecularDiffusion.modules.models.shepherd_arch.model.Model attribute) jump_length (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTSGenerator attribute) K k (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) K (MolecularDiffusion.modules.models.jodo.layers.CondGaussianLayer attribute) (MolecularDiffusion.modules.models.jodo.layers.GaussianLayer attribute) k (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) k_a_proj (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer attribute) k_e_proj (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer attribute) k_norm (MolecularDiffusion.modules.models.chefnmr.layers.Attention attribute) k_pairs (MolecularDiffusion.modules.tasks.ssl3d.PairwiseDistObjective attribute) k_proj (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer attribute) k_t (MolecularDiffusion.modules.models.ipdiff.score_model.IPDiffScorePosNet3D attribute) k_w (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) kabsch_align() (in module MolecularDiffusion.modules.models.ditmc.flow_matching) (in module MolecularDiffusion.modules.models.syncogen.api.ops.coordinates_ops) (in module MolecularDiffusion.utils.geom_metrics) kabsch_align_to() (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates method) kabsch_batch() (in module MolecularDiffusion.modules.models.nextmol.dgt) (in module MolecularDiffusion.modules.tasks.diffusion_jodo) keep_atoms (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMConstrainedGenerator attribute) kekulize (MolecularDiffusion.runmodes.train.data.DataModule attribute) kekulize_bonds() (in module MolecularDiffusion.data.component.graph3d_dataset) kernel (MolecularDiffusion.modules.layers.e3x.modules.Tensor attribute) kernel_size (MolecularDiffusion.modules.models.diffspectra.specformer_layers.moving_avg attribute) key (MolecularDiffusion.modules.layers.e3x.modules.SelfAttention attribute) (MolecularDiffusion.modules.layers.tabasco.losses.InterDistancesLoss attribute) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.Interpolant attribute) key_pad_mask (MolecularDiffusion.modules.layers.tabasco.losses.InterDistancesLoss attribute) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.Interpolant attribute) keys (MolecularDiffusion.modules.models.difflinker.linker_size.DistributionNodes attribute) (MolecularDiffusion.modules.models.en_diffusion.DistributionNodes attribute) (MolecularDiffusion.modules.models.loqi.self_conditioning.BaseSelfConditioningModule attribute) keys() (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) KGDIFF_ATOM_VOCAB (in module MolecularDiffusion.data.component.kgdiff_data) kgdiff_collate() (in module MolecularDiffusion.data.component.kgdiff_data) KGDIFF_ELEMENTS (in module MolecularDiffusion.data.component.kgdiff_data) KGDiffDataModule (class in MolecularDiffusion.data.component.kgdiff_data) KGDiffDataset (class in MolecularDiffusion.data.component.kgdiff_data) KGDiffDiffusionTask (class in MolecularDiffusion.modules.tasks.diffusion_kgdiff) KGDiffPocketGenerator (class in MolecularDiffusion.modules.tasks.diffusion_kgdiff) kl() (MolecularDiffusion.modules.tasks.diffusion_ldm.DiagonalGaussianDistribution method) kl_prior() (MolecularDiffusion.modules.models.difflinker.edm.EDM method) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.ConditionalDDPM method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion method) kl_prior_with_pocket() (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) kl_weight (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) knn() (in module MolecularDiffusion.modules.layers.vn.vn_layers) kwargs (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataModule attribute) (MolecularDiffusion.data.component.diffdec_data.DiffDecDataModule attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataModule attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataModule attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataModule attribute) (MolecularDiffusion.data.component.goflow_data.GoFlowDataModule attribute) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataModule attribute) (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataModule attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) (MolecularDiffusion.runmodes.analyze.featurize.UMAFeaturizer attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_equiformer.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gcdm.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gfmdiff.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_painn.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_transformer.ModelTaskFactory attribute) L l (MolecularDiffusion.modules.models.goflow.ops.TensorInit attribute) l1 (MolecularDiffusion.modules.models.difflinker.noise.GammaNetwork attribute) (MolecularDiffusion.modules.models.en_diffusion.GammaNetwork attribute) (MolecularDiffusion.modules.models.ligandiff.noise.GammaNetwork attribute) l2 (MolecularDiffusion.modules.models.difflinker.noise.GammaNetwork attribute) (MolecularDiffusion.modules.models.en_diffusion.GammaNetwork attribute) (MolecularDiffusion.modules.models.ligandiff.noise.GammaNetwork attribute) l3 (MolecularDiffusion.modules.models.difflinker.noise.GammaNetwork attribute) (MolecularDiffusion.modules.models.en_diffusion.GammaNetwork attribute) (MolecularDiffusion.modules.models.ligandiff.noise.GammaNetwork attribute) LabelEmbedder (class in MolecularDiffusion.modules.models.ldm.denoisers.dit) LAM_SCALING (in module MolecularDiffusion.utils.geom_metrics) (in module MolecularDiffusion.utils.shepherd_score.score.constants) lambda_ (MolecularDiffusion.callbacks.train_helper.SP_regularizer attribute) lambda_2 (MolecularDiffusion.callbacks.train_helper.SP_regularizer attribute) lambda_train (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) lambda_update_step (MolecularDiffusion.callbacks.train_helper.SP_regularizer attribute) lambda_update_value (MolecularDiffusion.callbacks.train_helper.SP_regularizer attribute) lambdas (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) langevin_dynamics_sample() (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet method) laplacian_eigen() (in module MolecularDiffusion.modules.models.ditmc.graph_features) largest_component() (in module MolecularDiffusion.modules.models.tabasco.chem.utils) last_bond_types (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask attribute) last_layer (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) last_pocket (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolDiffusionTask attribute) lat_resolution (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Grid attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Grid attribute) (MolecularDiffusion.modules.layers.esen.common.so3.SO3_Grid attribute) latent_dim (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) latent_nf (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) latent_node_nf (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE attribute) LatentGraph (class in MolecularDiffusion.modules.models.ditmc.graphs) lattice_head (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.decoders.transformer.TransformerDecoder attribute) layer_cfg (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) (MolecularDiffusion.runmodes.train.tasks_gcdm.ModelTaskFactory attribute) layer_norm (MolecularDiffusion.modules.models.etflow.torchmd.GatedEquivariantBlock attribute) layer_num (MolecularDiffusion.modules.models.diffsmol.shape_ae.DecoderInner attribute) (MolecularDiffusion.modules.models.diffsmol.shape_ae.VNDGCNNEncoder attribute) (MolecularDiffusion.modules.models.diffsmol.shape_ae.VNResnetEncoder attribute) layernorm (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) layernorm_ (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) LAYERNORM_EPS (in module MolecularDiffusion.modules.models.ditmc.layers) layers (MolecularDiffusion.modules.layers.common.MLP attribute) (MolecularDiffusion.modules.layers.tabasco.transformer.Transformer attribute) (MolecularDiffusion.modules.models.chefnmr.embedders.TransformerEncoder attribute) (MolecularDiffusion.modules.models.diffspectra.specformer.TSTEncoder attribute) (MolecularDiffusion.modules.models.ditmc.dit.GenerativeModel attribute) (MolecularDiffusion.modules.models.ditmc.layers.E3MLP attribute) (MolecularDiffusion.modules.models.ditmc.layers.MLP attribute) (MolecularDiffusion.modules.models.ditmc.meshgraphnet.MeshGraphNetEncoder attribute) (MolecularDiffusion.modules.models.goflow.ops.MLP attribute) (MolecularDiffusion.modules.models.ligandiff.gvp_model.GVPNetwork attribute) (MolecularDiffusion.modules.models.loqi.fn_model.MLP attribute) (MolecularDiffusion.modules.models.pmdm.common.MultiLayerPerceptron attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EquiInvDynamics attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiInvDynamics attribute) LazyChunkedDataset (class in MolecularDiffusion.data.component.dataset) LazyChunkedGraphDataset (class in MolecularDiffusion.data.component.dataset) lddt_loss_threshold (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) LDMTask (class in MolecularDiffusion.modules.tasks.diffusion_ldm) LDMTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_ldm) LearnedSinusodialposEmb (class in MolecularDiffusion.modules.models.jodo.layers) lecun_normal_() (in module MolecularDiffusion.modules.layers.e3x.initializers) LEFTNet (class in MolecularDiffusion.modules.models.oareactdiff.leftnet) legacy (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) len() (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataset method) length (MolecularDiffusion.modules.models.syncogen.models.semla.SemlaGenerator attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator attribute) lengths (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) LengthsMLP (class in MolecularDiffusion.modules.models.syncogen.models.semla) (class in MolecularDiffusion.modules.models.syncogen.models.semla_pharm) lg (in module MolecularDiffusion.utils.smilify) LIGAND_ATOM_ADD_AROMATIC_TYPES (in module MolecularDiffusion.modules.models.apo2mol.pminet) (in module MolecularDiffusion.modules.models.ipdiff.bapnet) ligand_atom_emb (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) ligand_atom_type_embed (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet attribute) ligand_class_index() (in module MolecularDiffusion.data.component.kgdiff_data) ligand_encoder (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) ligand_group_embedding (MolecularDiffusion.modules.models.ligandiff.egnn.Dynamics attribute) ligand_group_node_nf (MolecularDiffusion.modules.models.ligandiff.egnn.Dynamics attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) ligand_groups_from_geometry() (in module MolecularDiffusion.modules.models.ligandiff.utils) (in module MolecularDiffusion.modules.models.ligandiff_multi.utils) LIGAND_INDEX_TO_Z (in module MolecularDiffusion.data.component.kgdiff_data) ligand_pdbqt() (in module MolecularDiffusion.runmodes.analyze.docking) LigandDiffMultiTask (class in MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi) LigandDiffMultiTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi) LigandDiffMultiToPointCloud() (in module MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi) LigandDiffTask (class in MolecularDiffusion.modules.tasks.diffusion_ligandiff) LigandDiffTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_ligandiff) LigandDiffToPointCloud() (in module MolecularDiffusion.modules.tasks.diffusion_ligandiff) LigandGraph (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet attribute) LIGANDIFF_ATOM_VOCAB (in module MolecularDiffusion.modules.tasks.diffusion_ligandiff) (in module MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi) LIGANDIFF_FULL_VOCAB (in module MolecularDiffusion.modules.tasks.diffusion_ligandiff) LIGANDIFF_METAL_VOCAB (in module MolecularDiffusion.modules.tasks.diffusion_ligandiff) LIGANDIFF_MULTI_FULL_VOCAB (in module MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi) LIGANDIFF_MULTI_METAL_VOCAB (in module MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi) LIGANDIFF_MULTI_ROW_DATA_COLUMNS (in module MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi) LIGANDIFF_ROW_DATA_COLUMNS (in module MolecularDiffusion.modules.tasks.diffusion_ligandiff) LigandPocketSizePrior (class in MolecularDiffusion.modules.tasks.diffusion_diffsbdd) LigandSizeDistribution (class in MolecularDiffusion.modules.tasks.diffusion_pmdm) LIGHTNING_AVAILABLE (in module MolecularDiffusion.cli.train) lightning_module (MolecularDiffusion.modules.models.tabasco.sample.guided_sampling.GuidedSampling attribute) lightning_wrapper() (in module MolecularDiffusion.cli.train) LightningTabasco (class in MolecularDiffusion.modules.models.tabasco.lightning_tabasco) limit (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataModule attribute) (MolecularDiffusion.data.component.diffdec_data.DiffDecDataModule attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataModule attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataModule attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataModule attribute) (MolecularDiffusion.data.component.goflow_data.GoFlowDataModule attribute) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataModule attribute) (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataModule attribute) lin (MolecularDiffusion.modules.layers.conv.EtoX attribute) (MolecularDiffusion.modules.layers.conv.Etoy attribute) (MolecularDiffusion.modules.layers.conv.Xtoy attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.SAGPoolNet attribute) (MolecularDiffusion.modules.models.midi.layers.EtoX attribute) (MolecularDiffusion.modules.models.midi.layers.Etoy attribute) (MolecularDiffusion.modules.models.midi.layers.Xtoy attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.SeparableFCTP attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.CtoE attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.EtoC attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.EtoX attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.Etoy attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.Xtoy attribute) lin1 (MolecularDiffusion.modules.layers.gfmdiff.blocks.FeedForwardNetwork attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.CFConvS2V attribute) lin2 (MolecularDiffusion.modules.layers.gfmdiff.blocks.FeedForwardNetwork attribute) lin3 (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiUpdate attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) lin_cat (MolecularDiffusion.modules.layers.gfmdiff.blocks.Low2High attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.SimLow2High attribute) lin_dist1 (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) lin_edge0 (MolecularDiffusion.modules.models.jodo.layers.EdgeGateTransLayer attribute) (MolecularDiffusion.modules.models.jodo.layers.Trans_Layer attribute) (MolecularDiffusion.modules.models.jodo.layers.TransMixLayer attribute) (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) lin_edge1 (MolecularDiffusion.modules.models.jodo.layers.EdgeGateTransLayer attribute) (MolecularDiffusion.modules.models.jodo.layers.Trans_Layer attribute) (MolecularDiffusion.modules.models.jodo.layers.TransMixLayer attribute) (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) lin_key (MolecularDiffusion.modules.models.jodo.layers.EdgeGateTransLayer attribute) (MolecularDiffusion.modules.models.jodo.layers.Trans_Layer attribute) (MolecularDiffusion.modules.models.jodo.layers.TransMixLayer attribute) lin_norm_pos1 (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) lin_norm_pos2 (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) lin_query (MolecularDiffusion.modules.models.jodo.layers.EdgeGateTransLayer attribute) (MolecularDiffusion.modules.models.jodo.layers.Trans_Layer attribute) (MolecularDiffusion.modules.models.jodo.layers.TransMixLayer attribute) lin_value (MolecularDiffusion.modules.models.jodo.layers.EdgeGateTransLayer attribute) (MolecularDiffusion.modules.models.jodo.layers.Trans_Layer attribute) (MolecularDiffusion.modules.models.jodo.layers.TransMixLayer attribute) line (in module MolecularDiffusion.utils.pretty) linE1 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) linE2 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) linear (MolecularDiffusion.modules.layers.gfmdiff.blocks.DistEncoder attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.RBF_Emb attribute) (MolecularDiffusion.modules.models.chefnmr.layers.FinalLayer attribute) (MolecularDiffusion.modules.models.esen.Linear_Force_Head attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.FinalLayer attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.OneLayerActivation attribute) linear() (MolecularDiffusion.callbacks.train_helper.SP_regularizer method) linear1 (MolecularDiffusion.modules.layers.gfmdiff.blocks.Low2High attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.SimLow2High attribute) linear2 (MolecularDiffusion.modules.layers.gfmdiff.blocks.Low2High attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.SimLow2High attribute) linear_after_conv (MolecularDiffusion.modules.models.chefnmr.embedders.SpectraTokenizerConv1D attribute) linear_alpha_t() (MolecularDiffusion.modules.models.flowmol.interpolant_scheduler.InterpolantScheduler method) linear_alpha_t_prime() (MolecularDiffusion.modules.models.flowmol.interpolant_scheduler.InterpolantScheduler method) linear_attn (MolecularDiffusion.modules.models.apo2mol.attn.RetAugmentationLinearAttention attribute) linear_embed (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) Linear_Force_Head (class in MolecularDiffusion.modules.models.esen) linear_list (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Linear attribute) linear_schedule() (in module MolecularDiffusion.modules.models.oareactdiff.schedule) LinearInterpolator (class in MolecularDiffusion.modules.models.syncogen.diffusion.interpolation.linear) LinearNoise (class in MolecularDiffusion.modules.models.syncogen.diffusion.noise.linear) LinearRS (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) LinearSchedule (class in MolecularDiffusion.modules.models.loqi.interpolant) LinearSigmoidSmearing (class in MolecularDiffusion.modules.models.shepherd_arch.ocp_compat) linker_id2size (MolecularDiffusion.modules.models.difflinker.size_gnn.LinkerSizePredictor attribute) linker_sample() (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet method) LinkerSizePredictor (class in MolecularDiffusion.modules.models.difflinker.size_gnn) linX1 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) linX2 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) list_cmd() (in module MolecularDiffusion.cli.zoo) literal_eval() (in module MolecularDiffusion.utils.io) lm_batch_size (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolGenerator attribute) lmax (MolecularDiffusion.modules.layers.equiformer_v2.activation.GateActivation attribute) (MolecularDiffusion.modules.layers.equiformer_v2.activation.S2Activation attribute) (MolecularDiffusion.modules.layers.equiformer_v2.activation.SeparableS2Activation attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantDegreeLayerScale attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantLayerNormArray attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Grid attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_LinearV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Rotation attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.GateActivation attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.S2Activation attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.SeparableS2Activation attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantDegreeLayerScale attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantLayerNormArray attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantRMSNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Grid attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_LinearV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Rotation attribute) (MolecularDiffusion.modules.layers.esen.common.so3.CoefficientMapping attribute) (MolecularDiffusion.modules.layers.esen.common.so3.SO3_Grid attribute) (MolecularDiffusion.modules.layers.esen.esen_block.Edgewise attribute) (MolecularDiffusion.modules.layers.esen.esen_block.eSEN_Block attribute) (MolecularDiffusion.modules.layers.esen.esen_block.GridAtomwise attribute) (MolecularDiffusion.modules.layers.esen.esen_block.SpectralAtomwise attribute) (MolecularDiffusion.modules.layers.esen.nn.activation.GateActivation attribute) (MolecularDiffusion.modules.layers.esen.nn.activation.S2Activation attribute) (MolecularDiffusion.modules.layers.esen.nn.activation.SeparableS2Activation attribute) (MolecularDiffusion.modules.layers.esen.nn.embedding.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantDegreeLayerScale attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantLayerNormArray attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2SymmetricTensorHead attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Linear attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_m_Conv attribute) (MolecularDiffusion.modules.layers.esen.nn.so3_layers.SO3_Linear attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.esen.eSEN_VelocityFFN attribute) (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) lmax_list (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_m_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.CoefficientMappingModule attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_m_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.CoefficientMappingModule attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.models.equiformer_v2_backbone.EquiformerV2Backbone attribute) (MolecularDiffusion.modules.models.equiformer_v2_dynamics.EquiformerV2_dynamics attribute) (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) (MolecularDiffusion.modules.models.tabasco_equiformer.equiformer_backbone.EquiformerV2TabascoBackbone attribute) lmax_tensor_size() (in module MolecularDiffusion.modules.models.goflow.gotennet) lmdb (in module MolecularDiffusion.data.component.dataset) ln (MolecularDiffusion.modules.layers.gfmdiff.blocks.Low2High attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.SimLow2High attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.CondEquiUpdate attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.MultiCondEquiUpdate attribute) ln_emb (MolecularDiffusion.modules.models.oareactdiff.leftnet.NeighborEmb attribute) load() (MolecularDiffusion.core.engine.Engine method) (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataModule method) (MolecularDiffusion.data.component.diffdec_data.DiffDecDataModule method) (MolecularDiffusion.data.component.diffint_data.DiffIntDataModule method) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataModule method) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataModule method) (MolecularDiffusion.data.component.goflow_data.GoFlowDataModule method) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataModule method) (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule method) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule method) (MolecularDiffusion.data.component.pmdm_data.PMDMDataModule method) (MolecularDiffusion.modules.models.syncogen.datamodule.SyncogenDataModule method) (MolecularDiffusion.runmodes.train.data.DataModule method) load_bonds (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataset attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenSizePrior attribute) load_checkpoint_weights() (in module MolecularDiffusion.cli.eval_predict) load_conditioning_pool() (in module MolecularDiffusion.utils.conformer_pool) load_config_dict() (MolecularDiffusion.core.engine.Engine class method) load_csv() (MolecularDiffusion.data.component.dataset.GraphDataset method) (MolecularDiffusion.data.component.dataset.PointCloudDataset method) load_db() (MolecularDiffusion.data.component.dataset.GraphDataset method) (MolecularDiffusion.data.component.dataset.PointCloudDataset method) (MolecularDiffusion.data.component.graph3d_dataset.Graph3DDataset method) load_file_list_from_dir() (in module MolecularDiffusion.runmodes.analyze.xyz2mol) load_from_checkpoint() (MolecularDiffusion.core.engine.Engine class method) load_lightning_model() (in module MolecularDiffusion.cli.generate) load_mlps_layer (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) load_model() (in module MolecularDiffusion.cli.generate) (in module MolecularDiffusion.cli.predict) load_molecules_from_xyz() (in module MolecularDiffusion.utils.geom_metrics) load_mollama() (in module MolecularDiffusion.modules.models.nextmol.mollama) load_npy() (MolecularDiffusion.data.component.dataset.GraphDataset method) (MolecularDiffusion.data.component.dataset.PointCloudDataset method) load_pharmacophores (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataset attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenSizePrior attribute) load_pickle() (MolecularDiffusion.data.component.dataset.GraphDataset method) (MolecularDiffusion.data.component.dataset.PointCloudDataset method) (MolecularDiffusion.data.component.graph3d_dataset.Graph3DDataset method) load_pkl (MolecularDiffusion.runmodes.train.data.DataModule attribute) load_pose() (in module MolecularDiffusion.runmodes.analyze.docking) load_reference_source() (in module MolecularDiffusion.runmodes.analyze.similarity3d) load_shape_ae() (in module MolecularDiffusion.modules.models.diffsmol.shape_ae) load_shape_cache() (in module MolecularDiffusion.modules.tasks.diffusion_diffsmol) load_sidecar() (in module MolecularDiffusion.modules.models.chefnmr.sidecar) load_smiles() (MolecularDiffusion.data.component.dataset.GraphDataset method) load_ssl3d_task() (in module MolecularDiffusion.runmodes.analyze.ssl3d_embed) load_state_dict() (MolecularDiffusion.modules.models.syncogen.data.dataloader.FaultTolerantDistributedSampler method) (MolecularDiffusion.modules.models.syncogen.data.dataloader.RandomFaultTolerantSampler method) (MolecularDiffusion.modules.models.syncogen.models.ema.ExponentialMovingAverage method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer method) load_valency_table() (in module MolecularDiffusion.utils.geom_stability) load_vocabulary() (in module MolecularDiffusion.modules.models.syncogen.constants.constants) load_weights() (in module MolecularDiffusion.cli.train) load_xyz() (MolecularDiffusion.data.component.dataset.GraphDataset method) (MolecularDiffusion.data.component.dataset.PointCloudDataset method) local_geometry_calc() (in module MolecularDiffusion.modules.layers.gfmdiff.blocks) local_path() (in module MolecularDiffusion.assets) localize() (in module MolecularDiffusion.modules.models.gcdm.gcp_utils) log (in module MolecularDiffusion.cli.eval_predict) (in module MolecularDiffusion.cli.generate) (in module MolecularDiffusion.cli.predict) (in module MolecularDiffusion.cli.train) (in module MolecularDiffusion.modules.models.goflow.gotennet) (in module MolecularDiffusion.modules.models.tabasco.callbacks.dataset_stats) (in module MolecularDiffusion.modules.models.tabasco.callbacks.molecule_metrics) (in module MolecularDiffusion.modules.models.tabasco.callbacks.posebusters) (in module MolecularDiffusion.modules.models.tabasco.callbacks.save_molecules) (in module MolecularDiffusion.modules.models.tabasco.chem.convert) (in module MolecularDiffusion.modules.models.tabasco.utils.metric_utils) (in module MolecularDiffusion.modules.models.tabasco.utils.metrics) (in module MolecularDiffusion.utils.pretty) log() (in module MolecularDiffusion.modules.models.chefnmr.utils) (MolecularDiffusion.core.logger.LoggerBase method) (MolecularDiffusion.core.logger.LoggingLogger method) (MolecularDiffusion.core.logger.WandbLogger method) (MolecularDiffusion.core.meter.Meter method) (MolecularDiffusion.modules.models.tabasco.utils.pylogger.RankedLogger method) (MolecularDiffusion.utils.io.RankedLogger method) log_1_min_a() (in module MolecularDiffusion.modules.models.apo2mol.score_model) (in module MolecularDiffusion.modules.models.diffsmol.score_model) (in module MolecularDiffusion.modules.models.kgdiff.score_model) log_add_exp() (in module MolecularDiffusion.modules.models.apo2mol.score_model) (in module MolecularDiffusion.modules.models.diffsmol.score_model) (in module MolecularDiffusion.modules.models.kgdiff.score_model) log_alphas_cumprod_v (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) log_alphas_v (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) log_categorical() (in module MolecularDiffusion.modules.models.apo2mol.score_model) (in module MolecularDiffusion.modules.models.diffsmol.score_model) (in module MolecularDiffusion.modules.models.kgdiff.score_model) log_config() (MolecularDiffusion.core.logger.LoggerBase method) (MolecularDiffusion.core.logger.LoggingLogger method) (MolecularDiffusion.core.logger.WandbLogger method) (MolecularDiffusion.core.meter.Meter method) log_constant_of_p_x_given_z0() (MolecularDiffusion.modules.models.difflinker.edm.EDM method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) log_constants_p_h_given_z0() (MolecularDiffusion.modules.models.geoldm.diffusion.EnLatentDiffusion method) log_constants_p_x_given_z0() (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion method) log_constants_p_x_given_z0_pyG() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) log_hyperparameters() (in module MolecularDiffusion.cli.eval_predict) (in module MolecularDiffusion.cli.generate) (in module MolecularDiffusion.cli.predict) (in module MolecularDiffusion.cli.train) log_info() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) log_interval (MolecularDiffusion.core.meter.Meter attribute) (MolecularDiffusion.runmodes.train.logger.Logger attribute) log_normal() (in module MolecularDiffusion.modules.models.apo2mol.score_model) (in module MolecularDiffusion.modules.models.diffsmol.score_model) (in module MolecularDiffusion.modules.models.kgdiff.score_model) log_one_minus_alphas_cumprod_v (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) log_one_minus_alphas_v (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) log_p_xh_given_z0_without_constants() (MolecularDiffusion.modules.models.difflinker.edm.EDM method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) log_pN() (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) log_prob() (MolecularDiffusion.modules.models.difflinker.linker_size.DistributionNodes method) (MolecularDiffusion.modules.models.diffpharma.distributions.DistributionNodes method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.DistributionNodes method) (MolecularDiffusion.modules.models.en_diffusion.DistributionNodes method) log_prob_n1_given_n2() (MolecularDiffusion.modules.models.diffpharma.distributions.DistributionNodes method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.DistributionNodes method) log_prob_n2_given_n1() (MolecularDiffusion.modules.models.diffpharma.distributions.DistributionNodes method) log_pxh_given_z0_without_constants() (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnLatentDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion method) log_pxh_given_z0_without_constants_pyG() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) log_sample_categorical() (in module MolecularDiffusion.modules.models.apo2mol.score_model) (in module MolecularDiffusion.modules.models.diffsmol.score_model) (in module MolecularDiffusion.modules.models.kgdiff.score_model) log_system_info() (in module MolecularDiffusion.cli.main) (in module MolecularDiffusion.molcraftdiff) logaritmic() (MolecularDiffusion.callbacks.train_helper.SP_regularizer method) Logger (class in MolecularDiffusion.runmodes.train.logger) logger (in module MolecularDiffusion.callbacks.train_helper) (in module MolecularDiffusion.cli.data) (in module MolecularDiffusion.cli.main) (in module MolecularDiffusion.cli.zoo) (in module MolecularDiffusion.core.engine) (in module MolecularDiffusion.core.engine_lightning) (in module MolecularDiffusion.core.lightning_callbacks.ema_callback) (in module MolecularDiffusion.core.lightning_callbacks.generative_eval_callback) (in module MolecularDiffusion.core.meter) (in module MolecularDiffusion.data.component.apo2mol_data) (in module MolecularDiffusion.data.component.dataset) (in module MolecularDiffusion.data.component.diffdec_data) (in module MolecularDiffusion.data.component.diffpharma_data) (in module MolecularDiffusion.data.component.diffsbdd_data) (in module MolecularDiffusion.data.component.goflow_data) (in module MolecularDiffusion.data.component.graph3d_dataset) (in module MolecularDiffusion.data.component.kgdiff_data) (in module MolecularDiffusion.data.component.oareactdiff_data) (in module MolecularDiffusion.data.component.pharmacophore) (in module MolecularDiffusion.data.component.pmdm_data) (in module MolecularDiffusion.data.dataset) (in module MolecularDiffusion.data.lightning_data_module) (in module MolecularDiffusion.modules.models.apo2mol.pminet) (in module MolecularDiffusion.modules.models.apo2mol.score_model) (in module MolecularDiffusion.modules.models.chefnmr.sidecar) (in module MolecularDiffusion.modules.models.chefnmr.unknown) (in module MolecularDiffusion.modules.models.en_diffusion) (in module MolecularDiffusion.modules.models.etflow.features) (in module MolecularDiffusion.modules.models.pharmacophore_dynamics) (in module MolecularDiffusion.modules.models.syncogen.datamodule) (in module MolecularDiffusion.modules.models.tabasco.data.transforms) (in module MolecularDiffusion.modules.tasks.diffusion) (in module MolecularDiffusion.modules.tasks.diffusion_apo2mol) (in module MolecularDiffusion.modules.tasks.diffusion_chefnmr) (in module MolecularDiffusion.modules.tasks.diffusion_diffspectra) (in module MolecularDiffusion.modules.tasks.diffusion_ditmc) (in module MolecularDiffusion.modules.tasks.diffusion_etflow) (in module MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d) (in module MolecularDiffusion.modules.tasks.diffusion_jodo) (in module MolecularDiffusion.modules.tasks.diffusion_loqi) (in module MolecularDiffusion.modules.tasks.diffusion_midi) (in module MolecularDiffusion.modules.tasks.diffusion_nextmol) (in module MolecularDiffusion.modules.tasks.diffusion_syncogen) (in module MolecularDiffusion.modules.tasks.elucidation_generator) (in module MolecularDiffusion.modules.tasks.pharmacophore) (in module MolecularDiffusion.molcraftdiff) (in module MolecularDiffusion.runmodes.analyze.conformer_metrics) (in module MolecularDiffusion.runmodes.analyze.similarity3d) (in module MolecularDiffusion.runmodes.analyze.xtb_electronic) (in module MolecularDiffusion.runmodes.data.ase_ops) (in module MolecularDiffusion.runmodes.data.augmentation) (in module MolecularDiffusion.runmodes.data.featurization) (in module MolecularDiffusion.runmodes.data.graph3d_import) (in module MolecularDiffusion.runmodes.data.preparation) (in module MolecularDiffusion.runmodes.generate.tasks_conformer) (in module MolecularDiffusion.runmodes.generate.tasks_generate) (in module MolecularDiffusion.runmodes.train.data) (in module MolecularDiffusion.runmodes.train.tasks_egcl) (in module MolecularDiffusion.runmodes.train.tasks_egt) (in module MolecularDiffusion.runmodes.train.tasks_equiformer) (in module MolecularDiffusion.runmodes.train.tasks_esen) (in module MolecularDiffusion.runmodes.train.tasks_gcdm) (in module MolecularDiffusion.runmodes.train.tasks_gfmdiff) (in module MolecularDiffusion.runmodes.train.tasks_painn) (in module MolecularDiffusion.runmodes.train.tasks_transformer) (in module MolecularDiffusion.utils.conformer_pool) (in module MolecularDiffusion.utils.file) (in module MolecularDiffusion.utils.geom_constraint) (in module MolecularDiffusion.utils.geom_metrics) (in module MolecularDiffusion.utils.shepherd_utils) (MolecularDiffusion.core.logger.LoggingLogger attribute) (MolecularDiffusion.core.meter.Meter attribute) (MolecularDiffusion.runmodes.train.logger.Logger attribute) LoggerBase (class in MolecularDiffusion.core.logger) LoggingLogger (class in MolecularDiffusion.core.logger) logistic() (MolecularDiffusion.callbacks.train_helper.SP_regularizer method) LogLinearNoise (class in MolecularDiffusion.modules.models.syncogen.diffusion.noise.loglinear) logP() (in module MolecularDiffusion.modules.tasks.metrics) logvar (MolecularDiffusion.modules.tasks.diffusion_ldm.DiagonalGaussianDistribution attribute) long_array() (in module MolecularDiffusion.utils.pretty) LoQIConformerTask (class in MolecularDiffusion.modules.tasks.diffusion_loqi) LoQINodeDistribution (class in MolecularDiffusion.modules.tasks.diffusion_loqi) loss() (MolecularDiffusion.modules.models.ditmc.flow_matching.FlowMatching method) loss_a (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) loss_c (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) loss_cat (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) loss_chi_weight (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) loss_clamp (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory attribute) loss_coefs (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) loss_exp_weight (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) loss_from_bounds() (MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance.UFFBoundGuidance method) loss_param (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) loss_pos_type (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) loss_scale (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory attribute) loss_t_scale (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant attribute) loss_type (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM attribute) (MolecularDiffusion.modules.models.diffsmol.shape_ae.DecoderInner attribute) (MolecularDiffusion.modules.models.diffsmol.shape_ae.PointCloudAE attribute) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative attribute) loss_v_weight (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) loss_weight (MolecularDiffusion.modules.models.tabasco.flow.interpolate.Interpolant attribute) loss_weight_t() (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousDiffusionInterpolant method) (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant method) loss_weight_type (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant attribute) loss_weighting (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) loss_weights (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) loss_weights() (MolecularDiffusion.modules.models.flowmol.interpolant_scheduler.InterpolantScheduler method) loss_x (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) LossBase (class in MolecularDiffusion.modules.models.syncogen.diffusion.loss.base) losses (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.base.LossList attribute) LossList (class in MolecularDiffusion.modules.models.syncogen.diffusion.loss.base) LossMode (in module MolecularDiffusion.modules.models.syncogen.diffusion.loss.base) Low2High (class in MolecularDiffusion.modules.layers.gfmdiff.blocks) low2high_dropout (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) lr (MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance.UFFBoundGuidance attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) M m (MolecularDiffusion.callbacks.train_helper.gradient_clipping attribute) (MolecularDiffusion.callbacks.train_helper.gradient_clipping_0 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_m_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_m_Convolution attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_m_Conv attribute) (MolecularDiffusion.modules.models.difflinker.linker_size.DistributionNodes attribute) (MolecularDiffusion.modules.models.diffpharma.distributions.DistributionNodes attribute) (MolecularDiffusion.modules.models.en_diffusion.DistributionNodes attribute) (MolecularDiffusion.modules.models.ligandiff.gvp.GVP attribute) m_0_num_coefficients (MolecularDiffusion.modules.layers.equiformer_v2.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.esen.nn.embedding.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EdgeDegreeEmbedding attribute) m_all_num_coefficents (MolecularDiffusion.modules.layers.equiformer_v2.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.esen.nn.embedding.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EdgeDegreeEmbedding attribute) m_dim (MolecularDiffusion.modules.models.pmdm.encoders.EGNNSparseLayer attribute) m_output_channels (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_m_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_m_Convolution attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Linear attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_m_Conv attribute) m_para() (in module MolecularDiffusion.modules.models.equifm.paths) m_size (MolecularDiffusion.modules.layers.esen.common.so3.CoefficientMapping attribute) mae_eval (MolecularDiffusion.runmodes.train.eval.TaskEvalConfig attribute) main() (in module MolecularDiffusion.cli.main) (in module MolecularDiffusion.molcraftdiff) (in module MolecularDiffusion.runmodes.analyze.xyz2mol) (in module MolecularDiffusion.runmodes.data.graph3d_import) (in module MolecularDiffusion.runmodes.generate.sweep) make_beta_schedule() (in module MolecularDiffusion.modules.models.reactot.schedule) make_configurable() (in module MolecularDiffusion.core.core) make_graph_fully_connected() (in module MolecularDiffusion.modules.models.loqi.graph_utils) make_item() (in module MolecularDiffusion.data.component.diffint_data) make_molecular_dit() (in module MolecularDiffusion.modules.models.ditmc.build) make_molecular_dit_so3() (in module MolecularDiffusion.modules.models.ditmc.build) manager (MolecularDiffusion.modules.models.syncogen.datamodule.SyncogenDataModule attribute) MANIFEST (in module MolecularDiffusion.assets) manifest() (in module MolecularDiffusion.assets) MAP_ATOM_TYPE_AROMATIC_TO_INDEX (in module MolecularDiffusion.data.component.kgdiff_data) map_to_dir (MolecularDiffusion.modules.layers.vn.vn_layers.VNLeakyReLU attribute) (MolecularDiffusion.modules.layers.vn.vn_layers.VNLinearLeakyReLU attribute) (MolecularDiffusion.modules.layers.vn.vn_layers.VNMaxPool attribute) map_to_feat (MolecularDiffusion.modules.layers.vn.vn_layers.VNLinear attribute) (MolecularDiffusion.modules.layers.vn.vn_layers.VNLinearLeakyReLU attribute) MAPPING (in module MolecularDiffusion.modules.models.reactot.en_sb) mapping (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Grid attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Rotation attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Grid attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Rotation attribute) (MolecularDiffusion.modules.layers.esen.common.so3.SO3_Grid attribute) (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) (MolecularDiffusion.modules.models.noisemodel.NoiseModel attribute) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) MAPPING_INITIAL (in module MolecularDiffusion.modules.models.reactot.en_sb) mapping_initial (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) mappingReduced (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.esen.esen_block.Edgewise attribute) (MolecularDiffusion.modules.layers.esen.nn.embedding.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Linear attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) marginal (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.LigandPocketSizePrior attribute) marginal_alpha() (MolecularDiffusion.modules.models.jodo.noise_schedule.NoiseScheduleVP method) (MolecularDiffusion.modules.models.nextmol.scheduler.NoiseScheduleVPV2 method) marginal_log_mean_coeff() (MolecularDiffusion.modules.models.jodo.noise_schedule.NoiseScheduleVP method) (MolecularDiffusion.modules.models.nextmol.scheduler.NoiseScheduleVPV2 method) marginal_prob() (MolecularDiffusion.modules.models.jodo.noise_schedule.NoiseScheduleVP method) (MolecularDiffusion.modules.models.nextmol.scheduler.NoiseScheduleVPV2 method) marginal_size_distribution() (in module MolecularDiffusion.modules.models.kgdiff.atom_num) marginal_std() (MolecularDiffusion.modules.models.jodo.noise_schedule.NoiseScheduleVP method) (MolecularDiffusion.modules.models.nextmol.scheduler.NoiseScheduleVPV2 method) MarginalUniformTransition (class in MolecularDiffusion.modules.models.midi.noise_model) mask() (MolecularDiffusion.modules.models.gcdm.gcp_utils.ScalarVector method) (MolecularDiffusion.modules.models.midi.placeholder.PlaceHolder method) mask_and_zero_com() (in module MolecularDiffusion.modules.models.tabasco.utils.tensor_ops) MASK_CHANNEL (in module MolecularDiffusion.modules.models.syncogen.api.ops.graph_ops) mask_idxs (MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field.CTMCVectorField attribute) mask_indices_cache (MolecularDiffusion.modules.layers.equiformer_v2.so3.CoefficientMappingModule attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.CoefficientMappingModule attribute) mask_rate (MolecularDiffusion.modules.tasks.ssl3d.MaskedAtomTypeObjective attribute) mask_token (MolecularDiffusion.modules.tasks.ssl3d.MaskedAtomTypeObjective attribute) mask_value (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.TabascoEGNNDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.TabascoEquiformerDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.TabascoGVPDiffusionTask attribute) maskable_channels (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) masked() (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph class method) masked_mean() (in module MolecularDiffusion.modules.layers.functional) masked_softmax() (in module MolecularDiffusion.modules.layers.conv) (in module MolecularDiffusion.modules.models.midi.layers) MaskedAtomTypeObjective (class in MolecularDiffusion.modules.tasks.ssl3d) matthews_corrcoef() (in module MolecularDiffusion.modules.tasks.metrics) max_atom (MolecularDiffusion.data.component.graph3d_dataset.Graph3DDataset attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolGenerator attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) max_atoms (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.HierarchicalPositionalEmbedding attribute) MAX_ATOMS_PER_BB (in module MolecularDiffusion.modules.models.syncogen.constants.constants) max_bbs (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenSizePrior attribute) MAX_CHI (in module MolecularDiffusion.data.component.apo2mol_data) (in module MolecularDiffusion.modules.models.apo2mol.residue_ops) max_consecutive_bad_batches (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) max_degree (MolecularDiffusion.modules.layers.e3x.modules.Dense attribute) (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.embedding.RadialSphericalEdgeEmbedding attribute) (MolecularDiffusion.modules.models.ditmc.layers.EquivariantLayerNorm attribute) max_degree_qk (MolecularDiffusion.modules.layers.e3x.modules.SelfAttention attribute) max_fragments (MolecularDiffusion.modules.models.syncogen.models.layers.HierarchicalPositionalEmbedding attribute) max_frequency (MolecularDiffusion.modules.models.ditmc.embedding.DiTEdgeEmbed attribute) max_grad_norm (MolecularDiffusion.callbacks.train_helper.gradient_clipping attribute) (MolecularDiffusion.callbacks.train_helper.gradient_clipping_0 attribute) max_grad_norms (MolecularDiffusion.callbacks.train_helper.gradient_clipping attribute) (MolecularDiffusion.callbacks.train_helper.gradient_clipping_0 attribute) max_len (MolecularDiffusion.callbacks.train_helper.gradient_clipping attribute) (MolecularDiffusion.callbacks.train_helper.gradient_clipping_0 attribute) (MolecularDiffusion.callbacks.train_helper.Queue attribute) (MolecularDiffusion.modules.layers.tabasco.positional_encoder.SinusoidEncoding attribute) (MolecularDiffusion.modules.layers.tabasco.positional_encoder.TimeFourierEncoding attribute) MAX_LIG_LEN (in module MolecularDiffusion.modules.models.apo2mol.score_model) MAX_LIGAND_SIZE (in module MolecularDiffusion.modules.tasks.diffusion_pmdm) max_lmax (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork attribute) max_min_norm() (MolecularDiffusion.modules.models.goflow.ops.VecLayerNorm method) max_mol_size (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) max_molecules (MolecularDiffusion.runmodes.generate.tasks_conformer.ConformerFactory attribute) max_n_atoms (MolecularDiffusion.modules.models.chefnmr.sidecar.ChefNMRSidecar property) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) max_n_conformers (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) max_n_lig (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.ModelTaskFactory attribute) max_n_nodes (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeNodeDistribution property) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.TabascoEGNNDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.TabascoEquiformerDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.TabascoGVPDiffusionTask attribute) max_n_pocket (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.ModelTaskFactory attribute) max_neighbors (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) max_node_types_x4 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) MAX_NUM_AA (in module MolecularDiffusion.data.component.kgdiff_data) (in module MolecularDiffusion.data.component.pmdm_data) max_num_elements (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.esen.nn.embedding.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.decoders.transformer.TransformerDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.transformer.TransformerEncoder attribute) max_num_neighbors (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask attribute) MAX_PHARM (in module MolecularDiffusion.modules.models.syncogen.constants.constants) max_radius (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) max_records (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) max_retries (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTSGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTSGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTSGenerator attribute) (MolecularDiffusion.modules.tasks.pocket_generator.PocketGenerator attribute) max_sample_attempts (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask attribute) MAX_SEED_VALUE (in module MolecularDiffusion.utils.torch) max_sf_tokens (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolGenerator attribute) max_t (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant attribute) max_value (MolecularDiffusion.modules.models.tabasco.flow.time_factor.BaseTimeFactor attribute) max_z (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) MDLM (class in MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.mdlm) mean (MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf.GaussianRadialBasisLayer attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf.GaussianRadialBasisLayer attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.DiagonalGaussianDistribution attribute) mean() (in module MolecularDiffusion.utils.torch) (MolecularDiffusion.callbacks.train_helper.Queue method) mean_init_max (MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf.GaussianRadialBasisLayer attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf.GaussianRadialBasisLayer attribute) mean_init_min (MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf.GaussianRadialBasisLayer attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf.GaussianRadialBasisLayer attribute) mean_pool() (in module MolecularDiffusion.modules.layers.vn.vn_layers) mean_shift (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNorm attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNormV2 attribute) mean_w_mask() (in module MolecularDiffusion.modules.models.tabasco.utils.tensor_ops) mean_with_nan() (in module MolecularDiffusion.modules.layers.functional) means (MolecularDiffusion.modules.models.jodo.layers.CondGaussianLayer attribute) (MolecularDiffusion.modules.models.jodo.layers.GaussianLayer attribute) MegaFNV3Conf (class in MolecularDiffusion.modules.models.loqi.fn_model) merge_cmd() (in module MolecularDiffusion.cli.data) merge_dbs() (in module MolecularDiffusion.runmodes.data.ase_ops) MeshGraphNetEncoder (class in MolecularDiffusion.modules.models.ditmc.meshgraphnet) MeshGraphNetLayer (class in MolecularDiffusion.modules.models.ditmc.meshgraphnet) message() (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv method) (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention method) (MolecularDiffusion.modules.models.etflow.torchmd.NeighborEmbedding method) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPMessagePassing method) (MolecularDiffusion.modules.models.goflow.gotennet.GATA method) (MolecularDiffusion.modules.models.goflow.ops.NodeInit method) (MolecularDiffusion.modules.models.jodo.layers.EdgeGateTransLayer method) (MolecularDiffusion.modules.models.jodo.layers.Trans_Layer method) (MolecularDiffusion.modules.models.jodo.layers.TransMixLayer method) (MolecularDiffusion.modules.models.ligandiff.conv_layer.GVPMessagePassing method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.CFConvS2V method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiMessage method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.NeighborEmb method) message_ff (MolecularDiffusion.modules.models.syncogen.models.semla.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiMessagePassingLayer attribute) message_fusion (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPMessagePassing attribute) message_input_size (MolecularDiffusion.modules.models.loqi.fn_model.XEGNNK attribute) message_layer (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer attribute) message_layer_norm (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) message_layers (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) message_mlp (MolecularDiffusion.modules.models.shepherd_arch.egnn.EGNN attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.BondRefine attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EdgeMessages attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.BondRefine attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EdgeMessages attribute) message_mlp_embedding_dim (MolecularDiffusion.modules.models.shepherd_arch.egnn.EGNN attribute) message_norm (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) message_passing() (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer method) meta (MolecularDiffusion.data.component.reaction_data.Reaction attribute), [1] (MolecularDiffusion.modules.models.chefnmr.sidecar.ChefNMRSidecar attribute) (MolecularDiffusion.modules.tasks.elucidation_generator.Candidate attribute) meta_path (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) METAL_Z (in module MolecularDiffusion.modules.models.ligandiff.utils) (in module MolecularDiffusion.modules.models.ligandiff_multi.utils) Meter (class in MolecularDiffusion.core.meter) meter (MolecularDiffusion.core.engine.Engine attribute) method (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTSGenerator attribute) metric (MolecularDiffusion.core.lightning_callbacks.generative_eval_callback.GenerativeEvalCallback attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) metric_key (MolecularDiffusion.runmodes.train.eval.TaskEvalConfig attribute) metrics() (in module MolecularDiffusion.cli.analyze) mha (MolecularDiffusion.modules.layers.tabasco.attention.AdaLNAttention attribute) (MolecularDiffusion.modules.layers.tabasco.attention.Attention attribute) (MolecularDiffusion.modules.layers.tabasco.attention.CrossAdaLNAttention attribute) mid_in_indices (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Vec2AttnHeads attribute) mid_max_degree (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) mid_num_parity (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) MidiDiffusionTask (class in MolecularDiffusion.modules.tasks.diffusion_midi) MIN_ATOM_SEPARATION (in module MolecularDiffusion.modules.tasks.diffusion_pmdm) MIN_SEED_VALUE (in module MolecularDiffusion.utils.torch) min_t (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.FlowMatchingInterpolant attribute) min_value (MolecularDiffusion.modules.models.tabasco.flow.time_factor.BaseTimeFactor attribute) mix_vectors (MolecularDiffusion.modules.models.goflow.outputs.GatedEquivariantBlock attribute) mixed_coupling_paths (MolecularDiffusion.modules.layers.e3x.modules.Tensor attribute) mixing_mlp (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) mixture_tau_bool (MolecularDiffusion.modules.models.ditmc.flow_matching.FlowMatching attribute) MLP (class in MolecularDiffusion.modules.layers.common) (class in MolecularDiffusion.modules.models.apo2mol.common) Mlp (class in MolecularDiffusion.modules.models.chefnmr.layers) MLP (class in MolecularDiffusion.modules.models.diffsmol.common) (class in MolecularDiffusion.modules.models.ditmc.layers) (class in MolecularDiffusion.modules.models.goflow.ops) (class in MolecularDiffusion.modules.models.kgdiff.common) Mlp (class in MolecularDiffusion.modules.models.ldm.denoisers.dit) MLP (class in MolecularDiffusion.modules.models.loqi.fn_model) (class in MolecularDiffusion.modules.models.oareactdiff.leftnet) mlp (MolecularDiffusion.modules.layers.conv.PositionsMLP attribute) (MolecularDiffusion.modules.models.chefnmr.layers.DiTBlock attribute) (MolecularDiffusion.modules.models.chefnmr.layers.TimestepEmbedder attribute) (MolecularDiffusion.modules.models.ditmc.dit.DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.embedding.EdgeAttributeEmbedding attribute) (MolecularDiffusion.modules.models.ditmc.embedding.NodeAttributeEmbedding attribute) (MolecularDiffusion.modules.models.ditmc.embedding.TimeEmbedding attribute) (MolecularDiffusion.modules.models.goflow.gotennet.TimestepEmbedding attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiTBlock attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.TimestepEmbedder attribute) (MolecularDiffusion.modules.models.loqi.fn_model.TimestepEmbedder attribute) (MolecularDiffusion.modules.models.midi.layers.PositionsMLP attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.MLP attribute) (MolecularDiffusion.modules.models.pmdm.encoders.MLPEdgeEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.egnn.MultiLayerPerceptron attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.PositionsMLP attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.TimestepEmbedding attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.MLPRegressor_padded attribute) (MolecularDiffusion.modules.tasks.regression.MLPRegressor_pernode attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) mlp_batch_norm (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) mlp_dim (MolecularDiffusion.runmodes.train.tasks_transformer.ModelTaskFactory attribute) mlp_dropout (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) MLP_EFS_Head (class in MolecularDiffusion.modules.models.esen) MLP_Energy_Head (class in MolecularDiffusion.modules.models.esen) mlp_final (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) mlp_hidden_dim (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) mlp_in_E (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer attribute) mlp_in_pos (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer attribute) mlp_in_X (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer attribute) mlp_in_y (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer attribute) mlp_out_E (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer attribute) mlp_out_pos (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer attribute) mlp_out_X (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer attribute) mlp_ratio (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) mlp_type (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) MLPEdgeEncoder (class in MolecularDiffusion.modules.models.pmdm.encoders) MLPRegressor_padded (class in MolecularDiffusion.modules.tasks.regression) MLPRegressor_pernode (class in MolecularDiffusion.modules.tasks.regression) mmax (MolecularDiffusion.modules.layers.equiformer_v2.activation.GateActivation attribute) (MolecularDiffusion.modules.layers.equiformer_v2.activation.S2Activation attribute) (MolecularDiffusion.modules.layers.equiformer_v2.activation.SeparableS2Activation attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Grid attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.GateActivation attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.S2Activation attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.SeparableS2Activation attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Grid attribute) (MolecularDiffusion.modules.layers.esen.common.so3.CoefficientMapping attribute) (MolecularDiffusion.modules.layers.esen.common.so3.SO3_Grid attribute) (MolecularDiffusion.modules.layers.esen.esen_block.Edgewise attribute) (MolecularDiffusion.modules.layers.esen.esen_block.eSEN_Block attribute) (MolecularDiffusion.modules.layers.esen.esen_block.GridAtomwise attribute) (MolecularDiffusion.modules.layers.esen.esen_block.SpectralAtomwise attribute) (MolecularDiffusion.modules.layers.esen.nn.activation.GateActivation attribute) (MolecularDiffusion.modules.layers.esen.nn.activation.S2Activation attribute) (MolecularDiffusion.modules.layers.esen.nn.activation.SeparableS2Activation attribute) (MolecularDiffusion.modules.layers.esen.nn.embedding.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Linear attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_m_Conv attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) mmax_list (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_m_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.CoefficientMappingModule attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_m_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.CoefficientMappingModule attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) (MolecularDiffusion.modules.models.tabasco_equiformer.equiformer_backbone.EquiformerV2TabascoBackbone attribute) MODALITIES (in module MolecularDiffusion.modules.models.midi.noise_model) modality_weights (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative attribute) mode (MolecularDiffusion.modules.models.geoldm.networks.EGNN_decoder_QM9 attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_dynamics_QM9 attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_encoder_QM9 attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.base.LossBase attribute) (MolecularDiffusion.modules.models.tabasco.utils.metrics.PoseCheckStrainEnergy attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMConstrainedGenerator attribute) mode() (MolecularDiffusion.modules.tasks.diffusion_ldm.DiagonalGaussianDistribution method) Model (class in MolecularDiffusion.modules.models.shepherd_arch.model) model (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.modules.models.difflinker.egnn.Dynamics attribute) (MolecularDiffusion.modules.models.ligandiff.egnn.Dynamics attribute) (MolecularDiffusion.modules.models.oareactdiff.dynamics.BaseDynamics attribute) (MolecularDiffusion.modules.models.pharmacophore_dynamics.PharmacophoreModelWrapper attribute) (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco attribute) (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask property) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask property) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask property) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTask property) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTask property) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask property) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask property) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask property) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTask property) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.IPDiffDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.KGDiffDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask property) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask property) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask property) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask property) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask property) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask property) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask property) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask property) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) (MolecularDiffusion.modules.tasks.ssl3d.SSL3D attribute) model_class (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) model_config (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) (MolecularDiffusion.modules.models.oareactdiff.dynamics.BaseDynamics attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) model_kwargs (MolecularDiffusion.modules.tasks.diffusion_apo2mol.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.ModelTaskFactory attribute) model_mean_type (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) model_mode (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) model_output() (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTask method) ModelTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_apo2mol) (class in MolecularDiffusion.modules.tasks.diffusion_diffint) (class in MolecularDiffusion.modules.tasks.diffusion_diffsbdd) (class in MolecularDiffusion.modules.tasks.diffusion_goflow) (class in MolecularDiffusion.modules.tasks.diffusion_ipdiff) (class in MolecularDiffusion.modules.tasks.diffusion_jodo) (class in MolecularDiffusion.modules.tasks.diffusion_kgdiff) (class in MolecularDiffusion.modules.tasks.diffusion_loqi) (class in MolecularDiffusion.modules.tasks.diffusion_midi) (class in MolecularDiffusion.modules.tasks.diffusion_oareactdiff) (class in MolecularDiffusion.modules.tasks.diffusion_pmdm) (class in MolecularDiffusion.modules.tasks.diffusion_reactot) (class in MolecularDiffusion.modules.tasks.diffusion_syncogen) (class in MolecularDiffusion.modules.tasks.diffusion_tabasco) (class in MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn) (class in MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer) (class in MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp) (class in MolecularDiffusion.runmodes.train.tasks_egcl) (class in MolecularDiffusion.runmodes.train.tasks_egt) (class in MolecularDiffusion.runmodes.train.tasks_equiformer) (class in MolecularDiffusion.runmodes.train.tasks_esen) (class in MolecularDiffusion.runmodes.train.tasks_gcdm) (class in MolecularDiffusion.runmodes.train.tasks_gfmdiff) (class in MolecularDiffusion.runmodes.train.tasks_painn) (class in MolecularDiffusion.runmodes.train.tasks_transformer) (in module MolecularDiffusion.modules.tasks.diffusion_ditmc) (in module MolecularDiffusion.modules.tasks.diffusion_equifm) (in module MolecularDiffusion.modules.tasks.diffusion_etflow) (in module MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d) (in module MolecularDiffusion.modules.tasks.diffusion_nextmol) MODES (in module MolecularDiffusion.modules.tasks.diffusion_diffsbdd) modulate() (in module MolecularDiffusion.modules.models.chefnmr.layers) (in module MolecularDiffusion.modules.models.jodo.mol_gnn) (in module MolecularDiffusion.modules.models.ldm.denoisers.dit) (in module MolecularDiffusion.modules.models.loqi.fn_model) modulate_adaLN() (in module MolecularDiffusion.modules.models.ditmc.layers) modulate_E3adaLN() (in module MolecularDiffusion.modules.models.ditmc.layers) module MolecularDiffusion MolecularDiffusion.assets MolecularDiffusion.callbacks MolecularDiffusion.callbacks.train_helper MolecularDiffusion.cli MolecularDiffusion.cli.analyze MolecularDiffusion.cli.data MolecularDiffusion.cli.eval_predict MolecularDiffusion.cli.generate MolecularDiffusion.cli.main MolecularDiffusion.cli.predict MolecularDiffusion.cli.train MolecularDiffusion.cli.zoo MolecularDiffusion.core MolecularDiffusion.core.core MolecularDiffusion.core.engine MolecularDiffusion.core.engine_lightning MolecularDiffusion.core.lightning_callbacks MolecularDiffusion.core.lightning_callbacks.ema_callback MolecularDiffusion.core.lightning_callbacks.generative_eval_callback MolecularDiffusion.core.logger MolecularDiffusion.core.meter MolecularDiffusion.data MolecularDiffusion.data.component MolecularDiffusion.data.component.apo2mol_data MolecularDiffusion.data.component.dataset MolecularDiffusion.data.component.diffdec_data MolecularDiffusion.data.component.diffint_data MolecularDiffusion.data.component.diffint_prep MolecularDiffusion.data.component.diffpharma_data MolecularDiffusion.data.component.diffpharma_prep MolecularDiffusion.data.component.diffsbdd_data MolecularDiffusion.data.component.feature MolecularDiffusion.data.component.goflow_data MolecularDiffusion.data.component.graph3d_dataset MolecularDiffusion.data.component.kgdiff_data MolecularDiffusion.data.component.oareactdiff_data MolecularDiffusion.data.component.pharmacophore MolecularDiffusion.data.component.pmdm_data MolecularDiffusion.data.component.pointcloud MolecularDiffusion.data.component.reaction_data MolecularDiffusion.data.dataloader MolecularDiffusion.data.dataset MolecularDiffusion.data.lightning_data_module MolecularDiffusion.data.valency_tables MolecularDiffusion.modules.layers.atomic_data MolecularDiffusion.modules.layers.common MolecularDiffusion.modules.layers.conv MolecularDiffusion.modules.layers.e3x MolecularDiffusion.modules.layers.e3x.activations MolecularDiffusion.modules.layers.e3x.features MolecularDiffusion.modules.layers.e3x.indexed MolecularDiffusion.modules.layers.e3x.initializers MolecularDiffusion.modules.layers.e3x.modules MolecularDiffusion.modules.layers.e3x.radial MolecularDiffusion.modules.layers.e3x.so3 MolecularDiffusion.modules.layers.equiformer_v2 MolecularDiffusion.modules.layers.equiformer_v2.activation MolecularDiffusion.modules.layers.equiformer_v2.drop MolecularDiffusion.modules.layers.equiformer_v2.edge_rot_mat MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20 MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf MolecularDiffusion.modules.layers.equiformer_v2.input_block MolecularDiffusion.modules.layers.equiformer_v2.layer_norm MolecularDiffusion.modules.layers.equiformer_v2.module_list MolecularDiffusion.modules.layers.equiformer_v2.radial_function MolecularDiffusion.modules.layers.equiformer_v2.so2_ops MolecularDiffusion.modules.layers.equiformer_v2.so3 MolecularDiffusion.modules.layers.equiformer_v2.transformer_block MolecularDiffusion.modules.layers.equiformer_v2.wigner MolecularDiffusion.modules.layers.equiformer_v2_s MolecularDiffusion.modules.layers.equiformer_v2_s.activation MolecularDiffusion.modules.layers.equiformer_v2_s.drop MolecularDiffusion.modules.layers.equiformer_v2_s.edge_rot_mat MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20 MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf MolecularDiffusion.modules.layers.equiformer_v2_s.input_block MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm MolecularDiffusion.modules.layers.equiformer_v2_s.module_list MolecularDiffusion.modules.layers.equiformer_v2_s.radial_function MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops MolecularDiffusion.modules.layers.equiformer_v2_s.so3 MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block MolecularDiffusion.modules.layers.equiformer_v2_s.wigner MolecularDiffusion.modules.layers.esen MolecularDiffusion.modules.layers.esen.common MolecularDiffusion.modules.layers.esen.common.rotation MolecularDiffusion.modules.layers.esen.common.so3 MolecularDiffusion.modules.layers.esen.esen_block MolecularDiffusion.modules.layers.esen.nn MolecularDiffusion.modules.layers.esen.nn.activation MolecularDiffusion.modules.layers.esen.nn.embedding MolecularDiffusion.modules.layers.esen.nn.gaussian_embedding MolecularDiffusion.modules.layers.esen.nn.layer_norm MolecularDiffusion.modules.layers.esen.nn.radial MolecularDiffusion.modules.layers.esen.nn.rank2 MolecularDiffusion.modules.layers.esen.nn.so2_layers MolecularDiffusion.modules.layers.esen.nn.so3_layers MolecularDiffusion.modules.layers.esen.nn.utils MolecularDiffusion.modules.layers.functional MolecularDiffusion.modules.layers.gfmdiff MolecularDiffusion.modules.layers.gfmdiff.blocks MolecularDiffusion.modules.layers.graph_module MolecularDiffusion.modules.layers.gvp MolecularDiffusion.modules.layers.gvp.gvp MolecularDiffusion.modules.layers.tabasco MolecularDiffusion.modules.layers.tabasco.attention MolecularDiffusion.modules.layers.tabasco.common MolecularDiffusion.modules.layers.tabasco.losses MolecularDiffusion.modules.layers.tabasco.positional_encoder MolecularDiffusion.modules.layers.tabasco.transformer MolecularDiffusion.modules.layers.tabasco.transformer_module MolecularDiffusion.modules.layers.tabasco.transition MolecularDiffusion.modules.layers.vn MolecularDiffusion.modules.layers.vn.vn_layers MolecularDiffusion.modules.models MolecularDiffusion.modules.models.apo2mol MolecularDiffusion.modules.models.apo2mol.attn MolecularDiffusion.modules.models.apo2mol.common MolecularDiffusion.modules.models.apo2mol.pminet MolecularDiffusion.modules.models.apo2mol.residue_ops MolecularDiffusion.modules.models.apo2mol.score_model MolecularDiffusion.modules.models.apo2mol.uni_transformer MolecularDiffusion.modules.models.chefnmr MolecularDiffusion.modules.models.chefnmr.diffusion MolecularDiffusion.modules.models.chefnmr.embedders MolecularDiffusion.modules.models.chefnmr.layers MolecularDiffusion.modules.models.chefnmr.score_models MolecularDiffusion.modules.models.chefnmr.sidecar MolecularDiffusion.modules.models.chefnmr.unknown MolecularDiffusion.modules.models.chefnmr.utils MolecularDiffusion.modules.models.difflinker MolecularDiffusion.modules.models.difflinker.edm MolecularDiffusion.modules.models.difflinker.egnn MolecularDiffusion.modules.models.difflinker.linker_size MolecularDiffusion.modules.models.difflinker.noise MolecularDiffusion.modules.models.difflinker.size_gnn MolecularDiffusion.modules.models.difflinker.utils MolecularDiffusion.modules.models.diffpharma MolecularDiffusion.modules.models.diffpharma.conditional_ddpm MolecularDiffusion.modules.models.diffpharma.distributions MolecularDiffusion.modules.models.diffpharma.dynamics MolecularDiffusion.modules.models.diffpharma.egnn MolecularDiffusion.modules.models.diffsbdd MolecularDiffusion.modules.models.diffsbdd.dynamics MolecularDiffusion.modules.models.diffsbdd.egnn MolecularDiffusion.modules.models.diffsbdd.en_diffusion MolecularDiffusion.modules.models.diffsmol MolecularDiffusion.modules.models.diffsmol.bond_tables MolecularDiffusion.modules.models.diffsmol.common MolecularDiffusion.modules.models.diffsmol.score_model MolecularDiffusion.modules.models.diffsmol.shape_ae MolecularDiffusion.modules.models.diffsmol.shape_utils MolecularDiffusion.modules.models.diffsmol.uni_transformer MolecularDiffusion.modules.models.diffspectra MolecularDiffusion.modules.models.diffspectra.dmt MolecularDiffusion.modules.models.diffspectra.specformer MolecularDiffusion.modules.models.diffspectra.specformer_layers MolecularDiffusion.modules.models.ditmc MolecularDiffusion.modules.models.ditmc.build MolecularDiffusion.modules.models.ditmc.dit MolecularDiffusion.modules.models.ditmc.embedding MolecularDiffusion.modules.models.ditmc.flow_matching MolecularDiffusion.modules.models.ditmc.graph_features MolecularDiffusion.modules.models.ditmc.graphs MolecularDiffusion.modules.models.ditmc.layers MolecularDiffusion.modules.models.ditmc.meshgraphnet MolecularDiffusion.modules.models.ditmc.priors MolecularDiffusion.modules.models.ditmc.readout MolecularDiffusion.modules.models.egcl MolecularDiffusion.modules.models.egt MolecularDiffusion.modules.models.en_diffusion MolecularDiffusion.modules.models.equifm MolecularDiffusion.modules.models.equifm.cnflows MolecularDiffusion.modules.models.equifm.eot MolecularDiffusion.modules.models.equifm.paths MolecularDiffusion.modules.models.equiformer_v2_backbone MolecularDiffusion.modules.models.equiformer_v2_dynamics MolecularDiffusion.modules.models.esen MolecularDiffusion.modules.models.etflow MolecularDiffusion.modules.models.etflow.features MolecularDiffusion.modules.models.etflow.flow MolecularDiffusion.modules.models.etflow.torchmd MolecularDiffusion.modules.models.flowmol MolecularDiffusion.modules.models.flowmol.graph_utils MolecularDiffusion.modules.models.flowmol.interpolant_scheduler MolecularDiffusion.modules.models.flowmol.priors MolecularDiffusion.modules.models.flowmol.vector_field MolecularDiffusion.modules.models.flowmol_graph3d MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_utils MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field MolecularDiffusion.modules.models.flowmol_graph3d.graph_utils MolecularDiffusion.modules.models.flowmol_graph3d.priors MolecularDiffusion.modules.models.flowmol_graph3d.self_conditioning MolecularDiffusion.modules.models.flowmol_graph3d.vector_field MolecularDiffusion.modules.models.gcdm MolecularDiffusion.modules.models.gcdm.dynamics MolecularDiffusion.modules.models.gcdm.gcp_layers MolecularDiffusion.modules.models.gcdm.gcp_utils MolecularDiffusion.modules.models.geoldm MolecularDiffusion.modules.models.geoldm.diffusion MolecularDiffusion.modules.models.geoldm.egnn MolecularDiffusion.modules.models.geoldm.networks MolecularDiffusion.modules.models.gfmdiff MolecularDiffusion.modules.models.gfmdiff.dynamics MolecularDiffusion.modules.models.gfmdiff.equignn MolecularDiffusion.modules.models.goflow MolecularDiffusion.modules.models.goflow.cgr_graph_utils MolecularDiffusion.modules.models.goflow.flow MolecularDiffusion.modules.models.goflow.gotennet MolecularDiffusion.modules.models.goflow.ops MolecularDiffusion.modules.models.goflow.outputs MolecularDiffusion.modules.models.ipdiff MolecularDiffusion.modules.models.ipdiff.bapnet MolecularDiffusion.modules.models.ipdiff.score_model MolecularDiffusion.modules.models.jodo MolecularDiffusion.modules.models.jodo.layers MolecularDiffusion.modules.models.jodo.mol_gnn MolecularDiffusion.modules.models.jodo.noise_schedule MolecularDiffusion.modules.models.jodo.utils MolecularDiffusion.modules.models.kgdiff MolecularDiffusion.modules.models.kgdiff.atom_num MolecularDiffusion.modules.models.kgdiff.atom_num_config MolecularDiffusion.modules.models.kgdiff.common MolecularDiffusion.modules.models.kgdiff.score_model MolecularDiffusion.modules.models.kgdiff.uni_transformer MolecularDiffusion.modules.models.ldm MolecularDiffusion.modules.models.ldm.decoders MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward MolecularDiffusion.modules.models.ldm.decoders.transformer MolecularDiffusion.modules.models.ldm.denoisers MolecularDiffusion.modules.models.ldm.denoisers.dit MolecularDiffusion.modules.models.ldm.encoders MolecularDiffusion.modules.models.ldm.encoders.equiformer MolecularDiffusion.modules.models.ldm.encoders.transformer MolecularDiffusion.modules.models.ligandiff MolecularDiffusion.modules.models.ligandiff.conv_layer MolecularDiffusion.modules.models.ligandiff.dropout MolecularDiffusion.modules.models.ligandiff.edm MolecularDiffusion.modules.models.ligandiff.egnn MolecularDiffusion.modules.models.ligandiff.gvp MolecularDiffusion.modules.models.ligandiff.gvp_model MolecularDiffusion.modules.models.ligandiff.layer_norm MolecularDiffusion.modules.models.ligandiff.noise MolecularDiffusion.modules.models.ligandiff.utils MolecularDiffusion.modules.models.ligandiff_multi MolecularDiffusion.modules.models.ligandiff_multi.utils MolecularDiffusion.modules.models.loqi MolecularDiffusion.modules.models.loqi.fn_model MolecularDiffusion.modules.models.loqi.graph_utils MolecularDiffusion.modules.models.loqi.interpolant MolecularDiffusion.modules.models.loqi.self_conditioning MolecularDiffusion.modules.models.midi MolecularDiffusion.modules.models.midi.diffusion_utils MolecularDiffusion.modules.models.midi.layers MolecularDiffusion.modules.models.midi.noise_model MolecularDiffusion.modules.models.midi.placeholder MolecularDiffusion.modules.models.midi.transformer_model MolecularDiffusion.modules.models.nextmol MolecularDiffusion.modules.models.nextmol.dgt MolecularDiffusion.modules.models.nextmol.featurize MolecularDiffusion.modules.models.nextmol.mollama MolecularDiffusion.modules.models.nextmol.scheduler MolecularDiffusion.modules.models.noisemodel MolecularDiffusion.modules.models.oareactdiff MolecularDiffusion.modules.models.oareactdiff.dynamics MolecularDiffusion.modules.models.oareactdiff.en_diffusion MolecularDiffusion.modules.models.oareactdiff.graph_tools MolecularDiffusion.modules.models.oareactdiff.leftnet MolecularDiffusion.modules.models.oareactdiff.normalizer MolecularDiffusion.modules.models.oareactdiff.schedule MolecularDiffusion.modules.models.painn_backbone MolecularDiffusion.modules.models.painn_dynamics MolecularDiffusion.modules.models.pharmacophore_dynamics MolecularDiffusion.modules.models.pmdm MolecularDiffusion.modules.models.pmdm.common MolecularDiffusion.modules.models.pmdm.encoders MolecularDiffusion.modules.models.pmdm.epsnet MolecularDiffusion.modules.models.reactot MolecularDiffusion.modules.models.reactot.en_sb MolecularDiffusion.modules.models.reactot.schedule MolecularDiffusion.modules.models.shepherd_arch MolecularDiffusion.modules.models.shepherd_arch.egnn MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder MolecularDiffusion.modules.models.shepherd_arch.inference MolecularDiffusion.modules.models.shepherd_arch.inference.initialization MolecularDiffusion.modules.models.shepherd_arch.inference.noise MolecularDiffusion.modules.models.shepherd_arch.inference.sampler MolecularDiffusion.modules.models.shepherd_arch.inference.steps MolecularDiffusion.modules.models.shepherd_arch.model MolecularDiffusion.modules.models.shepherd_arch.ocp_compat MolecularDiffusion.modules.models.shepherd_arch.utils MolecularDiffusion.modules.models.syncogen MolecularDiffusion.modules.models.syncogen.api MolecularDiffusion.modules.models.syncogen.api.atomics MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates MolecularDiffusion.modules.models.syncogen.api.atomics.pharmacophores MolecularDiffusion.modules.models.syncogen.api.graph MolecularDiffusion.modules.models.syncogen.api.graph.building_block MolecularDiffusion.modules.models.syncogen.api.graph.graph MolecularDiffusion.modules.models.syncogen.api.graph.reaction MolecularDiffusion.modules.models.syncogen.api.ops MolecularDiffusion.modules.models.syncogen.api.ops.coordinates_ops MolecularDiffusion.modules.models.syncogen.api.ops.graph_ops MolecularDiffusion.modules.models.syncogen.api.rdkit MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly MolecularDiffusion.modules.models.syncogen.constants MolecularDiffusion.modules.models.syncogen.constants.constants MolecularDiffusion.modules.models.syncogen.constants.utils MolecularDiffusion.modules.models.syncogen.core MolecularDiffusion.modules.models.syncogen.data MolecularDiffusion.modules.models.syncogen.data.dataloader MolecularDiffusion.modules.models.syncogen.data.utils MolecularDiffusion.modules.models.syncogen.datamodule MolecularDiffusion.modules.models.syncogen.diffusion MolecularDiffusion.modules.models.syncogen.diffusion.interpolation MolecularDiffusion.modules.models.syncogen.diffusion.interpolation.base MolecularDiffusion.modules.models.syncogen.diffusion.interpolation.geometric MolecularDiffusion.modules.models.syncogen.diffusion.interpolation.linear MolecularDiffusion.modules.models.syncogen.diffusion.loss MolecularDiffusion.modules.models.syncogen.diffusion.loss.base MolecularDiffusion.modules.models.syncogen.diffusion.loss.bond_length MolecularDiffusion.modules.models.syncogen.diffusion.loss.mse MolecularDiffusion.modules.models.syncogen.diffusion.loss.nll MolecularDiffusion.modules.models.syncogen.diffusion.loss.pairwise_distance MolecularDiffusion.modules.models.syncogen.diffusion.loss.smooth_lddt MolecularDiffusion.modules.models.syncogen.diffusion.noise MolecularDiffusion.modules.models.syncogen.diffusion.noise.base MolecularDiffusion.modules.models.syncogen.diffusion.noise.brownian MolecularDiffusion.modules.models.syncogen.diffusion.noise.cosine MolecularDiffusion.modules.models.syncogen.diffusion.noise.geometric MolecularDiffusion.modules.models.syncogen.diffusion.noise.linear MolecularDiffusion.modules.models.syncogen.diffusion.noise.loglinear MolecularDiffusion.modules.models.syncogen.diffusion.sampling MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.base MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.mdlm MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.p2 MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.utils MolecularDiffusion.modules.models.syncogen.diffusion.sampling.integrators MolecularDiffusion.modules.models.syncogen.diffusion.sampling.integrators.base MolecularDiffusion.modules.models.syncogen.diffusion.sampling.integrators.euler MolecularDiffusion.modules.models.syncogen.models MolecularDiffusion.modules.models.syncogen.models.ema MolecularDiffusion.modules.models.syncogen.models.layers MolecularDiffusion.modules.models.syncogen.models.semla MolecularDiffusion.modules.models.syncogen.models.semla_pharm MolecularDiffusion.modules.models.syncogen.models.semla_utils MolecularDiffusion.modules.models.syncogen.utils MolecularDiffusion.modules.models.syncogen.utils.file_readers MolecularDiffusion.modules.models.syncogen.utils.rdkit MolecularDiffusion.modules.models.syncogen.vocab MolecularDiffusion.modules.models.tabasco MolecularDiffusion.modules.models.tabasco.callbacks MolecularDiffusion.modules.models.tabasco.callbacks.dataset_stats MolecularDiffusion.modules.models.tabasco.callbacks.ema MolecularDiffusion.modules.models.tabasco.callbacks.molecule_metrics MolecularDiffusion.modules.models.tabasco.callbacks.posebusters MolecularDiffusion.modules.models.tabasco.callbacks.save_molecules MolecularDiffusion.modules.models.tabasco.chem MolecularDiffusion.modules.models.tabasco.chem.constants MolecularDiffusion.modules.models.tabasco.chem.convert MolecularDiffusion.modules.models.tabasco.chem.utils MolecularDiffusion.modules.models.tabasco.data MolecularDiffusion.modules.models.tabasco.data.transforms MolecularDiffusion.modules.models.tabasco.data.utils MolecularDiffusion.modules.models.tabasco.flow MolecularDiffusion.modules.models.tabasco.flow.interpolate MolecularDiffusion.modules.models.tabasco.flow.path MolecularDiffusion.modules.models.tabasco.flow.time_factor MolecularDiffusion.modules.models.tabasco.flow.utils MolecularDiffusion.modules.models.tabasco.flow_model MolecularDiffusion.modules.models.tabasco.lightning_tabasco MolecularDiffusion.modules.models.tabasco.sample MolecularDiffusion.modules.models.tabasco.sample.guided_sampling MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance MolecularDiffusion.modules.models.tabasco.sample.noise_schedule MolecularDiffusion.modules.models.tabasco.utils MolecularDiffusion.modules.models.tabasco.utils.metric_utils MolecularDiffusion.modules.models.tabasco.utils.metrics MolecularDiffusion.modules.models.tabasco.utils.pylogger MolecularDiffusion.modules.models.tabasco.utils.tensor_ops MolecularDiffusion.modules.models.tabasco_egnn MolecularDiffusion.modules.models.tabasco_egnn.egnn_backbone MolecularDiffusion.modules.models.tabasco_equiformer MolecularDiffusion.modules.models.tabasco_equiformer.equiformer_backbone MolecularDiffusion.modules.models.tabasco_gvp MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone MolecularDiffusion.modules.models.transformer_dynamics MolecularDiffusion.modules.tasks MolecularDiffusion.modules.tasks.diffusion MolecularDiffusion.modules.tasks.diffusion_apo2mol MolecularDiffusion.modules.tasks.diffusion_chefnmr MolecularDiffusion.modules.tasks.diffusion_diffdec MolecularDiffusion.modules.tasks.diffusion_diffint MolecularDiffusion.modules.tasks.diffusion_difflinker MolecularDiffusion.modules.tasks.diffusion_diffpharma MolecularDiffusion.modules.tasks.diffusion_diffsbdd MolecularDiffusion.modules.tasks.diffusion_diffsmol MolecularDiffusion.modules.tasks.diffusion_diffspectra MolecularDiffusion.modules.tasks.diffusion_ditmc MolecularDiffusion.modules.tasks.diffusion_equifm MolecularDiffusion.modules.tasks.diffusion_etflow MolecularDiffusion.modules.tasks.diffusion_flowmol MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d MolecularDiffusion.modules.tasks.diffusion_geoldm MolecularDiffusion.modules.tasks.diffusion_goflow MolecularDiffusion.modules.tasks.diffusion_ipdiff MolecularDiffusion.modules.tasks.diffusion_jodo MolecularDiffusion.modules.tasks.diffusion_kgdiff MolecularDiffusion.modules.tasks.diffusion_ldm MolecularDiffusion.modules.tasks.diffusion_ligandiff MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi MolecularDiffusion.modules.tasks.diffusion_loqi MolecularDiffusion.modules.tasks.diffusion_midi MolecularDiffusion.modules.tasks.diffusion_nextmol MolecularDiffusion.modules.tasks.diffusion_oareactdiff MolecularDiffusion.modules.tasks.diffusion_pmdm MolecularDiffusion.modules.tasks.diffusion_reactot MolecularDiffusion.modules.tasks.diffusion_syncogen MolecularDiffusion.modules.tasks.diffusion_tabasco MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp MolecularDiffusion.modules.tasks.elucidation_generator MolecularDiffusion.modules.tasks.metrics MolecularDiffusion.modules.tasks.pharmacophore MolecularDiffusion.modules.tasks.pocket_generator MolecularDiffusion.modules.tasks.regression MolecularDiffusion.modules.tasks.ssl3d MolecularDiffusion.modules.tasks.task MolecularDiffusion.modules.tasks.ts_generator MolecularDiffusion.modules.tasks.vae_geoldm MolecularDiffusion.molcraftdiff MolecularDiffusion.optional MolecularDiffusion.runmodes MolecularDiffusion.runmodes.analyze MolecularDiffusion.runmodes.analyze.compare_to_optimized MolecularDiffusion.runmodes.analyze.compute_metrics MolecularDiffusion.runmodes.analyze.conformer_metrics MolecularDiffusion.runmodes.analyze.docking MolecularDiffusion.runmodes.analyze.druglike MolecularDiffusion.runmodes.analyze.featurize MolecularDiffusion.runmodes.analyze.similarity3d MolecularDiffusion.runmodes.analyze.ssl3d_embed MolecularDiffusion.runmodes.analyze.uma_embeddings MolecularDiffusion.runmodes.analyze.xtb_electronic MolecularDiffusion.runmodes.analyze.xtb_optimization MolecularDiffusion.runmodes.analyze.xyz2mol MolecularDiffusion.runmodes.data.ase_ops MolecularDiffusion.runmodes.data.augmentation MolecularDiffusion.runmodes.data.featurization MolecularDiffusion.runmodes.data.graph3d_import MolecularDiffusion.runmodes.data.preparation MolecularDiffusion.runmodes.generate MolecularDiffusion.runmodes.generate.sweep MolecularDiffusion.runmodes.generate.tasks_conformer MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize MolecularDiffusion.runmodes.generate.tasks_generate MolecularDiffusion.runmodes.train MolecularDiffusion.runmodes.train.data MolecularDiffusion.runmodes.train.eval MolecularDiffusion.runmodes.train.logger MolecularDiffusion.runmodes.train.tasks_egcl MolecularDiffusion.runmodes.train.tasks_egt MolecularDiffusion.runmodes.train.tasks_equiformer MolecularDiffusion.runmodes.train.tasks_esen MolecularDiffusion.runmodes.train.tasks_gcdm MolecularDiffusion.runmodes.train.tasks_gfmdiff MolecularDiffusion.runmodes.train.tasks_painn MolecularDiffusion.runmodes.train.tasks_transformer MolecularDiffusion.runmodes.train.trainer MolecularDiffusion.utils MolecularDiffusion.utils.comm MolecularDiffusion.utils.conformer_pool MolecularDiffusion.utils.diffusion_utils MolecularDiffusion.utils.file MolecularDiffusion.utils.geom_analyzer MolecularDiffusion.utils.geom_constant MolecularDiffusion.utils.geom_constraint MolecularDiffusion.utils.geom_metrics MolecularDiffusion.utils.geom_stability MolecularDiffusion.utils.geom_utils MolecularDiffusion.utils.io MolecularDiffusion.utils.molgraph_utils MolecularDiffusion.utils.plot_function MolecularDiffusion.utils.pretty MolecularDiffusion.utils.sascore MolecularDiffusion.utils.shape_measure MolecularDiffusion.utils.shepherd_score MolecularDiffusion.utils.shepherd_score.alignment MolecularDiffusion.utils.shepherd_score.alignment.utils MolecularDiffusion.utils.shepherd_score.alignment.utils.pca MolecularDiffusion.utils.shepherd_score.alignment.utils.pca_np MolecularDiffusion.utils.shepherd_score.alignment.utils.se3 MolecularDiffusion.utils.shepherd_score.alignment.utils.se3_np MolecularDiffusion.utils.shepherd_score.extract_profiles MolecularDiffusion.utils.shepherd_score.generate_point_cloud MolecularDiffusion.utils.shepherd_score.pharm_utils MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmacophore MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec MolecularDiffusion.utils.shepherd_score.score MolecularDiffusion.utils.shepherd_score.score.analytical_gradients MolecularDiffusion.utils.shepherd_score.score.constants MolecularDiffusion.utils.shepherd_score.score.electrostatic_scoring MolecularDiffusion.utils.shepherd_score.score.electrostatic_scoring_np MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap_np MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring_np MolecularDiffusion.utils.shepherd_utils MolecularDiffusion.utils.smilify MolecularDiffusion.utils.substituent_builder MolecularDiffusion.utils.substituent_geometries MolecularDiffusion.utils.torch MolecularDiffusion.utils.xyz2mol MolecularDiffusion.utils.xyz2mol.converter MolecularDiffusion.utils.xyz2mol.elements module (in module MolecularDiffusion.core.engine) (in module MolecularDiffusion.utils.sascore) module_cfg (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) (MolecularDiffusion.runmodes.train.tasks_gcdm.ModelTaskFactory attribute) ModuleListInfo (class in MolecularDiffusion.modules.layers.equiformer_v2.module_list) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.module_list) modules_dict (MolecularDiffusion.modules.models.loqi.self_conditioning.BaseSelfConditioningModule attribute) mol (MolecularDiffusion.modules.tasks.elucidation_generator.Candidate attribute), [1] mol2_to_bonds() (in module MolecularDiffusion.modules.models.syncogen.utils.file_readers) mol2_to_coordinates() (in module MolecularDiffusion.modules.models.syncogen.utils.file_readers) mol2smiles() (in module MolecularDiffusion.utils.geom_analyzer) mol_converter (MolecularDiffusion.modules.models.tabasco.callbacks.molecule_metrics.MoleculeMetricsCallback attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.save_molecules.SaveGeneratedMolsCallback attribute) (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco attribute) (MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance.UFFBoundGuidance attribute) mol_file (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMConstrainedGenerator attribute) mol_idx (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) mol_metrics (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco attribute) mol_size (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeGenerator attribute) (MolecularDiffusion.modules.tasks.pocket_generator.PocketGenerator attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) mol_to_atom_array() (MolecularDiffusion.modules.models.tabasco.chem.convert.MoleculeConverter method) mol_to_pharm_cond() (in module MolecularDiffusion.modules.models.syncogen.utils.rdkit) mol_to_row() (in module MolecularDiffusion.runmodes.data.graph3d_import) molblocks_and_charges (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) MolCraftDiff (class in MolecularDiffusion.molcraftdiff) MOLECULAR_LEVEL_GROUPS (in module MolecularDiffusion.runmodes.analyze.xtb_electronic) MolecularConnectivity (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) MolecularDiffusion module MolecularDiffusion.assets module MolecularDiffusion.callbacks module MolecularDiffusion.callbacks.train_helper module MolecularDiffusion.cli module MolecularDiffusion.cli.analyze module MolecularDiffusion.cli.data module MolecularDiffusion.cli.eval_predict module MolecularDiffusion.cli.generate module MolecularDiffusion.cli.main module MolecularDiffusion.cli.predict module MolecularDiffusion.cli.train module MolecularDiffusion.cli.zoo module MolecularDiffusion.core module MolecularDiffusion.core.core module MolecularDiffusion.core.engine module MolecularDiffusion.core.engine_lightning module MolecularDiffusion.core.lightning_callbacks module MolecularDiffusion.core.lightning_callbacks.ema_callback module MolecularDiffusion.core.lightning_callbacks.generative_eval_callback module MolecularDiffusion.core.logger module MolecularDiffusion.core.meter module MolecularDiffusion.data module MolecularDiffusion.data.component module MolecularDiffusion.data.component.apo2mol_data module MolecularDiffusion.data.component.dataset module MolecularDiffusion.data.component.diffdec_data module MolecularDiffusion.data.component.diffint_data module MolecularDiffusion.data.component.diffint_prep module MolecularDiffusion.data.component.diffpharma_data module MolecularDiffusion.data.component.diffpharma_prep module MolecularDiffusion.data.component.diffsbdd_data module MolecularDiffusion.data.component.feature module MolecularDiffusion.data.component.goflow_data module MolecularDiffusion.data.component.graph3d_dataset module MolecularDiffusion.data.component.kgdiff_data module MolecularDiffusion.data.component.oareactdiff_data module MolecularDiffusion.data.component.pharmacophore module MolecularDiffusion.data.component.pmdm_data module MolecularDiffusion.data.component.pointcloud module MolecularDiffusion.data.component.reaction_data module MolecularDiffusion.data.dataloader module MolecularDiffusion.data.dataset module MolecularDiffusion.data.lightning_data_module module MolecularDiffusion.data.valency_tables module MolecularDiffusion.modules.layers.atomic_data module MolecularDiffusion.modules.layers.common module MolecularDiffusion.modules.layers.conv module MolecularDiffusion.modules.layers.e3x module MolecularDiffusion.modules.layers.e3x.activations module MolecularDiffusion.modules.layers.e3x.features module MolecularDiffusion.modules.layers.e3x.indexed module MolecularDiffusion.modules.layers.e3x.initializers module MolecularDiffusion.modules.layers.e3x.modules module MolecularDiffusion.modules.layers.e3x.radial module MolecularDiffusion.modules.layers.e3x.so3 module MolecularDiffusion.modules.layers.equiformer_v2 module MolecularDiffusion.modules.layers.equiformer_v2.activation module MolecularDiffusion.modules.layers.equiformer_v2.drop module MolecularDiffusion.modules.layers.equiformer_v2.edge_rot_mat module MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20 module MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf module MolecularDiffusion.modules.layers.equiformer_v2.input_block module MolecularDiffusion.modules.layers.equiformer_v2.layer_norm module MolecularDiffusion.modules.layers.equiformer_v2.module_list module MolecularDiffusion.modules.layers.equiformer_v2.radial_function module MolecularDiffusion.modules.layers.equiformer_v2.so2_ops module MolecularDiffusion.modules.layers.equiformer_v2.so3 module MolecularDiffusion.modules.layers.equiformer_v2.transformer_block module MolecularDiffusion.modules.layers.equiformer_v2.wigner module MolecularDiffusion.modules.layers.equiformer_v2_s module MolecularDiffusion.modules.layers.equiformer_v2_s.activation module MolecularDiffusion.modules.layers.equiformer_v2_s.drop module MolecularDiffusion.modules.layers.equiformer_v2_s.edge_rot_mat module MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20 module MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf module MolecularDiffusion.modules.layers.equiformer_v2_s.input_block module MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm module MolecularDiffusion.modules.layers.equiformer_v2_s.module_list module MolecularDiffusion.modules.layers.equiformer_v2_s.radial_function module MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops module MolecularDiffusion.modules.layers.equiformer_v2_s.so3 module MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block module MolecularDiffusion.modules.layers.equiformer_v2_s.wigner module MolecularDiffusion.modules.layers.esen module MolecularDiffusion.modules.layers.esen.common module MolecularDiffusion.modules.layers.esen.common.rotation module MolecularDiffusion.modules.layers.esen.common.so3 module MolecularDiffusion.modules.layers.esen.esen_block module MolecularDiffusion.modules.layers.esen.nn module MolecularDiffusion.modules.layers.esen.nn.activation module MolecularDiffusion.modules.layers.esen.nn.embedding module MolecularDiffusion.modules.layers.esen.nn.gaussian_embedding module MolecularDiffusion.modules.layers.esen.nn.layer_norm module MolecularDiffusion.modules.layers.esen.nn.radial module MolecularDiffusion.modules.layers.esen.nn.rank2 module MolecularDiffusion.modules.layers.esen.nn.so2_layers module MolecularDiffusion.modules.layers.esen.nn.so3_layers module MolecularDiffusion.modules.layers.esen.nn.utils module MolecularDiffusion.modules.layers.functional module MolecularDiffusion.modules.layers.gfmdiff module MolecularDiffusion.modules.layers.gfmdiff.blocks module MolecularDiffusion.modules.layers.graph_module module MolecularDiffusion.modules.layers.gvp module MolecularDiffusion.modules.layers.gvp.gvp module MolecularDiffusion.modules.layers.tabasco module MolecularDiffusion.modules.layers.tabasco.attention module MolecularDiffusion.modules.layers.tabasco.common module MolecularDiffusion.modules.layers.tabasco.losses module MolecularDiffusion.modules.layers.tabasco.positional_encoder module MolecularDiffusion.modules.layers.tabasco.transformer module MolecularDiffusion.modules.layers.tabasco.transformer_module module MolecularDiffusion.modules.layers.tabasco.transition module MolecularDiffusion.modules.layers.vn module MolecularDiffusion.modules.layers.vn.vn_layers module MolecularDiffusion.modules.models module MolecularDiffusion.modules.models.apo2mol module MolecularDiffusion.modules.models.apo2mol.attn module MolecularDiffusion.modules.models.apo2mol.common module MolecularDiffusion.modules.models.apo2mol.pminet module MolecularDiffusion.modules.models.apo2mol.residue_ops module MolecularDiffusion.modules.models.apo2mol.score_model module MolecularDiffusion.modules.models.apo2mol.uni_transformer module MolecularDiffusion.modules.models.chefnmr module MolecularDiffusion.modules.models.chefnmr.diffusion module MolecularDiffusion.modules.models.chefnmr.embedders module MolecularDiffusion.modules.models.chefnmr.layers module MolecularDiffusion.modules.models.chefnmr.score_models module MolecularDiffusion.modules.models.chefnmr.sidecar module MolecularDiffusion.modules.models.chefnmr.unknown module MolecularDiffusion.modules.models.chefnmr.utils module MolecularDiffusion.modules.models.difflinker module MolecularDiffusion.modules.models.difflinker.edm module MolecularDiffusion.modules.models.difflinker.egnn module MolecularDiffusion.modules.models.difflinker.linker_size module MolecularDiffusion.modules.models.difflinker.noise module MolecularDiffusion.modules.models.difflinker.size_gnn module MolecularDiffusion.modules.models.difflinker.utils module MolecularDiffusion.modules.models.diffpharma module MolecularDiffusion.modules.models.diffpharma.conditional_ddpm module MolecularDiffusion.modules.models.diffpharma.distributions module MolecularDiffusion.modules.models.diffpharma.dynamics module MolecularDiffusion.modules.models.diffpharma.egnn module MolecularDiffusion.modules.models.diffsbdd module MolecularDiffusion.modules.models.diffsbdd.dynamics module MolecularDiffusion.modules.models.diffsbdd.egnn module MolecularDiffusion.modules.models.diffsbdd.en_diffusion module MolecularDiffusion.modules.models.diffsmol module MolecularDiffusion.modules.models.diffsmol.bond_tables module MolecularDiffusion.modules.models.diffsmol.common module MolecularDiffusion.modules.models.diffsmol.score_model module MolecularDiffusion.modules.models.diffsmol.shape_ae module MolecularDiffusion.modules.models.diffsmol.shape_utils module MolecularDiffusion.modules.models.diffsmol.uni_transformer module MolecularDiffusion.modules.models.diffspectra module MolecularDiffusion.modules.models.diffspectra.dmt module MolecularDiffusion.modules.models.diffspectra.specformer module MolecularDiffusion.modules.models.diffspectra.specformer_layers module MolecularDiffusion.modules.models.ditmc module MolecularDiffusion.modules.models.ditmc.build module MolecularDiffusion.modules.models.ditmc.dit module MolecularDiffusion.modules.models.ditmc.embedding module MolecularDiffusion.modules.models.ditmc.flow_matching module MolecularDiffusion.modules.models.ditmc.graph_features module MolecularDiffusion.modules.models.ditmc.graphs module MolecularDiffusion.modules.models.ditmc.layers module MolecularDiffusion.modules.models.ditmc.meshgraphnet module MolecularDiffusion.modules.models.ditmc.priors module MolecularDiffusion.modules.models.ditmc.readout module MolecularDiffusion.modules.models.egcl module MolecularDiffusion.modules.models.egt module MolecularDiffusion.modules.models.en_diffusion module MolecularDiffusion.modules.models.equifm module MolecularDiffusion.modules.models.equifm.cnflows module MolecularDiffusion.modules.models.equifm.eot module MolecularDiffusion.modules.models.equifm.paths module MolecularDiffusion.modules.models.equiformer_v2_backbone module MolecularDiffusion.modules.models.equiformer_v2_dynamics module MolecularDiffusion.modules.models.esen module MolecularDiffusion.modules.models.etflow module MolecularDiffusion.modules.models.etflow.features module MolecularDiffusion.modules.models.etflow.flow module MolecularDiffusion.modules.models.etflow.torchmd module MolecularDiffusion.modules.models.flowmol module MolecularDiffusion.modules.models.flowmol.graph_utils module MolecularDiffusion.modules.models.flowmol.interpolant_scheduler module MolecularDiffusion.modules.models.flowmol.priors module MolecularDiffusion.modules.models.flowmol.vector_field module MolecularDiffusion.modules.models.flowmol_graph3d module MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_utils module MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field module MolecularDiffusion.modules.models.flowmol_graph3d.graph_utils module MolecularDiffusion.modules.models.flowmol_graph3d.priors module MolecularDiffusion.modules.models.flowmol_graph3d.self_conditioning module MolecularDiffusion.modules.models.flowmol_graph3d.vector_field module MolecularDiffusion.modules.models.gcdm module MolecularDiffusion.modules.models.gcdm.dynamics module MolecularDiffusion.modules.models.gcdm.gcp_layers module MolecularDiffusion.modules.models.gcdm.gcp_utils module MolecularDiffusion.modules.models.geoldm module MolecularDiffusion.modules.models.geoldm.diffusion module MolecularDiffusion.modules.models.geoldm.egnn module MolecularDiffusion.modules.models.geoldm.networks module MolecularDiffusion.modules.models.gfmdiff module MolecularDiffusion.modules.models.gfmdiff.dynamics module MolecularDiffusion.modules.models.gfmdiff.equignn module MolecularDiffusion.modules.models.goflow module MolecularDiffusion.modules.models.goflow.cgr_graph_utils module MolecularDiffusion.modules.models.goflow.flow module MolecularDiffusion.modules.models.goflow.gotennet module MolecularDiffusion.modules.models.goflow.ops module MolecularDiffusion.modules.models.goflow.outputs module MolecularDiffusion.modules.models.ipdiff module MolecularDiffusion.modules.models.ipdiff.bapnet module MolecularDiffusion.modules.models.ipdiff.score_model module MolecularDiffusion.modules.models.jodo module MolecularDiffusion.modules.models.jodo.layers module MolecularDiffusion.modules.models.jodo.mol_gnn module MolecularDiffusion.modules.models.jodo.noise_schedule module MolecularDiffusion.modules.models.jodo.utils module MolecularDiffusion.modules.models.kgdiff module MolecularDiffusion.modules.models.kgdiff.atom_num module MolecularDiffusion.modules.models.kgdiff.atom_num_config module MolecularDiffusion.modules.models.kgdiff.common module MolecularDiffusion.modules.models.kgdiff.score_model module MolecularDiffusion.modules.models.kgdiff.uni_transformer module MolecularDiffusion.modules.models.ldm module MolecularDiffusion.modules.models.ldm.decoders module MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward module MolecularDiffusion.modules.models.ldm.decoders.transformer module MolecularDiffusion.modules.models.ldm.denoisers module MolecularDiffusion.modules.models.ldm.denoisers.dit module MolecularDiffusion.modules.models.ldm.encoders module MolecularDiffusion.modules.models.ldm.encoders.equiformer module MolecularDiffusion.modules.models.ldm.encoders.transformer module MolecularDiffusion.modules.models.ligandiff module MolecularDiffusion.modules.models.ligandiff.conv_layer module MolecularDiffusion.modules.models.ligandiff.dropout module MolecularDiffusion.modules.models.ligandiff.edm module MolecularDiffusion.modules.models.ligandiff.egnn module MolecularDiffusion.modules.models.ligandiff.gvp module MolecularDiffusion.modules.models.ligandiff.gvp_model module MolecularDiffusion.modules.models.ligandiff.layer_norm module MolecularDiffusion.modules.models.ligandiff.noise module MolecularDiffusion.modules.models.ligandiff.utils module MolecularDiffusion.modules.models.ligandiff_multi module MolecularDiffusion.modules.models.ligandiff_multi.utils module MolecularDiffusion.modules.models.loqi module MolecularDiffusion.modules.models.loqi.fn_model module MolecularDiffusion.modules.models.loqi.graph_utils module MolecularDiffusion.modules.models.loqi.interpolant module MolecularDiffusion.modules.models.loqi.self_conditioning module MolecularDiffusion.modules.models.midi module MolecularDiffusion.modules.models.midi.diffusion_utils module MolecularDiffusion.modules.models.midi.layers module MolecularDiffusion.modules.models.midi.noise_model module MolecularDiffusion.modules.models.midi.placeholder module MolecularDiffusion.modules.models.midi.transformer_model module MolecularDiffusion.modules.models.nextmol module MolecularDiffusion.modules.models.nextmol.dgt module MolecularDiffusion.modules.models.nextmol.featurize module MolecularDiffusion.modules.models.nextmol.mollama module MolecularDiffusion.modules.models.nextmol.scheduler module MolecularDiffusion.modules.models.noisemodel module MolecularDiffusion.modules.models.oareactdiff module MolecularDiffusion.modules.models.oareactdiff.dynamics module MolecularDiffusion.modules.models.oareactdiff.en_diffusion module MolecularDiffusion.modules.models.oareactdiff.graph_tools module MolecularDiffusion.modules.models.oareactdiff.leftnet module MolecularDiffusion.modules.models.oareactdiff.normalizer module MolecularDiffusion.modules.models.oareactdiff.schedule module MolecularDiffusion.modules.models.painn_backbone module MolecularDiffusion.modules.models.painn_dynamics module MolecularDiffusion.modules.models.pharmacophore_dynamics module MolecularDiffusion.modules.models.pmdm module MolecularDiffusion.modules.models.pmdm.common module MolecularDiffusion.modules.models.pmdm.encoders module MolecularDiffusion.modules.models.pmdm.epsnet module MolecularDiffusion.modules.models.reactot module MolecularDiffusion.modules.models.reactot.en_sb module MolecularDiffusion.modules.models.reactot.schedule module MolecularDiffusion.modules.models.shepherd_arch module MolecularDiffusion.modules.models.shepherd_arch.egnn module MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations module MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder module MolecularDiffusion.modules.models.shepherd_arch.inference module MolecularDiffusion.modules.models.shepherd_arch.inference.initialization module MolecularDiffusion.modules.models.shepherd_arch.inference.noise module MolecularDiffusion.modules.models.shepherd_arch.inference.sampler module MolecularDiffusion.modules.models.shepherd_arch.inference.steps module MolecularDiffusion.modules.models.shepherd_arch.model module MolecularDiffusion.modules.models.shepherd_arch.ocp_compat module MolecularDiffusion.modules.models.shepherd_arch.utils module MolecularDiffusion.modules.models.syncogen module MolecularDiffusion.modules.models.syncogen.api module MolecularDiffusion.modules.models.syncogen.api.atomics module MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates module MolecularDiffusion.modules.models.syncogen.api.atomics.pharmacophores module MolecularDiffusion.modules.models.syncogen.api.graph module MolecularDiffusion.modules.models.syncogen.api.graph.building_block module MolecularDiffusion.modules.models.syncogen.api.graph.graph module MolecularDiffusion.modules.models.syncogen.api.graph.reaction module MolecularDiffusion.modules.models.syncogen.api.ops module MolecularDiffusion.modules.models.syncogen.api.ops.coordinates_ops module MolecularDiffusion.modules.models.syncogen.api.ops.graph_ops module MolecularDiffusion.modules.models.syncogen.api.rdkit module MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly module MolecularDiffusion.modules.models.syncogen.constants module MolecularDiffusion.modules.models.syncogen.constants.constants module MolecularDiffusion.modules.models.syncogen.constants.utils module MolecularDiffusion.modules.models.syncogen.core module MolecularDiffusion.modules.models.syncogen.data module MolecularDiffusion.modules.models.syncogen.data.dataloader module MolecularDiffusion.modules.models.syncogen.data.utils module MolecularDiffusion.modules.models.syncogen.datamodule module MolecularDiffusion.modules.models.syncogen.diffusion module MolecularDiffusion.modules.models.syncogen.diffusion.interpolation module MolecularDiffusion.modules.models.syncogen.diffusion.interpolation.base module MolecularDiffusion.modules.models.syncogen.diffusion.interpolation.geometric module MolecularDiffusion.modules.models.syncogen.diffusion.interpolation.linear module MolecularDiffusion.modules.models.syncogen.diffusion.loss module MolecularDiffusion.modules.models.syncogen.diffusion.loss.base module MolecularDiffusion.modules.models.syncogen.diffusion.loss.bond_length module MolecularDiffusion.modules.models.syncogen.diffusion.loss.mse module MolecularDiffusion.modules.models.syncogen.diffusion.loss.nll module MolecularDiffusion.modules.models.syncogen.diffusion.loss.pairwise_distance module MolecularDiffusion.modules.models.syncogen.diffusion.loss.smooth_lddt module MolecularDiffusion.modules.models.syncogen.diffusion.noise module MolecularDiffusion.modules.models.syncogen.diffusion.noise.base module MolecularDiffusion.modules.models.syncogen.diffusion.noise.brownian module MolecularDiffusion.modules.models.syncogen.diffusion.noise.cosine module MolecularDiffusion.modules.models.syncogen.diffusion.noise.geometric module MolecularDiffusion.modules.models.syncogen.diffusion.noise.linear module MolecularDiffusion.modules.models.syncogen.diffusion.noise.loglinear module MolecularDiffusion.modules.models.syncogen.diffusion.sampling module MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies module MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.base module MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.mdlm module MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.p2 module MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.utils module MolecularDiffusion.modules.models.syncogen.diffusion.sampling.integrators module MolecularDiffusion.modules.models.syncogen.diffusion.sampling.integrators.base module MolecularDiffusion.modules.models.syncogen.diffusion.sampling.integrators.euler module MolecularDiffusion.modules.models.syncogen.models module MolecularDiffusion.modules.models.syncogen.models.ema module MolecularDiffusion.modules.models.syncogen.models.layers module MolecularDiffusion.modules.models.syncogen.models.semla module MolecularDiffusion.modules.models.syncogen.models.semla_pharm module MolecularDiffusion.modules.models.syncogen.models.semla_utils module MolecularDiffusion.modules.models.syncogen.utils module MolecularDiffusion.modules.models.syncogen.utils.file_readers module MolecularDiffusion.modules.models.syncogen.utils.rdkit module MolecularDiffusion.modules.models.syncogen.vocab module MolecularDiffusion.modules.models.tabasco module MolecularDiffusion.modules.models.tabasco.callbacks module MolecularDiffusion.modules.models.tabasco.callbacks.dataset_stats module MolecularDiffusion.modules.models.tabasco.callbacks.ema module MolecularDiffusion.modules.models.tabasco.callbacks.molecule_metrics module MolecularDiffusion.modules.models.tabasco.callbacks.posebusters module MolecularDiffusion.modules.models.tabasco.callbacks.save_molecules module MolecularDiffusion.modules.models.tabasco.chem module MolecularDiffusion.modules.models.tabasco.chem.constants module MolecularDiffusion.modules.models.tabasco.chem.convert module MolecularDiffusion.modules.models.tabasco.chem.utils module MolecularDiffusion.modules.models.tabasco.data module MolecularDiffusion.modules.models.tabasco.data.transforms module MolecularDiffusion.modules.models.tabasco.data.utils module MolecularDiffusion.modules.models.tabasco.flow module MolecularDiffusion.modules.models.tabasco.flow.interpolate module MolecularDiffusion.modules.models.tabasco.flow.path module MolecularDiffusion.modules.models.tabasco.flow.time_factor module MolecularDiffusion.modules.models.tabasco.flow.utils module MolecularDiffusion.modules.models.tabasco.flow_model module MolecularDiffusion.modules.models.tabasco.lightning_tabasco module MolecularDiffusion.modules.models.tabasco.sample module MolecularDiffusion.modules.models.tabasco.sample.guided_sampling module MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance module MolecularDiffusion.modules.models.tabasco.sample.noise_schedule module MolecularDiffusion.modules.models.tabasco.utils module MolecularDiffusion.modules.models.tabasco.utils.metric_utils module MolecularDiffusion.modules.models.tabasco.utils.metrics module MolecularDiffusion.modules.models.tabasco.utils.pylogger module MolecularDiffusion.modules.models.tabasco.utils.tensor_ops module MolecularDiffusion.modules.models.tabasco_egnn module MolecularDiffusion.modules.models.tabasco_egnn.egnn_backbone module MolecularDiffusion.modules.models.tabasco_equiformer module MolecularDiffusion.modules.models.tabasco_equiformer.equiformer_backbone module MolecularDiffusion.modules.models.tabasco_gvp module MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone module MolecularDiffusion.modules.models.transformer_dynamics module MolecularDiffusion.modules.tasks module MolecularDiffusion.modules.tasks.diffusion module MolecularDiffusion.modules.tasks.diffusion_apo2mol module MolecularDiffusion.modules.tasks.diffusion_chefnmr module MolecularDiffusion.modules.tasks.diffusion_diffdec module MolecularDiffusion.modules.tasks.diffusion_diffint module MolecularDiffusion.modules.tasks.diffusion_difflinker module MolecularDiffusion.modules.tasks.diffusion_diffpharma module MolecularDiffusion.modules.tasks.diffusion_diffsbdd module MolecularDiffusion.modules.tasks.diffusion_diffsmol module MolecularDiffusion.modules.tasks.diffusion_diffspectra module MolecularDiffusion.modules.tasks.diffusion_ditmc module MolecularDiffusion.modules.tasks.diffusion_equifm module MolecularDiffusion.modules.tasks.diffusion_etflow module MolecularDiffusion.modules.tasks.diffusion_flowmol module MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d module MolecularDiffusion.modules.tasks.diffusion_geoldm module MolecularDiffusion.modules.tasks.diffusion_goflow module MolecularDiffusion.modules.tasks.diffusion_ipdiff module MolecularDiffusion.modules.tasks.diffusion_jodo module MolecularDiffusion.modules.tasks.diffusion_kgdiff module MolecularDiffusion.modules.tasks.diffusion_ldm module MolecularDiffusion.modules.tasks.diffusion_ligandiff module MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi module MolecularDiffusion.modules.tasks.diffusion_loqi module MolecularDiffusion.modules.tasks.diffusion_midi module MolecularDiffusion.modules.tasks.diffusion_nextmol module MolecularDiffusion.modules.tasks.diffusion_oareactdiff module MolecularDiffusion.modules.tasks.diffusion_pmdm module MolecularDiffusion.modules.tasks.diffusion_reactot module MolecularDiffusion.modules.tasks.diffusion_syncogen module MolecularDiffusion.modules.tasks.diffusion_tabasco module MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn module MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer module MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp module MolecularDiffusion.modules.tasks.elucidation_generator module MolecularDiffusion.modules.tasks.metrics module MolecularDiffusion.modules.tasks.pharmacophore module MolecularDiffusion.modules.tasks.pocket_generator module MolecularDiffusion.modules.tasks.regression module MolecularDiffusion.modules.tasks.ssl3d module MolecularDiffusion.modules.tasks.task module MolecularDiffusion.modules.tasks.ts_generator module MolecularDiffusion.modules.tasks.vae_geoldm module MolecularDiffusion.molcraftdiff module MolecularDiffusion.optional module MolecularDiffusion.runmodes module MolecularDiffusion.runmodes.analyze module MolecularDiffusion.runmodes.analyze.compare_to_optimized module MolecularDiffusion.runmodes.analyze.compute_metrics module MolecularDiffusion.runmodes.analyze.conformer_metrics module MolecularDiffusion.runmodes.analyze.docking module MolecularDiffusion.runmodes.analyze.druglike module MolecularDiffusion.runmodes.analyze.featurize module MolecularDiffusion.runmodes.analyze.similarity3d module MolecularDiffusion.runmodes.analyze.ssl3d_embed module MolecularDiffusion.runmodes.analyze.uma_embeddings module MolecularDiffusion.runmodes.analyze.xtb_electronic module MolecularDiffusion.runmodes.analyze.xtb_optimization module MolecularDiffusion.runmodes.analyze.xyz2mol module MolecularDiffusion.runmodes.data.ase_ops module MolecularDiffusion.runmodes.data.augmentation module MolecularDiffusion.runmodes.data.featurization module MolecularDiffusion.runmodes.data.graph3d_import module MolecularDiffusion.runmodes.data.preparation module MolecularDiffusion.runmodes.generate module MolecularDiffusion.runmodes.generate.sweep module MolecularDiffusion.runmodes.generate.tasks_conformer module MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize module MolecularDiffusion.runmodes.generate.tasks_generate module MolecularDiffusion.runmodes.train module MolecularDiffusion.runmodes.train.data module MolecularDiffusion.runmodes.train.eval module MolecularDiffusion.runmodes.train.logger module MolecularDiffusion.runmodes.train.tasks_egcl module MolecularDiffusion.runmodes.train.tasks_egt module MolecularDiffusion.runmodes.train.tasks_equiformer module MolecularDiffusion.runmodes.train.tasks_esen module MolecularDiffusion.runmodes.train.tasks_gcdm module MolecularDiffusion.runmodes.train.tasks_gfmdiff module MolecularDiffusion.runmodes.train.tasks_painn module MolecularDiffusion.runmodes.train.tasks_transformer module MolecularDiffusion.runmodes.train.trainer module MolecularDiffusion.utils module MolecularDiffusion.utils.comm module MolecularDiffusion.utils.conformer_pool module MolecularDiffusion.utils.diffusion_utils module MolecularDiffusion.utils.file module MolecularDiffusion.utils.geom_analyzer module MolecularDiffusion.utils.geom_constant module MolecularDiffusion.utils.geom_constraint module MolecularDiffusion.utils.geom_metrics module MolecularDiffusion.utils.geom_stability module MolecularDiffusion.utils.geom_utils module MolecularDiffusion.utils.io module MolecularDiffusion.utils.molgraph_utils module MolecularDiffusion.utils.plot_function module MolecularDiffusion.utils.pretty module MolecularDiffusion.utils.sascore module MolecularDiffusion.utils.shape_measure module MolecularDiffusion.utils.shepherd_score module MolecularDiffusion.utils.shepherd_score.alignment module MolecularDiffusion.utils.shepherd_score.alignment.utils module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca_np module MolecularDiffusion.utils.shepherd_score.alignment.utils.se3 module MolecularDiffusion.utils.shepherd_score.alignment.utils.se3_np module MolecularDiffusion.utils.shepherd_score.extract_profiles module MolecularDiffusion.utils.shepherd_score.generate_point_cloud module MolecularDiffusion.utils.shepherd_score.pharm_utils module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmacophore module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmvec module MolecularDiffusion.utils.shepherd_score.score module MolecularDiffusion.utils.shepherd_score.score.analytical_gradients module MolecularDiffusion.utils.shepherd_score.score.constants module MolecularDiffusion.utils.shepherd_score.score.electrostatic_scoring module MolecularDiffusion.utils.shepherd_score.score.electrostatic_scoring_np module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap_np module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring_np module MolecularDiffusion.utils.shepherd_utils module MolecularDiffusion.utils.smilify module MolecularDiffusion.utils.substituent_builder module MolecularDiffusion.utils.substituent_geometries module MolecularDiffusion.utils.torch module MolecularDiffusion.utils.xyz2mol module MolecularDiffusion.utils.xyz2mol.converter module MolecularDiffusion.utils.xyz2mol.elements module MolecularDiffusionDataModule (class in MolecularDiffusion.data.lightning_data_module) MolecularDiversity (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) MolecularLipinski (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) MolecularLogP (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) MolecularNovelty (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) MolecularQEDValue (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) MolecularUniqueness (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) MolecularValidity (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) Molecule (class in MolecularDiffusion.utils.smilify) (in module MolecularDiffusion.runmodes.data.preparation) molecule_default() (in module MolecularDiffusion.data.component.feature) MoleculeConverter (class in MolecularDiffusion.modules.models.tabasco.chem.convert) MoleculeFeatureCache (class in MolecularDiffusion.modules.models.ditmc.graph_features) (class in MolecularDiffusion.modules.tasks.diffusion_nextmol) MoleculeMetricsCallback (class in MolecularDiffusion.modules.models.tabasco.callbacks.molecule_metrics) MoleculeReconstructionEvaluator (class in MolecularDiffusion.utils.geom_utils) mollama_model (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolGenerator attribute) monitor_metric (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) (MolecularDiffusion.core.lightning_callbacks.generative_eval_callback.GenerativeEvalCallback attribute) move_P_device() (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel method) move_shadow_params_to_device() (MolecularDiffusion.modules.models.syncogen.models.ema.ExponentialMovingAverage method) move_stray_tensor_attrs() (in module MolecularDiffusion.utils.torch) move_to_device() (in module MolecularDiffusion.modules.tasks.elucidation_generator) moving_avg (class in MolecularDiffusion.modules.models.diffspectra.specformer_layers) (MolecularDiffusion.modules.models.diffspectra.specformer_layers.series_decomp attribute) mpnn_layers (MolecularDiffusion.modules.models.pmdm.encoders.EGNNSparseNetwork attribute) mse_loss (MolecularDiffusion.modules.layers.tabasco.losses.InterDistancesLoss attribute) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.CenteredMetricInterpolant attribute) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.SDEMetricInterpolant attribute) MSELoss (class in MolecularDiffusion.modules.models.syncogen.diffusion.loss.mse) mu (MolecularDiffusion.modules.models.ditmc.priors.GaussianPrior attribute) (MolecularDiffusion.modules.models.ligandiff.gvp.GVP attribute) mu_x0 (MolecularDiffusion.modules.models.reactot.schedule.SBSchedule attribute), [1] mu_x1 (MolecularDiffusion.modules.models.reactot.schedule.SBSchedule attribute), [1] mul (MolecularDiffusion.modules.layers.equiformer_v2.drop.EquivariantDropout attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.EquivariantDropout attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Gate attribute) multi_slice() (in module MolecularDiffusion.modules.layers.functional) multi_slice_mask() (in module MolecularDiffusion.modules.layers.functional) MultiCondEquiUpdate (class in MolecularDiffusion.modules.models.jodo.mol_gnn) MultiLayerPerceptron (class in MolecularDiffusion.modules.models.pmdm.common) (class in MolecularDiffusion.modules.models.shepherd_arch.egnn) multinomial() (in module MolecularDiffusion.modules.layers.functional) multitask_args (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) multivectors (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) N n (MolecularDiffusion.modules.models.ligandiff.gvp.GVP attribute) n1_given_n2 (MolecularDiffusion.modules.models.diffpharma.distributions.DistributionNodes attribute) n2_given_n1 (MolecularDiffusion.modules.models.diffpharma.distributions.DistributionNodes attribute) n_adapter_context (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.equiformer_v2_dynamics.EquiformerV2_dynamics attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.TabascoEGNNDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.TabascoEquiformerDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.TabascoGVPDiffusionTask attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_equiformer.ModelTaskFactory attribute) n_atom_basis (MolecularDiffusion.modules.models.goflow.gotennet.EQFF attribute) (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) N_ATOM_FEATURES (in module MolecularDiffusion.modules.models.syncogen.constants.constants) n_atom_rdkit_feats (MolecularDiffusion.data.component.goflow_data.GoFlowDataModule attribute) n_atom_types (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.PointCloudToDGLAdapter attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.Graph3DToDGLAdapter attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) n_atoms (MolecularDiffusion.data.component.dataset.LazyChunkedDataset attribute) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRRecord attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraRecord attribute) n_atoms_hist (MolecularDiffusion.data.component.graph3d_dataset.Graph3DStats attribute) n_atoms_histogram() (MolecularDiffusion.data.component.graph3d_dataset.Graph3DStats method) n_attn_heads (MolecularDiffusion.modules.models.syncogen.models.semla.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.NodeAttention attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.NodeAttention attribute) n_bins (MolecularDiffusion.modules.models.chefnmr.unknown.Channel attribute), [1] n_blocks (MolecularDiffusion.modules.models.nextmol.dgt.DGTDiffusion attribute) N_BOND_CLASSES (in module MolecularDiffusion.data.component.graph3d_dataset) (in module MolecularDiffusion.modules.tasks.diffusion_ditmc) (in module MolecularDiffusion.modules.tasks.diffusion_nextmol) N_BOND_FEATURES (in module MolecularDiffusion.modules.models.syncogen.constants.constants) N_BOND_TYPES (in module MolecularDiffusion.modules.models.diffsmol.uni_transformer) n_bond_types (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.Graph3DToDGLAdapter attribute) N_BOND_TYPES_KEKULIZED (in module MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d) N_BUILDING_BLOCKS (in module MolecularDiffusion.modules.models.syncogen.constants.constants) n_calls (MolecularDiffusion.callbacks.train_helper.SP_regularizer attribute) n_cat_feats (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) N_CENTERS (in module MolecularDiffusion.modules.models.syncogen.constants.constants) N_CHARGE_CLASSES (in module MolecularDiffusion.modules.tasks.diffusion_loqi) n_charge_classes (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.Graph3DToDGLAdapter attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) n_charges (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.PointCloudToDGLAdapter attribute) n_concat_context (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.equiformer_v2_dynamics.EquiformerV2_dynamics attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.TabascoEGNNDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.TabascoEquiformerDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.TabascoGVPDiffusionTask attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_equiformer.ModelTaskFactory attribute) n_conf (MolecularDiffusion.modules.models.chefnmr.sidecar.ChefNMRSidecar attribute) n_coord_sets (MolecularDiffusion.modules.models.syncogen.models.semla.CoordNorm attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EdgeMessages attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EquiInvDynamics attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.CoordNorm attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EdgeMessages attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiInvDynamics attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiMessagePassingLayer attribute) n_cp_feats (MolecularDiffusion.modules.layers.gvp.gvp.GVP attribute) (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) n_dim_data (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) n_dims (MolecularDiffusion.modules.models.difflinker.edm.EDM attribute) (MolecularDiffusion.modules.models.difflinker.egnn.Dynamics attribute) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM attribute) (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.diffsbdd.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.egt.EGT_dynamics attribute) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows attribute) (MolecularDiffusion.modules.models.equiformer_v2_dynamics.EquiformerV2_dynamics attribute) (MolecularDiffusion.modules.models.esen.eSEN_dynamics attribute) (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_decoder_QM9 attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_dynamics_QM9 attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_encoder_QM9 attribute) (MolecularDiffusion.modules.models.gfmdiff.dynamics.GFMDiffDynamics attribute) (MolecularDiffusion.modules.models.ligandiff.edm.EDM attribute) (MolecularDiffusion.modules.models.ligandiff.egnn.Dynamics attribute) (MolecularDiffusion.modules.models.painn_dynamics.PaiNNDynamics attribute) (MolecularDiffusion.modules.models.transformer_dynamics.TransformerDynamics attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) n_dist_basis (MolecularDiffusion.modules.tasks.ssl3d.PairwiseDistObjective attribute) N_EDGE_CLASSES (in module MolecularDiffusion.modules.models.loqi.graph_utils) n_edge_features (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) n_edge_types (MolecularDiffusion.modules.models.syncogen.models.semla.SemlaGenerator attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator attribute) N_ELEMENT (in module MolecularDiffusion.data.component.oareactdiff_data) n_extra_heads (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) n_feats (MolecularDiffusion.modules.models.flowmol.interpolant_scheduler.InterpolantScheduler attribute) n_fragments (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask attribute) n_frames (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) n_frequencies (MolecularDiffusion.modules.layers.common.SinusoidsEmbeddingNew attribute) (MolecularDiffusion.modules.models.difflinker.egnn.SinusoidsEmbeddingNew attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.SinusoidsEmbeddingNew attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.SinusoidsEmbeddingNew attribute) (MolecularDiffusion.modules.models.geoldm.egnn.SinusoidsEmbeddingNew attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.SinusoidsEmbeddingNew attribute) n_head (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) n_heads (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) n_hidden (MolecularDiffusion.modules.models.goflow.outputs.GatedEquivariantBlock attribute) n_hidden_edge_feats (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) n_hidden_scalars (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone attribute) n_interactions (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet attribute) n_jobs (MolecularDiffusion.runmodes.analyze.featurize.SOAPFeaturizer attribute) n_layers (MolecularDiffusion.modules.layers.conv.EquivariantBlock attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.EquivariantBlock attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EGNN attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.difflinker.egnn.GNN attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EGNN attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EGNN attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.diffspectra.dmt.DMT attribute) (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EGNN attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.geoldm.egnn.GNN attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.EquivariantBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) n_message_gvps (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) n_molecule_updates (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone attribute) n_molecules (MolecularDiffusion.data.component.graph3d_dataset.Graph3DStats attribute) n_neigh (MolecularDiffusion.runmodes.train.data.DataModule attribute) n_new_atoms (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMConstrainedGenerator attribute) n_node_dist (MolecularDiffusion.modules.models.diffpharma.distributions.DistributionNodes property) (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask property) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask property) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTask property) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDTask property) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.LigandPocketSizePrior attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeNodeDistribution attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask property) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTask property) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask property) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask property) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.IPDiffDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.KGDiffDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.PocketSizePrior attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask property) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask property) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask property) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQINodeDistribution attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_pmdm.LigandSizeDistribution attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenSizePrior property) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoNodeDistribution attribute) n_node_types (MolecularDiffusion.modules.models.syncogen.models.semla.SemlaGenerator attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator attribute) n_nodes (MolecularDiffusion.modules.models.difflinker.linker_size.DistributionNodes attribute) (MolecularDiffusion.modules.models.en_diffusion.DistributionNodes attribute) n_nodes_to_idx (MolecularDiffusion.modules.models.diffpharma.distributions.DistributionNodes attribute) n_overfit (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) N_PHARM (in module MolecularDiffusion.modules.models.syncogen.constants.constants) n_pharm (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator attribute) n_rbf (MolecularDiffusion.modules.models.goflow.ops.ExpNormalSmearing attribute) N_REACTIONS (in module MolecularDiffusion.modules.models.syncogen.constants.constants) n_real_atom_types (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) n_recycles (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone attribute) n_rows (MolecularDiffusion.modules.models.chefnmr.sidecar.ChefNMRSidecar property) n_samples (MolecularDiffusion.core.lightning_callbacks.generative_eval_callback.GenerativeEvalCallback attribute) n_sin (MolecularDiffusion.modules.models.goflow.outputs.GatedEquivariantBlock attribute) n_sout (MolecularDiffusion.modules.models.goflow.outputs.GatedEquivariantBlock attribute) n_steps (MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance.UFFBoundGuidance attribute) n_update_gvps (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) n_vars (MolecularDiffusion.modules.models.diffspectra.specformer.Flatten_Head attribute) n_vec_channels (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone attribute) n_vector_features (MolecularDiffusion.modules.models.loqi.fn_model.MegaFNV3Conf attribute) n_vin (MolecularDiffusion.modules.models.goflow.outputs.GatedEquivariantBlock attribute) n_vocab (MolecularDiffusion.modules.tasks.diffusion_difflinker.PointCloudToDiffLinkerBatch attribute) n_volume_bins (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolTaskFactory attribute) n_vout (MolecularDiffusion.modules.models.goflow.outputs.GatedEquivariantBlock attribute) N_x1 (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) N_x1_sampling (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) N_x4 (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) name (MolecularDiffusion.modules.models.chefnmr.unknown.Channel attribute), [1] (MolecularDiffusion.modules.models.ditmc.priors.GaussianPrior attribute) (MolecularDiffusion.modules.models.ditmc.priors.HarmonicPrior attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.base.LossBase property) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRRecord attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraRecord attribute) (MolecularDiffusion.utils.geom_analyzer.Histogram_cont attribute) (MolecularDiffusion.utils.geom_analyzer.Histogram_discrete attribute) name_to_idx() (MolecularDiffusion.modules.models.tabasco.utils.metrics.AtomTypeDistribution method) name_wandb (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.runmodes.train.logger.Logger attribute) NATIVE_BOND_VOCAB_SIZE (in module MolecularDiffusion.data.component.goflow_data) natoms (MolecularDiffusion.modules.layers.atomic_data.AtomicData attribute) natoms_file (MolecularDiffusion.runmodes.train.data.DataModule attribute) ndim_extra (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask attribute) nedges (MolecularDiffusion.modules.layers.atomic_data.AtomicData attribute) needs_generative (MolecularDiffusion.runmodes.train.eval.TaskEvalConfig attribute) neg_infinity (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) negative_slope (MolecularDiffusion.modules.layers.vn.vn_layers.VNLeakyReLU attribute) (MolecularDiffusion.modules.layers.vn.vn_layers.VNLinearLeakyReLU attribute) negative_target_values (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) neighbor_emb (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) neighbor_embedding (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet attribute) NeighborEmb (class in MolecularDiffusion.modules.models.oareactdiff.leftnet) NeighborEmbedding (class in MolecularDiffusion.modules.models.etflow.torchmd) neighbors (MolecularDiffusion.modules.layers.graph_module.GraphData attribute) net (MolecularDiffusion.modules.layers.equiformer_v2.radial_function.RadialFunction attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.radial_function.RadialFunction attribute) (MolecularDiffusion.modules.layers.esen.nn.radial.RadialMLP attribute) (MolecularDiffusion.modules.layers.tabasco.transition.FeedForward attribute) (MolecularDiffusion.modules.models.apo2mol.common.MLP attribute) (MolecularDiffusion.modules.models.chefnmr.embedders.FeedForward attribute) (MolecularDiffusion.modules.models.diffsmol.common.MLP attribute) (MolecularDiffusion.modules.models.kgdiff.common.MLP attribute) (MolecularDiffusion.modules.models.tabasco.flow_model.FlowMatchingModel attribute) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTask attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask attribute) net() (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet method) net_cond (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.IPDiffDiffusionTask attribute) net_cond_ckpt (MolecularDiffusion.modules.tasks.diffusion_apo2mol.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.ModelTaskFactory attribute) net_target() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) network (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask attribute) neural_network_forward() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) neutral_charge_index (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.PointCloudToDGLAdapter attribute) next_compute (MolecularDiffusion.modules.models.tabasco.callbacks.molecule_metrics.MoleculeMetricsCallback attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.posebusters.PoseBustersCallback attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.save_molecules.SaveGeneratedMolsCallback attribute) NextMolGenerator (class in MolecularDiffusion.modules.tasks.diffusion_nextmol) NextMolTask (class in MolecularDiffusion.modules.tasks.diffusion_nextmol) NextMolTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_nextmol) nf (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) nfe (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask attribute) nhead (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT attribute) NLLLoss (class in MolecularDiffusion.modules.models.syncogen.diffusion.loss.nll) NMRSpectraEmbedder (class in MolecularDiffusion.modules.models.chefnmr.embedders) nn_vector() (in module MolecularDiffusion.modules.models.oareactdiff.leftnet) NO_EDGE_CHANNEL (in module MolecularDiffusion.modules.models.syncogen.api.ops.graph_ops) no_rdkit_log() (in module MolecularDiffusion.modules.tasks.metrics) (in module MolecularDiffusion.utils.io) no_weight_decay() (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 method) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 method) (MolecularDiffusion.modules.layers.graph_module.GraphModelMixin method) (MolecularDiffusion.modules.models.esen.eSEN_Backbone method) (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder method) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 method) node2edge_lin (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) node_attn (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiMessagePassingLayer attribute) node_attn_dropout (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) node_attr (MolecularDiffusion.modules.models.ditmc.graphs.CondGraph attribute) (MolecularDiffusion.modules.models.ditmc.graphs.LatentGraph attribute) (MolecularDiffusion.modules.models.ditmc.graphs.PriorGraph attribute) NODE_ATTR_BLOCKS (in module MolecularDiffusion.modules.models.ditmc.graph_features) NODE_ATTR_DIM (in module MolecularDiffusion.modules.models.etflow.features) node_attr_dim (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) node_attr_dim() (in module MolecularDiffusion.modules.models.ditmc.graph_features) node_classifier_head (MolecularDiffusion.modules.models.syncogen.models.semla.SemlaGenerator attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator attribute) node_dims (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) node_dist_model (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask property) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask property) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDTask property) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTask property) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask property) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.IPDiffDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.KGDiffDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask property) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask property) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask property) node_dropout (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) node_emb (MolecularDiffusion.modules.models.diffspectra.dmt.DMT attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.Cond_DGT_concat attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.DGT_concat attribute) (MolecularDiffusion.modules.models.nextmol.dgt.DGTDiffusion attribute) node_embedding (MolecularDiffusion.modules.models.ditmc.dit.GenerativeModel attribute) (MolecularDiffusion.modules.models.ditmc.meshgraphnet.MeshGraphNetEncoder attribute) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPEmbedding attribute) node_feature (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) node_feature_choice (MolecularDiffusion.runmodes.train.data.DataModule attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) node_feature_dim (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) node_ff (MolecularDiffusion.modules.models.syncogen.models.semla.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.LengthsMLP attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiMessagePassingLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.LengthsMLP attribute) node_ffn (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) node_ffn_dropout (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) node_indicator (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) node_input_dims (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) node_ln (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer attribute) node_mask (MolecularDiffusion.modules.models.midi.placeholder.PlaceHolder attribute) (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) node_mask_index() (MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.base.DiscreteStrategyBase static method) node_message() (MolecularDiffusion.modules.models.oareactdiff.leftnet.GCLMessage method) node_mlp (MolecularDiffusion.modules.layers.conv.GCL attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.GCL attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.GCL attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.GCL attribute) (MolecularDiffusion.modules.models.ditmc.meshgraphnet.MeshGraphNetLayer attribute) (MolecularDiffusion.modules.models.geoldm.egnn.GCL attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.GCL attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.GCLMessage attribute) (MolecularDiffusion.modules.models.pmdm.encoders.EGNNSparseLayer attribute) (MolecularDiffusion.modules.models.shepherd_arch.egnn.EGNN attribute) node_mlp_embedding_dim (MolecularDiffusion.modules.models.shepherd_arch.egnn.EGNN attribute) node_model() (MolecularDiffusion.modules.layers.conv.GCL method) (MolecularDiffusion.modules.models.apo2mol.pminet.GCL method) (MolecularDiffusion.modules.models.difflinker.egnn.GCL method) (MolecularDiffusion.modules.models.diffpharma.egnn.GCL method) (MolecularDiffusion.modules.models.geoldm.egnn.GCL method) node_nf (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.diffsbdd.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) node_nfs (MolecularDiffusion.modules.models.oareactdiff.dynamics.BaseDynamics attribute) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) node_norm (MolecularDiffusion.modules.models.ditmc.meshgraphnet.MeshGraphNetLayer attribute) (MolecularDiffusion.modules.models.pmdm.encoders.EGNNSparseLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.BondRefine attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EdgeMessages attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.NodeFeedForward attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.BondRefine attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EdgeMessages attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.NodeFeedForward attribute) node_offset (MolecularDiffusion.modules.layers.graph_module.GraphData attribute) node_output_embedding (MolecularDiffusion.modules.models.shepherd_arch.egnn.EGNN attribute) node_output_embedding_dim (MolecularDiffusion.modules.models.shepherd_arch.egnn.EGNN attribute) node_output_head (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone attribute) node_output_layer (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer attribute) node_pair_fuse (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) node_position_updater (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone attribute) node_position_updaters (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) node_positions_weight (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPInteractions attribute) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) node_pred_mlp (MolecularDiffusion.modules.models.diffspectra.dmt.DMT attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.Cond_DGT_concat attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.DGT_concat attribute) node_proj (MolecularDiffusion.modules.models.syncogen.models.semla.BondRefine attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EdgeMessages attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EquivariantMLP attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.BondRefine attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EdgeMessages attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquivariantMLP attribute) node_residual_mlp (MolecularDiffusion.modules.models.flowmol_graph3d.self_conditioning.SelfConditioningResidualLayer attribute) NODE_SETS (in module MolecularDiffusion.modules.tasks.diffusion_diffpharma) node_size (MolecularDiffusion.modules.models.painn_backbone.EquivNetHParams attribute) node_time_embedding (MolecularDiffusion.modules.models.loqi.fn_model.MegaFNV3Conf attribute) node_time_mlp (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) node_update (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) node_vector_features() (in module MolecularDiffusion.modules.models.gcdm.gcp_utils) NodeAttention (class in MolecularDiffusion.modules.models.syncogen.models.semla) (class in MolecularDiffusion.modules.models.syncogen.models.semla_pharm) NodeAttributeEmbedding (class in MolecularDiffusion.modules.models.ditmc.embedding) NodeEdgeBlock (class in MolecularDiffusion.modules.layers.conv) (class in MolecularDiffusion.modules.models.midi.transformer_model) NodeFeaturizer (class in MolecularDiffusion.data.component.feature) NodeFeedForward (class in MolecularDiffusion.modules.models.syncogen.models.semla) (class in MolecularDiffusion.modules.models.syncogen.models.semla_pharm) NodeInit (class in MolecularDiffusion.modules.models.goflow.ops) NodePositionUpdate (class in MolecularDiffusion.modules.layers.gvp.gvp) (class in MolecularDiffusion.modules.models.flowmol.vector_field) NodeTransformerLayer (class in MolecularDiffusion.modules.layers.gfmdiff.blocks) noise_align (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) noise_level (MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize.GCDMOptimizeFactory attribute) noise_scale (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion attribute) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.CenteredMetricInterpolant attribute) noise_schedule (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTSGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) noise_schedule_dict (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) noise_scheduler (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.Graph3DBatchToNextMolAdapter attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask attribute) noise_sigma (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant attribute) noise_sigma_max (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) noise_sigma_min (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) NoiseBase (class in MolecularDiffusion.modules.models.syncogen.diffusion.noise.base) noised_coords_in_network() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) noised_representation() (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion method) NoiseModel (class in MolecularDiffusion.modules.models.midi.noise_model) (class in MolecularDiffusion.modules.models.noisemodel) NoiseScheduleVP (class in MolecularDiffusion.modules.models.jodo.noise_schedule) NoiseScheduleVPV2 (class in MolecularDiffusion.modules.models.nextmol.scheduler) none_norm() (MolecularDiffusion.modules.models.goflow.ops.VecLayerNorm method) NONLINEARITIES (in module MolecularDiffusion.modules.models.apo2mol.common) (in module MolecularDiffusion.modules.models.kgdiff.common) (in module MolecularDiffusion.modules.models.loqi.fn_model) nonlinearities (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) nonlinearity_slope (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPLayerConfig attribute) norm (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.tabasco.attention.AdaLNAttention attribute) (MolecularDiffusion.modules.layers.tabasco.attention.AttentionBlock attribute) (MolecularDiffusion.modules.layers.tabasco.attention.CrossAdaLNAttention attribute) (MolecularDiffusion.modules.layers.tabasco.transformer.Transformer attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.chefnmr.embedders.PreNorm attribute) (MolecularDiffusion.modules.models.chefnmr.layers.Mlp attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.ditmc.embedding.EdgeAttributeEmbedding attribute) (MolecularDiffusion.modules.models.ditmc.embedding.NodeAttributeEmbedding attribute) (MolecularDiffusion.modules.models.ditmc.readout.EquivariantReadout attribute) (MolecularDiffusion.modules.models.ditmc.readout.SimpleReadout attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.Mlp attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.ligandiff.conv_layer.GVPConvLayer attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.FullyConnectedTensorProductRescaleNorm attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.SeparableFCTP attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.CoordNorm attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.CoordNorm attribute) norm00 (MolecularDiffusion.modules.models.ditmc.layers.EquivariantLayerNorm attribute) norm1 (MolecularDiffusion.modules.models.chefnmr.layers.DiTBlock attribute) (MolecularDiffusion.modules.models.ditmc.dit.DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiTBlock attribute) (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) (MolecularDiffusion.modules.models.pmdm.encoders.CrossAttentionBlock attribute) norm1_edge (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) norm1_node (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) norm1p (MolecularDiffusion.modules.models.pmdm.encoders.CrossAttentionBlock attribute) norm2 (MolecularDiffusion.modules.models.chefnmr.layers.DiTBlock attribute) (MolecularDiffusion.modules.models.ditmc.dit.DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiTBlock attribute) (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) (MolecularDiffusion.modules.models.pmdm.encoders.CrossAttentionBlock attribute) norm2_edge (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) norm2_node (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.EquivariantMixBlock attribute) norm2p (MolecularDiffusion.modules.models.pmdm.encoders.CrossAttentionBlock attribute) norm3 (MolecularDiffusion.modules.models.pmdm.encoders.CrossAttentionBlock attribute) norm3p (MolecularDiffusion.modules.models.pmdm.encoders.CrossAttentionBlock attribute) norm_1 (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.TransBlockV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.TransBlockV2 attribute) (MolecularDiffusion.modules.layers.esen.esen_block.eSEN_Block attribute) norm_2 (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.TransBlockV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.TransBlockV2 attribute) (MolecularDiffusion.modules.layers.esen.esen_block.eSEN_Block attribute) norm_biases (MolecularDiffusion.modules.models.difflinker.edm.EDM attribute) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM attribute) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.ligandiff.edm.EDM attribute) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.oareactdiff.normalizer.Normalizer attribute) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) norm_const (MolecularDiffusion.modules.layers.esen.nn.radial.SphericalBesselBasis attribute) norm_constant (MolecularDiffusion.modules.layers.conv.EquivariantBlock attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.EquivariantBlock attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.EquivariantBlock attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) norm_diff (MolecularDiffusion.modules.layers.conv.EquivariantBlock attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.EquivariantBlock attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EGNN attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EGNN attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EGNN attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.EquivariantBlock attribute) norm_eps (MolecularDiffusion.modules.layers.tabasco.attention.AdaLNAttention attribute) (MolecularDiffusion.modules.layers.tabasco.attention.CrossAdaLNAttention attribute) norm_final (MolecularDiffusion.modules.models.chefnmr.layers.FinalLayer attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.FinalLayer attribute) norm_k (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) norm_l0 (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) norm_no_nan() (in module MolecularDiffusion.modules.models.diffsmol.common) (in module MolecularDiffusion.modules.models.gcdm.gcp_utils) norm_pos1 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) norm_q (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) norm_type (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) norm_values (MolecularDiffusion.modules.models.difflinker.edm.EDM attribute) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM attribute) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.ligandiff.edm.EDM attribute) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.oareactdiff.normalizer.Normalizer attribute) (MolecularDiffusion.modules.models.oareactdiff.schedule.DiffSchedule attribute) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTask property) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) norm_vector() (MolecularDiffusion.modules.models.gcdm.gcp_utils.GCPLayerNorm static method) norm_x_diff (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) normal_kl() (in module MolecularDiffusion.modules.models.apo2mol.score_model) (in module MolecularDiffusion.modules.models.diffsmol.score_model) (in module MolecularDiffusion.modules.models.kgdiff.score_model) normalization (MolecularDiffusion.modules.layers.conv.GCL attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantLayerNormArray attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantLayerNormArray attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantRMSNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantLayerNormArray attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNorm attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNormV2 attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) normalization_factor (MolecularDiffusion.modules.layers.conv.EquivariantBlock attribute) (MolecularDiffusion.modules.layers.conv.EquivariantUpdate attribute) (MolecularDiffusion.modules.layers.conv.GCL attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.EquivariantBlock attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.GCL attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EGNN attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.difflinker.egnn.GCL attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EGNN attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.GCL attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.GCL attribute) (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EGNN attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.geoldm.egnn.GCL attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.EquivariantBlock attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.GCL attribute) (MolecularDiffusion.modules.models.ligandiff.conv_layer.GVPMessagePassing attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) normalization_scale (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) normalize() (MolecularDiffusion.modules.models.difflinker.edm.EDM method) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) (MolecularDiffusion.modules.models.oareactdiff.normalizer.Normalizer method) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) (MolecularDiffusion.utils.geom_analyzer.Histogram_discrete method) normalize_condition (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.TabascoEGNNDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.TabascoEquiformerDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.TabascoGVPDiffusionTask attribute) normalize_distance_vectors (MolecularDiffusion.modules.models.shepherd_arch.egnn.EGNN attribute) normalize_factors (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) normalize_frame (MolecularDiffusion.modules.layers.vn.vn_layers.VNStdFeature attribute) normalize_histogram() (in module MolecularDiffusion.utils.geom_analyzer) normalize_pyG() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) normalize_tensor() (MolecularDiffusion.modules.models.en_diffusion.DistributionProperty method) normalize_threshold (MolecularDiffusion.modules.models.syncogen.diffusion.loss.smooth_lddt.SmoothLDDTLoss attribute) normalized_shape (MolecularDiffusion.modules.layers.conv.SE3Norm attribute) (MolecularDiffusion.modules.models.midi.layers.SE3Norm attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.SE3Norm attribute) Normalizer (class in MolecularDiffusion.modules.models.oareactdiff.normalizer) normalizer (MolecularDiffusion.modules.models.en_diffusion.DistributionProperty attribute) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute), [1] normE1 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) normE2 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) normX1 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) normX2 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) nu (MolecularDiffusion.modules.models.loqi.interpolant.CosineSchedule attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) nu_arr (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) (MolecularDiffusion.modules.models.noisemodel.NoiseModel attribute) num2symbol (in module MolecularDiffusion.utils.geom_analyzer) NUM_ALIGN_REPEATS (in module MolecularDiffusion.runmodes.analyze.similarity3d) num_atom (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) NUM_ATOM_CLASSES (in module MolecularDiffusion.data.component.diffsbdd_data) num_atom_classes (MolecularDiffusion.modules.models.loqi.fn_model.MegaFNV3Conf attribute) num_atom_type (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset property) num_atom_types (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.PointCloudToTensorDictAdapter attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.TabascoEGNNDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.TabascoEquiformerDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.TabascoGVPDiffusionTask attribute) NUM_ATOMIC_NUMBERS (in module MolecularDiffusion.modules.models.ditmc.embedding) num_atoms (MolecularDiffusion.data.component.dataset.GraphDataset property) (MolecularDiffusion.data.component.dataset.LazyChunkedDataset property) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset property) (MolecularDiffusion.data.component.dataset.PointCloudDataset property) (MolecularDiffusion.data.component.graph3d_dataset.Graph3DDataset property) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.BaseModel attribute) (MolecularDiffusion.modules.models.syncogen.api.graph.building_block.BuildingBlock attribute) (MolecularDiffusion.utils.smilify.Molecule attribute) num_basis (MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf.GaussianRadialBasisLayer attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf.GaussianRadialBasisLayer attribute) (MolecularDiffusion.modules.layers.esen.nn.gaussian_embedding.GaussianFeatureEmbedding attribute) (MolecularDiffusion.modules.models.esen.GaussianFeatureEmbedding attribute) num_beams (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolGenerator attribute) num_bins (MolecularDiffusion.modules.models.en_diffusion.DistributionProperty attribute) num_blocks (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) NUM_BOND_TYPES (in module MolecularDiffusion.modules.models.pmdm.common) num_candidates (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) num_channels (MolecularDiffusion.modules.layers.equiformer_v2.activation.GateActivation attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantDegreeLayerScale attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantLayerNormArray attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Embedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.GateActivation attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantDegreeLayerScale attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantLayerNormArray attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantRMSNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Embedding attribute) (MolecularDiffusion.modules.layers.esen.nn.activation.GateActivation attribute) (MolecularDiffusion.modules.layers.esen.nn.gaussian_embedding.GaussianFeatureEmbedding attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantDegreeLayerScale attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantLayerNormArray attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.models.esen.GaussianFeatureEmbedding attribute) num_class (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) num_classes (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_decoder_QM9 attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_encoder_QM9 attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.LabelEmbedder attribute) (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousDiffusionInterpolant attribute) (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant attribute) num_coefficients (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Embedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Embedding attribute) num_confs (MolecularDiffusion.modules.models.tabasco.utils.metrics.PoseCheckStrainEnergy attribute) num_context_node_features (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) num_diffusion_timesteps (MolecularDiffusion.modules.models.loqi.interpolant.CosineSchedule attribute) (MolecularDiffusion.modules.models.loqi.interpolant.LinearSchedule attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolTaskFactory attribute) num_display_mols (MolecularDiffusion.modules.models.tabasco.callbacks.save_molecules.SaveGeneratedMolsCallback attribute) num_distance_basis (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) num_edge_classes (MolecularDiffusion.modules.models.loqi.fn_model.MegaFNV3Conf attribute) num_edges (MolecularDiffusion.modules.layers.atomic_data.AtomicData property) num_encoder_layers (MolecularDiffusion.runmodes.train.tasks_gcdm.ModelTaskFactory attribute) num_epochs (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) num_features (MolecularDiffusion.modules.models.ditmc.dit.DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) (MolecularDiffusion.modules.models.ditmc.embedding.DiTEdgeEmbed attribute) (MolecularDiffusion.modules.models.ditmc.embedding.DiTNodeEmbed attribute) (MolecularDiffusion.modules.models.ditmc.layers.EquivariantLayerNorm attribute) (MolecularDiffusion.modules.models.ditmc.meshgraphnet.MeshGraphNetEncoder attribute) (MolecularDiffusion.modules.models.ditmc.readout.EquivariantReadout attribute) (MolecularDiffusion.modules.models.ditmc.readout.SimpleReadout attribute) num_feedforward_layers (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPLayerConfig attribute) num_fragments() (MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly.RDKitMoleculeAssembly method) num_fragments_probs (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) num_fragments_probs() (MolecularDiffusion.modules.models.syncogen.datamodule.SyncogenDataModule method) num_gaussians (MolecularDiffusion.modules.models.apo2mol.common.GaussianSmearing attribute) (MolecularDiffusion.modules.models.diffsmol.common.GaussianSmearing attribute) (MolecularDiffusion.modules.models.kgdiff.common.GaussianSmearing attribute) num_generate (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecScaffoldGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolGenerator attribute) (MolecularDiffusion.modules.tasks.pocket_generator.PocketGenerator attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) num_graphs (MolecularDiffusion.modules.layers.atomic_data.AtomicData property) (MolecularDiffusion.modules.models.ditmc.graphs.LatentGraph attribute) num_h2x (MolecularDiffusion.modules.models.apo2mol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) num_heads (MolecularDiffusion.modules.layers.e3x.modules.SelfAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer attribute) (MolecularDiffusion.modules.layers.tabasco.attention.AdaLNAttention attribute) (MolecularDiffusion.modules.layers.tabasco.attention.CrossAdaLNAttention attribute) (MolecularDiffusion.modules.models.chefnmr.layers.Attention attribute) (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Vec2AttnHeads attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) (MolecularDiffusion.runmodes.train.tasks_transformer.ModelTaskFactory attribute) num_init_h2x (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) num_init_x2h (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) num_interactions (MolecularDiffusion.modules.models.painn_backbone.EquivNetHParams attribute) (MolecularDiffusion.runmodes.train.tasks_painn.ModelTaskFactory attribute) num_irreps (MolecularDiffusion.modules.layers.equiformer_v2.drop.EquivariantDropout attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.EquivariantDropout attribute) num_k (MolecularDiffusion.modules.models.diffsmol.shape_ae.VNDGCNNEncoder attribute) (MolecularDiffusion.modules.models.diffsmol.shape_ae.VNResnetEncoder attribute) num_layers (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.ditmc.layers.E3MLP attribute) (MolecularDiffusion.modules.models.ditmc.layers.MLP attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.ldm.decoders.transformer.TransformerDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.transformer.TransformerEncoder attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gfmdiff.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_transformer.ModelTaskFactory attribute) NUM_LIGAND_CLASSES (in module MolecularDiffusion.data.component.kgdiff_data) num_message_layers (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPLayerConfig attribute) num_mlp_layer (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) num_molecules (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolGenerator attribute) num_node_types (MolecularDiffusion.modules.models.apo2mol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) num_nodes (MolecularDiffusion.modules.layers.atomic_data.AtomicData property) (MolecularDiffusion.modules.models.ditmc.graphs.LatentGraph property) (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) num_optimization_timesteps (MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize.GCDMOptimizeFactory attribute) num_output (MolecularDiffusion.modules.layers.esen.nn.radial.GaussianSmearing attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.GaussianSmearing attribute) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.GaussianSmearing attribute) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.LinearSigmoidSmearing attribute) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.SigmoidSmearing attribute) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.SiLUSmearing attribute) num_params (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 property) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 property) (MolecularDiffusion.modules.layers.graph_module.GraphModelMixin property) (MolecularDiffusion.modules.models.esen.eSEN_Backbone property) (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder property) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder property) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 property) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.BaseModel property) num_parity (MolecularDiffusion.modules.layers.e3x.modules.Dense attribute) (MolecularDiffusion.modules.models.ditmc.layers.EquivariantLayerNorm attribute) num_parity_qk (MolecularDiffusion.modules.layers.e3x.modules.SelfAttention attribute) NUM_POCKET_CLASSES (in module MolecularDiffusion.data.component.diffint_prep) num_points_x2 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) num_points_x3 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) num_r_gaussian (MolecularDiffusion.modules.models.apo2mol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) num_radial (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiMessage attribute) num_radial_basis (MolecularDiffusion.modules.models.ditmc.embedding.DiTEdgeEmbed attribute) (MolecularDiffusion.modules.models.ditmc.embedding.RadialSphericalEdgeEmbedding attribute) num_random_augmentations (MolecularDiffusion.modules.models.tabasco.flow_model.FlowMatchingModel attribute) num_rbf (MolecularDiffusion.modules.models.etflow.torchmd.ExpNormalSmearing attribute) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.RBFEmb attribute) num_resolutions (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_m_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.CoefficientMappingModule attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Embedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_m_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.CoefficientMappingModule attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Embedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) num_sample_steps (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) num_samples (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.molecule_metrics.MoleculeMetricsCallback attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.posebusters.PoseBustersCallback attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.save_molecules.SaveGeneratedMolsCallback attribute) num_sampling_steps (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.molecule_metrics.MoleculeMetricsCallback attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.posebusters.PoseBustersCallback attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.save_molecules.SaveGeneratedMolsCallback attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) NUM_SHORTEST_HOPS (in module MolecularDiffusion.modules.models.ditmc.embedding) num_sphere_samples (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) num_steps (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecScaffoldGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTask attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolGenerator attribute) (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.pocket_generator.PocketGenerator attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) num_sublayers (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) NUM_SURFACE_POINTS (in module MolecularDiffusion.runmodes.analyze.similarity3d) num_targets (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.BaseModel attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) num_timesteps (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.FlowMatchingInterpolant attribute) num_tokens() (MolecularDiffusion.modules.models.chefnmr.embedders.SpectraTokenizerConv1D static method) (MolecularDiffusion.modules.models.chefnmr.embedders.SpectraTokenizerPatch1D static method) num_trajectories (MolecularDiffusion.modules.models.tabasco.callbacks.save_molecules.SaveGeneratedMolsCallback attribute) num_updates (MolecularDiffusion.modules.models.syncogen.models.ema.ExponentialMovingAverage attribute) num_worker (MolecularDiffusion.core.engine.Engine attribute) num_workers (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataModule attribute) (MolecularDiffusion.data.component.diffdec_data.DiffDecDataModule attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataModule attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataModule attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataModule attribute) (MolecularDiffusion.data.component.goflow_data.GoFlowDataModule attribute) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataModule attribute) (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataModule attribute) (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule attribute) (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) (MolecularDiffusion.modules.models.syncogen.datamodule.SyncogenDataModule attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) num_x2h (MolecularDiffusion.modules.models.apo2mol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) num_x_dims (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) numbers_of_nodes() (MolecularDiffusion.modules.models.difflinker.edm.EDM static method) numBridgeheadsAndSpiro() (in module MolecularDiffusion.utils.sascore) O o3d (in module MolecularDiffusion.data.component.pharmacophore) (in module MolecularDiffusion.utils.shepherd_utils) o_proj (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) OAREACTDIFF_ATOM_VOCAB (in module MolecularDiffusion.data.component.oareactdiff_data) oareactdiff_collate() (in module MolecularDiffusion.data.component.oareactdiff_data) OAReactDiffDataModule (class in MolecularDiffusion.data.component.oareactdiff_data) OAReactDiffTask (class in MolecularDiffusion.modules.tasks.diffusion_oareactdiff) OAReactDiffTS1xDataset (class in MolecularDiffusion.data.component.oareactdiff_data) OAReactDiffTSGenerator (class in MolecularDiffusion.modules.tasks.diffusion_oareactdiff) object_aware (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) objectives (MolecularDiffusion.modules.tasks.ssl3d.SSL3D attribute) ode_sampling() (MolecularDiffusion.modules.models.reactot.en_sb.EnSB method) offset_distances (MolecularDiffusion.modules.layers.graph_module.GraphData attribute) ok (MolecularDiffusion.runmodes.generate.sweep.RunResult attribute) on_before_optimizer_step() (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) on_fit_start() (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.dataset_stats.DatasetStatsCallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) on_load_checkpoint() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) on_save_checkpoint() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback method) (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) on_test_batch_end() (MolecularDiffusion.core.engine_lightning.EngineLightning method) on_test_end() (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) on_test_epoch_end() (MolecularDiffusion.core.engine_lightning.EngineLightning method) on_test_start() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) on_train_batch_end() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback method) on_train_start() (MolecularDiffusion.core.engine_lightning.EngineLightning method) on_validation_batch_end() (MolecularDiffusion.core.engine_lightning.EngineLightning method) on_validation_end() (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) on_validation_epoch_end() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.core.lightning_callbacks.generative_eval_callback.GenerativeEvalCallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.molecule_metrics.MoleculeMetricsCallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.posebusters.PoseBustersCallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.save_molecules.SaveGeneratedMolsCallback method) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask method) on_validation_epoch_start() (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask method) on_validation_start() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) one_hot() (in module MolecularDiffusion.modules.layers.functional) one_hot_from_z() (in module MolecularDiffusion.data.component.diffsbdd_data) onehot() (in module MolecularDiffusion.data.component.feature) onehot_float() (in module MolecularDiffusion.modules.models.midi.diffusion_utils) OneLayerActivation (class in MolecularDiffusion.modules.models.oareactdiff.leftnet) only_h_nan_idx (MolecularDiffusion.modules.models.difflinker.utils.FoundNaNException attribute) (MolecularDiffusion.modules.models.ligandiff.utils.FoundNaNException attribute) only_x_nan_idx (MolecularDiffusion.modules.models.difflinker.utils.FoundNaNException attribute) (MolecularDiffusion.modules.models.ligandiff.utils.FoundNaNException attribute) OPENBABEL_VDW_RADII (in module MolecularDiffusion.modules.models.diffsmol.shape_utils) optimal_transport (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant attribute) optimize() (in module MolecularDiffusion.cli.analyze) optimize_ase_db() (in module MolecularDiffusion.runmodes.analyze.xtb_optimization) optimize_molecule() (in module MolecularDiffusion.runmodes.analyze.xtb_optimization) optimize_shape_alignment() (in module MolecularDiffusion.utils.geom_metrics) optimizer (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) optimizer_choice (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) optimizer_config (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) OptimSchedulerFactory (class in MolecularDiffusion.runmodes.train.trainer) optional_import_error() (in module MolecularDiffusion.optional) OptionalDependencyError original_smiles (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularNovelty attribute) ot_interpolate() (in module MolecularDiffusion.modules.models.equifm.paths) ot_ode (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask attribute) otf_graph (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) ouput_name (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2SymmetricTensorHead attribute) out (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.layers.e3x.modules.SelfAttention attribute) (MolecularDiffusion.modules.models.apo2mol.attn.RetAugmentationLinearAttention attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) out_atom_type_linear (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) out_channels (MolecularDiffusion.modules.layers.equiformer_v2.activation.ScaledSwiGLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2.activation.SwiGLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.ScaledSwiGLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.SwiGLU attribute) (MolecularDiffusion.modules.models.etflow.torchmd.GatedEquivariantBlock attribute) (MolecularDiffusion.modules.models.jodo.layers.EdgeGateTransLayer attribute) (MolecularDiffusion.modules.models.jodo.layers.Trans_Layer attribute) (MolecularDiffusion.modules.models.jodo.layers.TransMixLayer attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.GatedEquivariantBlock attribute) (MolecularDiffusion.modules.models.pmdm.encoders.MLPEdgeEncoder property) (MolecularDiffusion.modules.models.pmdm.encoders.SchNetProteinEncoder property) out_channels_half (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_m_Conv attribute) out_coord_linear (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) out_dim() (MolecularDiffusion.modules.layers.tabasco.positional_encoder.PositionalEncoding method) (MolecularDiffusion.modules.layers.tabasco.positional_encoder.SinusoidEncoding method) (MolecularDiffusion.modules.layers.tabasco.positional_encoder.TimeFourierEncoding method) out_dim_charges (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer attribute) out_dim_E (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer attribute) out_dim_X (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer attribute) out_dim_y (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer attribute) out_fc (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseX2HAttLayer attribute) out_features (MolecularDiffusion.modules.layers.e3x.modules.Dense attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_LinearV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_LinearV2 attribute) (MolecularDiffusion.modules.layers.esen.nn.so3_layers.SO3_Linear attribute) (MolecularDiffusion.modules.models.difflinker.noise.PositiveLinear attribute) (MolecularDiffusion.modules.models.ditmc.layers.E3MLP attribute) (MolecularDiffusion.modules.models.ditmc.layers.MLP attribute) (MolecularDiffusion.modules.models.en_diffusion.PositiveLinear attribute) (MolecularDiffusion.modules.models.ligandiff.noise.PositiveLinear attribute) out_gate (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer attribute) out_head (MolecularDiffusion.modules.models.transformer_dynamics.TransformerDynamics attribute) out_mask (MolecularDiffusion.modules.layers.esen.esen_block.Edgewise attribute) (MolecularDiffusion.modules.layers.esen.nn.embedding.EdgeDegreeEmbedding attribute) out_max_degree (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) out_net (MolecularDiffusion.modules.models.goflow.outputs.Atomwise3DOut attribute) out_node_nf (MolecularDiffusion.modules.models.difflinker.size_gnn.SizeGNN attribute) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_encoder_QM9 attribute) out_norm (MolecularDiffusion.modules.models.diffspectra.specformer.SpecFormer attribute) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) out_num_parity (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) out_pos (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) out_proj (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.NodeAttention attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.NodeAttention attribute) out_projection (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) outer_product() (in module MolecularDiffusion.modules.models.apo2mol.common) (in module MolecularDiffusion.modules.models.diffsmol.common) (in module MolecularDiffusion.modules.models.kgdiff.common) output (MolecularDiffusion.modules.models.ditmc.dit.GenerativeModel property) (MolecularDiffusion.modules.models.ditmc.readout.EquivariantReadout attribute) (MolecularDiffusion.modules.models.ditmc.readout.SimpleReadout attribute) output_channels (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) output_dim (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer attribute) (MolecularDiffusion.modules.models.goflow.gotennet.TimestepEmbedding attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseX2HAttLayer attribute) output_dims (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) output_dir (MolecularDiffusion.core.lightning_callbacks.generative_eval_callback.GenerativeEvalCallback attribute) output_layer (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTask attribute) output_model (MolecularDiffusion.modules.models.etflow.torchmd.TorchMDDynamics attribute) output_n_hidden (MolecularDiffusion.modules.tasks.diffusion_goflow.ModelTaskFactory attribute) output_name (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2SymmetricTensorHead attribute) output_network (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantVectorOutput attribute) output_norm (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer attribute) output_path (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecScaffoldGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolGenerator attribute) (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.pocket_generator.PocketGenerator attribute) (MolecularDiffusion.runmodes.generate.tasks_conformer.ConformerFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize.GCDMOptimizeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) OutputLayer (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet attribute) overfit (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) P p (MolecularDiffusion.callbacks.train_helper.SP_regularizer attribute) (MolecularDiffusion.modules.layers.esen.nn.radial.PolynomialEnvelope attribute) P_ALPHAS (in module MolecularDiffusion.utils.geom_metrics) (in module MolecularDiffusion.utils.shepherd_score.score.constants) p_drop_both (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) p_drop_c13nmr (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) p_drop_h1nmr (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) p_posterior() (MolecularDiffusion.modules.models.reactot.en_sb.EnSB method) P_TYPES (in module MolecularDiffusion.utils.geom_metrics) (in module MolecularDiffusion.utils.shepherd_score.score.constants) (in module MolecularDiffusion.utils.shepherd_utils) P_TYPES_LWRCASE (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring) (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring_np) pad() (MolecularDiffusion.modules.models.syncogen.api.atomics.pharmacophores.ShepherdPharmacophores method) pad_data() (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction method) pad_sigma() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) padded_to_variadic() (in module MolecularDiffusion.modules.layers.functional) PaiNNDynamics (class in MolecularDiffusion.modules.models.painn_dynamics) pair_attn (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) pair_attn_dropout (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) pair_dropout (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) pair_ffn (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) pair_ffn_dropout (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) pair_ln (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer attribute) pair_scale (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) pair_update (MolecularDiffusion.modules.models.nextmol.dgt.DGTDiffusion attribute) pairwise_distances() (in module MolecularDiffusion.modules.models.painn_backbone) PairwiseDistanceLoss (class in MolecularDiffusion.modules.models.syncogen.diffusion.loss.pairwise_distance) PairwiseDistObjective (class in MolecularDiffusion.modules.tasks.ssl3d) parameters (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) parametrization (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM attribute) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion attribute) params (MolecularDiffusion.modules.models.pharmacophore_dynamics.PharmacophoreModelWrapper attribute) (MolecularDiffusion.modules.models.shepherd_arch.model.Model attribute) parity_output (MolecularDiffusion.modules.models.ditmc.dit.SO3DiTLayer attribute) parity_switch (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask attribute) parse_mol2_file() (in module MolecularDiffusion.modules.models.syncogen.utils.file_readers) parse_pocket_pdb() (in module MolecularDiffusion.data.component.pmdm_data) parse_row_index() (in module MolecularDiffusion.modules.models.chefnmr.sidecar) parse_update_info() (in module MolecularDiffusion.modules.models.goflow.ops) parser (in module MolecularDiffusion.runmodes.analyze.xtb_optimization) partial_atom_mask (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) patch_len (MolecularDiffusion.modules.models.diffspectra.specformer.SpecFormer attribute) (MolecularDiffusion.modules.models.diffspectra.specformer.TSTiEncoder attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) patch_nums (MolecularDiffusion.modules.models.diffspectra.specformer.SpecFormer attribute) (MolecularDiffusion.modules.models.diffspectra.specformer.TSTiEncoder attribute) patch_size (MolecularDiffusion.modules.models.chefnmr.embedders.SpectraTokenizerPatch1D attribute) path (in module MolecularDiffusion.utils.sascore) path_cmd() (in module MolecularDiffusion.cli.zoo) PathPlanning (class in MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.p2) pattern_of_smarts() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmacophore) pbc (MolecularDiffusion.modules.layers.atomic_data.AtomicData attribute) pca_align() (in module MolecularDiffusion.utils.geom_metrics) Pcharges (MolecularDiffusion.modules.models.midi.noise_model.DiscreteUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.MarginalUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) Pe (MolecularDiffusion.modules.models.midi.noise_model.DiscreteUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.MarginalUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) pe (MolecularDiffusion.modules.models.syncogen.models.layers.SimplePositionalEmbedding attribute) pe_m (MolecularDiffusion.modules.models.syncogen.models.layers.EtoC attribute) pearsonr() (in module MolecularDiffusion.modules.tasks.metrics) penalized_logP() (in module MolecularDiffusion.modules.tasks.metrics) permute_atoms() (in module MolecularDiffusion.modules.models.tabasco.data.transforms) persistent_workers (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule attribute) pharm_cond_proj (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator attribute) pharm_coords (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates attribute) pharm_indices_to_onehot() (in module MolecularDiffusion.modules.models.syncogen.api.atomics.pharmacophores) pharm_padding_mask (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates attribute) pharm_subset (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask attribute) pharmacophore_collate_fn() (in module MolecularDiffusion.data.component.pharmacophore) pharmacophore_path (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataset attribute) pharmacophore_subset (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator attribute) PharmacophoreConditionGenerator (class in MolecularDiffusion.runmodes.generate.tasks_generate) PharmacophoreDataModule (class in MolecularDiffusion.data.component.pharmacophore) PharmacophoreDataset (class in MolecularDiffusion.data.component.pharmacophore) PharmacophoreEnVariationalDiff (class in MolecularDiffusion.modules.models.pharmacophore_dynamics) PharmacophoreGenerative (class in MolecularDiffusion.modules.tasks.pharmacophore) PharmacophoreModelWrapper (class in MolecularDiffusion.modules.models.pharmacophore_dynamics) pharmacophores (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates property) phi() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) phi_distillation() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) phi_message (MolecularDiffusion.modules.models.loqi.fn_model.XEGNNK attribute) phi_pyg() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) phi_x (MolecularDiffusion.modules.models.loqi.fn_model.XEGNNK attribute) phi_x_cross (MolecularDiffusion.modules.models.loqi.fn_model.XEGNNK attribute) phik_w_ra (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) pin_memory (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule attribute) (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) pkl_files (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) pkl_path (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffTS1xDataset attribute) place_fragment() (in module MolecularDiffusion.utils.substituent_builder) PlaceHolder (class in MolecularDiffusion.modules.models.midi.placeholder) plot() (MolecularDiffusion.utils.geom_analyzer.Histogram_cont method) (MolecularDiffusion.utils.geom_analyzer.Histogram_discrete method) plot_both() (MolecularDiffusion.utils.geom_analyzer.Histogram_cont method) plot_correlation_with_histograms() (in module MolecularDiffusion.utils.plot_function) plot_correlation_with_kde() (in module MolecularDiffusion.utils.plot_function) plot_cosine_scheduler() (in module MolecularDiffusion.modules.models.noisemodel) plot_embedding() (in module MolecularDiffusion.utils.plot_function) plot_histogram_distribution() (in module MolecularDiffusion.utils.plot_function) plot_kde_distribution() (in module MolecularDiffusion.utils.plot_function) plot_kde_distribution_multiple() (in module MolecularDiffusion.utils.plot_function) PMDM_ATOM_VOCAB (in module MolecularDiffusion.data.component.pmdm_data) pmdm_collate() (in module MolecularDiffusion.data.component.pmdm_data) PMDM_ELEMENTS (in module MolecularDiffusion.data.component.pmdm_data) PMDMConstrainedGenerator (class in MolecularDiffusion.modules.tasks.diffusion_pmdm) PMDMDataModule (class in MolecularDiffusion.data.component.pmdm_data) PMDMDataset (class in MolecularDiffusion.data.component.pmdm_data) PMDMDiffusionTask (class in MolecularDiffusion.modules.tasks.diffusion_pmdm) PMDMEpsNet (class in MolecularDiffusion.modules.models.pmdm.epsnet) PMDMPocketGenerator (class in MolecularDiffusion.modules.tasks.diffusion_pmdm) pocket_atom_type_embed (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet attribute) POCKET_ATOM_TYPES (in module MolecularDiffusion.modules.models.apo2mol.pminet) (in module MolecularDiffusion.modules.models.ipdiff.bapnet) pocket_conditioned (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) pocket_db (MolecularDiffusion.modules.tasks.diffusion_diffint.DiffIntPocketGenerator attribute) (MolecularDiffusion.modules.tasks.pocket_generator.PocketGenerator attribute) pocket_file (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMConstrainedGenerator attribute) pocket_index (MolecularDiffusion.modules.tasks.pocket_generator.PocketGenerator attribute) pocket_pdb (MolecularDiffusion.modules.tasks.diffusion_diffint.DiffIntPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaPocketGenerator attribute) pocket_residue_type_embed (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet attribute) pocket_type_fusion (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet attribute) PocketGenerator (class in MolecularDiffusion.modules.tasks.pocket_generator) PocketGraph (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet attribute) PocketSizePrior (class in MolecularDiffusion.modules.tasks.diffusion_kgdiff) POINT_CLOUD_SAMPLES (in module MolecularDiffusion.modules.models.diffsmol.shape_utils) pointcloud_collate() (in module MolecularDiffusion.data.dataloader) pointcloud_collate_v0() (in module MolecularDiffusion.data.dataloader) pointcloud_dataset (class in MolecularDiffusion.data.dataset) pointcloud_dataset_pyG (class in MolecularDiffusion.data.dataset) PointCloud_Mol (class in MolecularDiffusion.data.component.pointcloud) PointCloudAE (class in MolecularDiffusion.modules.models.diffsmol.shape_ae) PointCloudDataset (class in MolecularDiffusion.data.component.dataset) PointCloudToDGLAdapter (class in MolecularDiffusion.modules.tasks.diffusion_flowmol) PointCloudToDiffLinkerBatch (class in MolecularDiffusion.modules.tasks.diffusion_difflinker) PointCloudToLigandDiffBatch (class in MolecularDiffusion.modules.tasks.diffusion_ligandiff) PointCloudToLigandDiffMultiBatch (class in MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi) PointCloudToTensorDictAdapter (class in MolecularDiffusion.modules.tasks.diffusion_tabasco) policy_gradient_objective() (in module MolecularDiffusion.modules.layers.functional) polynomial() (MolecularDiffusion.callbacks.train_helper.SP_regularizer method) polynomial_schedule() (in module MolecularDiffusion.modules.models.difflinker.noise) (in module MolecularDiffusion.modules.models.diffpharma.conditional_ddpm) (in module MolecularDiffusion.modules.models.diffsbdd.en_diffusion) (in module MolecularDiffusion.modules.models.en_diffusion) (in module MolecularDiffusion.modules.models.ligandiff.noise) (in module MolecularDiffusion.modules.models.noisemodel) (in module MolecularDiffusion.modules.models.oareactdiff.schedule) PolynomialEnvelope (class in MolecularDiffusion.modules.layers.esen.nn.radial) pool (MolecularDiffusion.modules.models.diffsmol.shape_ae.VNDGCNNEncoder attribute) (MolecularDiffusion.modules.models.diffsmol.shape_ae.VNResnetEncoder attribute) pool1 (MolecularDiffusion.modules.models.apo2mol.uni_transformer.SAGPoolNet attribute) pool_nodes() (in module MolecularDiffusion.runmodes.analyze.ssl3d_embed) pooling (MolecularDiffusion.modules.models.chefnmr.embedders.NMRSpectraEmbedder attribute) (MolecularDiffusion.runmodes.analyze.featurize.SOAPFeaturizer attribute) (MolecularDiffusion.runmodes.analyze.featurize.SSL3DFeaturizer attribute) pos (MolecularDiffusion.data.component.reaction_data.ReactionSide attribute), [1] (MolecularDiffusion.modules.layers.atomic_data.AtomicData attribute) (MolecularDiffusion.modules.models.midi.placeholder.Dims attribute) (MolecularDiffusion.modules.models.midi.placeholder.PlaceHolder attribute) pos_att_mul (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) pos_dim (MolecularDiffusion.modules.models.oareactdiff.dynamics.BaseDynamics attribute) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.oareactdiff.normalizer.Normalizer attribute) (MolecularDiffusion.modules.models.pmdm.encoders.EGNNSparseLayer attribute) (MolecularDiffusion.modules.models.pmdm.encoders.EGNNSparseNetwork attribute) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) pos_emb (MolecularDiffusion.modules.models.syncogen.models.semla.SemlaGenerator attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator attribute) pos_embed (MolecularDiffusion.modules.models.chefnmr.score_models.DiffusionModuleTransformer attribute) (MolecularDiffusion.modules.models.transformer_dynamics.TransformerDynamics attribute) pos_embedder (MolecularDiffusion.modules.models.ldm.encoders.transformer.TransformerEncoder attribute) pos_enc_mode (MolecularDiffusion.modules.models.chefnmr.embedders.NMRSpectraEmbedder attribute) pos_encode() (MolecularDiffusion.modules.models.chefnmr.embedders.NMRSpectraEmbedder method) pos_expansion (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) pos_grad (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) pos_grad_weight (MolecularDiffusion.modules.tasks.diffusion_kgdiff.KGDiffPocketGenerator attribute) pos_head (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.decoders.transformer.TransformerDecoder attribute) pos_mlp (MolecularDiffusion.modules.models.ditmc.embedding.DiTNodeEmbed attribute) pos_noise_std (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_apo2mol.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.IPDiffDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.ModelTaskFactory attribute) pos_only (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) pos_require_grad (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) pos_std (MolecularDiffusion.modules.tasks.diffusion_nextmol.Graph3DBatchToNextMolAdapter attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) pos_update (MolecularDiffusion.modules.layers.gfmdiff.blocks.InterBlock attribute) pos_x_mul (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) posebuster_timeout (MolecularDiffusion.core.lightning_callbacks.generative_eval_callback.GenerativeEvalCallback attribute) PoseBusters (in module MolecularDiffusion.utils.geom_metrics) posebusters (MolecularDiffusion.modules.models.tabasco.callbacks.posebusters.PoseBustersCallback attribute) PoseBustersCallback (class in MolecularDiffusion.modules.models.tabasco.callbacks.posebusters) PoseBustersValidity (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) PoseCheckStrainEnergy (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) posenc_dim (MolecularDiffusion.modules.layers.tabasco.positional_encoder.SinusoidEncoding attribute) (MolecularDiffusion.modules.layers.tabasco.positional_encoder.TimeFourierEncoding attribute) positional_embedding_bool (MolecularDiffusion.modules.models.ditmc.embedding.DiTNodeEmbed attribute) positional_encoding() (in module MolecularDiffusion.modules.models.diffspectra.specformer_layers) (in module MolecularDiffusion.modules.models.shepherd_arch.utils) positional_encoding_bool (MolecularDiffusion.modules.models.ditmc.embedding.DiTNodeEmbed attribute) PositionalEncoding (class in MolecularDiffusion.modules.layers.tabasco.positional_encoder) PositionalEncoding() (in module MolecularDiffusion.modules.models.diffspectra.specformer_layers) positions (MolecularDiffusion.modules.models.ditmc.graphs.LatentGraph attribute) (MolecularDiffusion.utils.smilify.Molecule attribute) PositionsMLP (class in MolecularDiffusion.modules.layers.conv) (class in MolecularDiffusion.modules.models.midi.layers) (class in MolecularDiffusion.modules.models.syncogen.models.layers) PositiveLinear (class in MolecularDiffusion.modules.models.difflinker.noise) (class in MolecularDiffusion.modules.models.en_diffusion) (class in MolecularDiffusion.modules.models.ligandiff.noise) post_quant_conv (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) posterior_logvar (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) posterior_mean_c0_coef (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) posterior_mean_ct_coef (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) posterior_var (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) PosUpdate (class in MolecularDiffusion.modules.layers.gfmdiff.blocks) power (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) pre_compute_coefficient_idx() (MolecularDiffusion.modules.layers.esen.common.so3.CoefficientMapping method) pre_compute_rotate_inv_rescale() (MolecularDiffusion.modules.layers.esen.common.so3.CoefficientMapping method) pre_norm (MolecularDiffusion.modules.models.diffspectra.specformer.TSTEncoderLayer attribute) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPEmbedding attribute) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPInteractions attribute) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPLayerConfig attribute) pre_reduce() (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantVectorOutput method) pre_softmax (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) precision (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) precompute_distances() (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField method) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField method) pred_arrays_list (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator attribute) pred_bond_type (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) pred_data (MolecularDiffusion.modules.models.diffspectra.dmt.DMT attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.Cond_DGT_concat attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.DGT_concat attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) pred_exp_from_all (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) PredefinedNoiseSchedule (class in MolecularDiffusion.modules.models.difflinker.noise) (class in MolecularDiffusion.modules.models.diffpharma.conditional_ddpm) (class in MolecularDiffusion.modules.models.diffsbdd.en_diffusion) (class in MolecularDiffusion.modules.models.en_diffusion) (class in MolecularDiffusion.modules.models.ligandiff.noise) (class in MolecularDiffusion.modules.models.oareactdiff.schedule) predict() (in module MolecularDiffusion.cli.eval_predict) (in module MolecularDiffusion.cli.main) (MolecularDiffusion.modules.models.difflinker.size_gnn.LinkerSizePredictor method) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPredictionPointCloud method) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative method) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction method) (MolecularDiffusion.modules.tasks.ssl3d.SSL3D method) (MolecularDiffusion.modules.tasks.task.Task method) (MolecularDiffusion.molcraftdiff.MolCraftDiff method) predict_and_target() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask method) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask method) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask method) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTask method) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDTask method) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask method) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTask method) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTask method) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask method) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask method) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask method) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTask method) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.IPDiffDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.KGDiffDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask method) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask method) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask method) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask method) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask method) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask method) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask method) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask method) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask method) (MolecularDiffusion.modules.tasks.ssl3d.SSL3D method) (MolecularDiffusion.modules.tasks.task.Task method) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETask method) predict_denoised_atom_coords() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) predict_dense() (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPredictionPointCloud method) predict_main() (in module MolecularDiffusion.cli.predict) predict_velocity() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) prediction_activation (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) prediction_level (MolecularDiffusion.modules.tasks.regression.MLPRegressor_padded attribute) (MolecularDiffusion.modules.tasks.regression.MLPRegressor_pernode attribute) prediction_mlp_type (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) prediction_type (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant attribute) prefactor (MolecularDiffusion.modules.models.painn_backbone.BesselRBFLayer attribute) prefetch_factor (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule attribute) PreNorm (class in MolecularDiffusion.modules.models.chefnmr.embedders) prepare() (in module MolecularDiffusion.cli.data) prepare_coefficient_idx() (MolecularDiffusion.modules.layers.esen.common.so3.CoefficientMapping method) prepare_context() (in module MolecularDiffusion.utils.diffusion_utils) prepare_context_pyG() (in module MolecularDiffusion.utils.diffusion_utils) prepare_mol_for_conformer_eval() (in module MolecularDiffusion.runmodes.analyze.conformer_metrics) prepare_receptor() (in module MolecularDiffusion.runmodes.analyze.docking) preprocess() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask method) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask method) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask method) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask method) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative method) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction method) (MolecularDiffusion.modules.tasks.ssl3d.SSL3D method) (MolecularDiffusion.modules.tasks.task.Task method) preprocess_ref_structure() (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory method) PrettyPrinter (class in MolecularDiffusion.utils.pretty) print() (in module MolecularDiffusion.utils.pretty) prior (MolecularDiffusion.modules.models.ditmc.flow_matching.FlowMatching attribute) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTaskFactory attribute) prior() (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousDiffusionInterpolant method) (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant method) prior_func() (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant method) prior_noise_scale (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) prior_std (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) prior_type (MolecularDiffusion.modules.models.loqi.interpolant.Interpolant attribute) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask attribute) PriorGraph (class in MolecularDiffusion.modules.models.ditmc.graphs) PRIORS (in module MolecularDiffusion.modules.models.ditmc.priors) prob (MolecularDiffusion.modules.models.difflinker.linker_size.DistributionNodes attribute) (MolecularDiffusion.modules.models.diffpharma.distributions.DistributionNodes attribute) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.DistributionNodes attribute) (MolecularDiffusion.modules.models.en_diffusion.DistributionNodes attribute) PROBE_RADIUS (in module MolecularDiffusion.runmodes.analyze.similarity3d) probe_radius (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) probs (MolecularDiffusion.modules.models.tabasco.flow.utils.HistogramTimeDistribution attribute) process (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTask attribute) process_ligand_and_pocket() (in module MolecularDiffusion.data.component.diffpharma_prep) process_vector() (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCP method) process_vector_frames() (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCP method) process_vector_with_frames() (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCP2 method) process_vector_without_frames() (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCP2 method) product (MolecularDiffusion.data.component.reaction_data.Reaction attribute), [1] progress_bar_metrics (MolecularDiffusion.core.engine.Engine attribute) proj (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.models.chefnmr.embedders.AttnPoolToken attribute) (MolecularDiffusion.modules.models.chefnmr.embedders.SpectraTokenizerPatch1D attribute) (MolecularDiffusion.modules.models.chefnmr.layers.Attention attribute) proj_drop (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.TransBlockV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.TransBlockV2 attribute) (MolecularDiffusion.modules.models.chefnmr.layers.Attention attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.FeedForwardNetwork_equiformer attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) project_layer (MolecularDiffusion.modules.models.painn_backbone.EquivNet attribute) project_wandb (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.runmodes.train.logger.Logger attribute) promote_to_e3x() (in module MolecularDiffusion.modules.layers.e3x.features) prompt_ligand_attn (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) prompt_protein_mlp (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) prop_dist_model (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.IPDiffDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.KGDiffDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.TabascoEGNNDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.TabascoEquiformerDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.TabascoGVPDiffusionTask attribute) PROPERTY_GROUPS (in module MolecularDiffusion.runmodes.analyze.xtb_electronic) property_guidance() (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory method) property_names (MolecularDiffusion.modules.models.en_diffusion.DistributionProperty attribute) (MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize.GCDMOptimizeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) property_norms (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.TabascoEGNNDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.TabascoEquiformerDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.TabascoGVPDiffusionTask attribute) property_prediction() (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory method) ProperyPrediction (class in MolecularDiffusion.modules.tasks.regression) prot_sag_layer (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) protein_atom_emb (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) PROTEIN_ELEMENTS (in module MolecularDiffusion.data.component.kgdiff_data) protein_encoder (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) PROTEIN_FEATURE_DIM (in module MolecularDiffusion.data.component.kgdiff_data) protein_features() (in module MolecularDiffusion.data.component.kgdiff_data) protein_update_steps (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) prune_edges (MolecularDiffusion.modules.models.loqi.fn_model.XEGNNK attribute) PT (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmacophore) (in module MolecularDiffusion.utils.shepherd_utils) pt_path (MolecularDiffusion.data.component.diffdec_data.DiffDecDataset attribute) purity_sampling() (in module MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_utils) pv_joint_guide() (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D method) Px (MolecularDiffusion.modules.models.midi.noise_model.DiscreteUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.MarginalUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) Py (MolecularDiffusion.modules.models.midi.noise_model.DiscreteUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.MarginalUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) pybel (in module MolecularDiffusion.utils.geom_metrics) Q q (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) q_norm (MolecularDiffusion.modules.models.chefnmr.layers.Attention attribute) q_pos_posterior() (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.ipdiff.score_model.IPDiffScorePosNet3D method) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D method) q_proj (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer attribute) q_sample() (MolecularDiffusion.modules.models.reactot.en_sb.EnSB method) q_v_posterior() (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D method) q_v_pred() (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D method) q_v_pred_one_timestep() (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D method) q_v_sample() (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D method) q_w (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) QED() (in module MolecularDiffusion.modules.tasks.metrics) qk_norm (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) qkv (MolecularDiffusion.modules.models.chefnmr.layers.Attention attribute) qkv_features (MolecularDiffusion.modules.layers.e3x.modules.SelfAttention attribute) qkv_proj (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) QM9_RAW_ARTEFACTS (in module MolecularDiffusion.runmodes.data.graph3d_import) qm9_targets() (in module MolecularDiffusion.runmodes.data.graph3d_import) qm9_types (in module MolecularDiffusion.modules.models.nextmol.featurize) quant_conv (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) quaternion_from_axis_angle() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca) quaternion_from_axis_angle_np() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca_np) quaternion_mult() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca) quaternion_mult_np() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca_np) quaternion_product() (in module MolecularDiffusion.modules.models.apo2mol.residue_ops) quaternion_to_matrix() (in module MolecularDiffusion.modules.models.chefnmr.utils) quaternion_to_rotation_matrix() (in module MolecularDiffusion.modules.models.apo2mol.residue_ops) quaternions_for_principal_component_alignment() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca) quaternions_for_principal_component_alignment_np() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca_np) quaternions_to_rotation_matrix() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.se3) quaternions_to_rotation_matrix_np() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.se3_np) query (MolecularDiffusion.modules.layers.e3x.modules.SelfAttention attribute) Queue (class in MolecularDiffusion.callbacks.train_helper) R r2() (in module MolecularDiffusion.modules.tasks.metrics) r2tensor_MLP (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2Block attribute) r_feat_dim (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseX2HAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseX2HAttLayer attribute) r_max (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.painn_backbone.BesselRBFLayer attribute) rad_func (MolecularDiffusion.modules.layers.equiformer_v2.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.esen.nn.embedding.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Linear attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EdgeDegreeEmbedding attribute) radial_basis (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet attribute) radial_basis_bool (MolecularDiffusion.modules.models.ditmc.embedding.DiTEdgeEmbed attribute) radial_emb (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) radial_fn (MolecularDiffusion.modules.models.ditmc.embedding.RadialSphericalEdgeEmbedding attribute) radial_lin (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) RadialFunction (class in MolecularDiffusion.modules.layers.equiformer_v2.radial_function) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.radial_function) RadialMLP (class in MolecularDiffusion.modules.layers.esen.nn.radial) RadialSphericalEdgeEmbedding (class in MolecularDiffusion.modules.models.ditmc.embedding) radius (MolecularDiffusion.runmodes.train.data.DataModule attribute) radius_graph_pbc() (in module MolecularDiffusion.modules.layers.graph_module) raman (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraRecord attribute) random() (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates class method) random_permute (MolecularDiffusion.modules.layers.tabasco.positional_encoder.SinusoidEncoding attribute) (MolecularDiffusion.modules.layers.tabasco.positional_encoder.TimeFourierEncoding attribute) random_quaternions() (in module MolecularDiffusion.modules.models.chefnmr.utils) random_rotate() (in module MolecularDiffusion.modules.models.syncogen.api.ops.coordinates_ops) (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates method) random_rotation() (in module MolecularDiffusion.modules.layers.e3x.so3) (in module MolecularDiffusion.modules.models.tabasco.data.transforms) (in module MolecularDiffusion.utils.geom_utils) random_rotation_matrix() (in module MolecularDiffusion.utils.geom_utils) random_rotations() (in module MolecularDiffusion.modules.models.chefnmr.utils) random_translate() (in module MolecularDiffusion.modules.models.syncogen.api.ops.coordinates_ops) (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates method) RandomFaultTolerantSampler (class in MolecularDiffusion.modules.models.syncogen.data.dataloader) randomly_rotate() (in module MolecularDiffusion.modules.models.chefnmr.utils) range (MolecularDiffusion.utils.geom_analyzer.Histogram_cont attribute) rank (MolecularDiffusion.utils.io.RankState attribute) Rank2Block (class in MolecularDiffusion.modules.layers.esen.nn.rank2) Rank2DecompositionEdgeBlock (class in MolecularDiffusion.modules.layers.esen.nn.rank2) Rank2SymmetricTensorHead (class in MolecularDiffusion.modules.layers.esen.nn.rank2) rank_prefixed_message() (in module MolecularDiffusion.utils.io) rank_zero_only (MolecularDiffusion.modules.models.tabasco.utils.pylogger.RankedLogger attribute) (MolecularDiffusion.utils.io.RankedLogger attribute) RankedLogger (class in MolecularDiffusion.modules.models.tabasco.utils.pylogger) (class in MolecularDiffusion.utils.io) RankState (class in MolecularDiffusion.utils.io) rate_noise() (MolecularDiffusion.modules.models.syncogen.diffusion.noise.base.NoiseBase method) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.brownian.BrownianBridgeNoise method) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.cosine.CosineNoise method) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.cosine.CosineSqrNoise method) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.geometric.GeometricNoise method) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.linear.LinearNoise method) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.loglinear.LogLinearNoise method) RatioSampleNoiseSchedule (class in MolecularDiffusion.modules.models.tabasco.sample.noise_schedule) raw (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffTS1xDataset attribute) RBF (class in MolecularDiffusion.modules.layers.gfmdiff.blocks) rbf (MolecularDiffusion.modules.layers.esen.nn.radial.EnvelopedBesselBasis attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.DistEncoder attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.RBF_Emb attribute) rbf_dim (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.self_conditioning.SelfConditioningResidualLayer attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone attribute) rbf_dmax (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.self_conditioning.SelfConditioningResidualLayer attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone attribute) RBF_Emb (class in MolecularDiffusion.modules.layers.gfmdiff.blocks) rbf_layer (MolecularDiffusion.modules.models.painn_backbone.EquivNet attribute) rbf_param (MolecularDiffusion.modules.layers.gfmdiff.blocks.DistEncoder attribute) rbf_proj (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiMessage attribute) rbf_trainable (MolecularDiffusion.modules.models.oareactdiff.leftnet.RBFEmb attribute) rbf_type (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) RBFEmb (class in MolecularDiffusion.modules.models.oareactdiff.leftnet) rbound_lower (MolecularDiffusion.modules.models.oareactdiff.leftnet.RBFEmb attribute) rbound_upper (MolecularDiffusion.modules.models.oareactdiff.leftnet.RBFEmb attribute) rdEHTTools (in module MolecularDiffusion.utils.xyz2mol.converter) rdkit_bond_types() (in module MolecularDiffusion.data.component.graph3d_dataset) rdkit_mol (MolecularDiffusion.utils.smilify.Molecule attribute) rdkit_rmsd() (in module MolecularDiffusion.runmodes.analyze.druglike) RDKitMoleculeAssembly (class in MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly) RDLogger (in module MolecularDiffusion.runmodes.analyze.compute_metrics) reactant (MolecularDiffusion.data.component.reaction_data.Reaction attribute), [1] Reaction (class in MolecularDiffusion.data.component.reaction_data) (class in MolecularDiffusion.modules.models.syncogen.api.graph.reaction) REACTIONS (in module MolecularDiffusion.modules.models.syncogen.constants.constants) reactions (MolecularDiffusion.data.component.goflow_data.GoFlowRDB7Dataset attribute) (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) ReactionSide (class in MolecularDiffusion.data.component.reaction_data) ReactionSource (class in MolecularDiffusion.modules.tasks.ts_generator) ReactOTTask (class in MolecularDiffusion.modules.tasks.diffusion_reactot) ReactOTTSGenerator (class in MolecularDiffusion.modules.tasks.diffusion_reactot) read_fragment_scores() (in module MolecularDiffusion.runmodes.data.preparation) read_unknown_spectra() (in module MolecularDiffusion.modules.models.chefnmr.unknown) read_xyz() (in module MolecularDiffusion.modules.models.diffsmol.shape_utils) (in module MolecularDiffusion.runmodes.data.augmentation) read_xyz_file() (in module MolecularDiffusion.utils.geom_utils) (in module MolecularDiffusion.utils.xyz2mol.converter) read_xyz_ob() (in module MolecularDiffusion.utils.smilify) readFragmentScores() (in module MolecularDiffusion.utils.sascore) readout (MolecularDiffusion.modules.models.ditmc.dit.GenerativeModel attribute) (MolecularDiffusion.modules.models.painn_dynamics.PaiNNDynamics attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) readout_f() (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction method) readout_method (MolecularDiffusion.modules.tasks.regression.MLPRegressor_padded attribute) (MolecularDiffusion.modules.tasks.regression.MLPRegressor_pernode attribute) reason (MolecularDiffusion.runmodes.generate.sweep.RunResult attribute) rebuild_ema_params (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) receivers (MolecularDiffusion.modules.models.ditmc.graphs.CondGraph attribute) (MolecularDiffusion.modules.models.ditmc.graphs.LatentGraph attribute) (MolecularDiffusion.modules.models.ditmc.graphs.PriorGraph attribute) recenter_x1 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) recenter_x2 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) recenter_x3 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) recenter_x4 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) recipe_cmd() (in module MolecularDiffusion.cli.zoo) reciprocal_bernstein() (in module MolecularDiffusion.modules.layers.e3x.radial) reciprocal_mapping() (in module MolecularDiffusion.modules.layers.e3x.radial) reconstruct() (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE method) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask method) records (MolecularDiffusion.core.meter.Meter attribute) recover() (MolecularDiffusion.modules.models.gcdm.gcp_utils.ScalarVector static method) recursive_module_to_device() (in module MolecularDiffusion.utils.torch) reduce (MolecularDiffusion.modules.models.esen.MLP_Energy_Head attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNorm attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNormV2 attribute) reduce() (in module MolecularDiffusion.utils.comm) reduce_function (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPMessagePassing attribute) reduce_mean (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) reduce_node_mean (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) reencode_selfies() (in module MolecularDiffusion.modules.models.nextmol.mollama) ref_sdf (MolecularDiffusion.modules.tasks.diffusion_diffint.DiffIntPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaPocketGenerator attribute) reference_feature_stats (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) reference_freeze_mode (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) reference_indices (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) reference_ligand (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask attribute) reference_mol (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) reference_mol() (in module MolecularDiffusion.runmodes.analyze.similarity3d) reference_scaffold (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) reference_shape() (in module MolecularDiffusion.utils.shape_measure) refine_net (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) refine_net_type (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) reflect() (in module MolecularDiffusion.modules.layers.e3x.features) reflect_equiv (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiMessage attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiUpdate attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) reflection_equiv (MolecularDiffusion.modules.models.diffpharma.egnn.EGNN attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EquivariantUpdate attribute) register() (in module MolecularDiffusion.assets) (MolecularDiffusion.core.core.Registry class method) Registry (class in MolecularDiffusion.core.core) registry (in module MolecularDiffusion.modules.models.shepherd_arch.ocp_compat) regress_forces (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.esen.MLP_EFS_Head attribute) regress_stress (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.esen.MLP_EFS_Head attribute) regress_to_center (MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance.UFFBoundGuidance attribute) regress_x1_bool (MolecularDiffusion.modules.models.ditmc.flow_matching.FlowMatching attribute) regularizer (MolecularDiffusion.callbacks.train_helper.SP_regularizer attribute) rej() (MolecularDiffusion.modules.models.goflow.gotennet.GATA static method) remap_bonds_after_atom_removal() (in module MolecularDiffusion.data.component.graph3d_dataset) remap_values() (in module MolecularDiffusion.modules.models.shepherd_arch.model) remove_h_unit() (in module MolecularDiffusion.runmodes.data.augmentation) remove_mean() (in module MolecularDiffusion.modules.models.jodo.utils) (in module MolecularDiffusion.modules.models.nextmol.dgt) (in module MolecularDiffusion.utils.geom_utils) remove_mean_batch() (in module MolecularDiffusion.modules.models.oareactdiff.graph_tools) (in module MolecularDiffusion.modules.models.oareactdiff.leftnet) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM class method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.ConditionalDDPM class method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion static method) (MolecularDiffusion.modules.models.oareactdiff.dynamics.EGNNDynamics static method) remove_mean_batch_ligand() (in module MolecularDiffusion.modules.models.apo2mol.pminet) remove_mean_pyG() (in module MolecularDiffusion.utils.molgraph_utils) remove_mean_with_mask() (in module MolecularDiffusion.modules.layers.gfmdiff.blocks) (in module MolecularDiffusion.modules.models.difflinker.utils) (in module MolecularDiffusion.modules.models.jodo.utils) (in module MolecularDiffusion.modules.models.midi.placeholder) (in module MolecularDiffusion.utils.geom_utils) remove_mean_with_mask_v2() (in module MolecularDiffusion.utils.geom_utils) remove_noise_COM_x1 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) remove_noise_COM_x2 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) remove_noise_COM_x3 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) remove_noise_COM_x4 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) remove_partial_mean_with_mask() (in module MolecularDiffusion.modules.models.difflinker.utils) (in module MolecularDiffusion.modules.models.ligandiff.utils) remove_pocket_mean() (in module MolecularDiffusion.modules.models.ipdiff.bapnet) rename_cmd() (in module MolecularDiffusion.cli.data) rename_db_attribute() (in module MolecularDiffusion.runmodes.data.ase_ops) reorder_molecule_by_smiles() (in module MolecularDiffusion.modules.models.tabasco.chem.utils) repeat() (MolecularDiffusion.modules.models.gcdm.gcp_utils.ScalarVector method) replace() (MolecularDiffusion.modules.models.ditmc.graphs.LatentGraph method) replace_atoms (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMConstrainedGenerator attribute) representation (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTask attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.ModelTaskFactory attribute) representation_model (MolecularDiffusion.modules.models.etflow.torchmd.TorchMDDynamics attribute) require_modules() (in module MolecularDiffusion.optional) REQUIRED_FILES (in module MolecularDiffusion.modules.models.syncogen.vocab) res_attention (MolecularDiffusion.modules.models.diffspectra.specformer.TSTEncoder attribute) (MolecularDiffusion.modules.models.diffspectra.specformer.TSTEncoderLayer attribute) res_inference (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) res_size (MolecularDiffusion.modules.layers.esen.common.so3.CoefficientMapping attribute) resamplings (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTSGenerator attribute) rescale (MolecularDiffusion.modules.layers.esen.common.so3.SO3_Grid attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.TensorProductRescale attribute) rescale_factor (MolecularDiffusion.modules.layers.equiformer_v2.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.esen.nn.embedding.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EdgeDegreeEmbedding attribute) reset() (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularUniqueness method) reset_parameters() (MolecularDiffusion.modules.layers.conv.SE3Norm method) (MolecularDiffusion.modules.layers.e3x.modules.Dense method) (MolecularDiffusion.modules.models.difflinker.noise.PositiveLinear method) (MolecularDiffusion.modules.models.diffspectra.specformer.Flatten_Head method) (MolecularDiffusion.modules.models.diffspectra.specformer.SpecFormer method) (MolecularDiffusion.modules.models.diffspectra.specformer.TSTEncoder method) (MolecularDiffusion.modules.models.diffspectra.specformer.TSTEncoderLayer method) (MolecularDiffusion.modules.models.diffspectra.specformer.TSTiEncoder method) (MolecularDiffusion.modules.models.en_diffusion.PositiveLinear method) (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention method) (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantVectorOutput method) (MolecularDiffusion.modules.models.etflow.torchmd.ExpNormalSmearing method) (MolecularDiffusion.modules.models.etflow.torchmd.GatedEquivariantBlock method) (MolecularDiffusion.modules.models.etflow.torchmd.NeighborEmbedding method) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics method) (MolecularDiffusion.modules.models.etflow.torchmd.TorchMDDynamics method) (MolecularDiffusion.modules.models.goflow.gotennet.EQFF method) (MolecularDiffusion.modules.models.goflow.gotennet.GATA method) (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet method) (MolecularDiffusion.modules.models.goflow.ops.Dense method) (MolecularDiffusion.modules.models.goflow.ops.EdgeInit method) (MolecularDiffusion.modules.models.goflow.ops.ExpNormalSmearing method) (MolecularDiffusion.modules.models.goflow.ops.MLP method) (MolecularDiffusion.modules.models.goflow.ops.NodeInit method) (MolecularDiffusion.modules.models.goflow.ops.VecLayerNorm method) (MolecularDiffusion.modules.models.goflow.outputs.SNNDense method) (MolecularDiffusion.modules.models.jodo.layers.EdgeGateTransLayer method) (MolecularDiffusion.modules.models.jodo.layers.Trans_Layer method) (MolecularDiffusion.modules.models.jodo.layers.TransMixLayer method) (MolecularDiffusion.modules.models.ligandiff.conv_layer.GVPMessagePassing method) (MolecularDiffusion.modules.models.ligandiff.egnn.DenseLayer method) (MolecularDiffusion.modules.models.ligandiff.gvp.GVP method) (MolecularDiffusion.modules.models.ligandiff.noise.PositiveLinear method) (MolecularDiffusion.modules.models.loqi.fn_model.E3Norm method) (MolecularDiffusion.modules.models.midi.layers.SE3Norm method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiMessage method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiOutput method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiUpdate method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.GatedEquivariantBlock method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.RBFEmb method) (MolecularDiffusion.modules.models.syncogen.models.layers.SE3Norm method) (MolecularDiffusion.modules.models.syncogen.models.semla.CoordNorm method) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.CoordNorm method) reshape_features() (in module MolecularDiffusion.modules.layers.atomic_data) residual (MolecularDiffusion.modules.models.ligandiff.conv_layer.GVPConvLayer attribute) residue_decoder (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.diffsbdd.dynamics.EGNNDynamics attribute) residue_encoder (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.diffsbdd.dynamics.EGNNDynamics attribute) residue_nf (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM attribute) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion attribute) RESIDUE_TYPES (in module MolecularDiffusion.modules.models.apo2mol.pminet) (in module MolecularDiffusion.modules.models.ipdiff.bapnet) ResnetBlockFC (class in MolecularDiffusion.modules.layers.vn.vn_layers) resolve() (in module MolecularDiffusion.assets) resolve_connectors() (in module MolecularDiffusion.utils.geom_constraint) resolve_tensor_output() (in module MolecularDiffusion.modules.layers.e3x.modules) restarting (MolecularDiffusion.modules.models.syncogen.data.dataloader.FaultTolerantDistributedSampler attribute) (MolecularDiffusion.modules.models.syncogen.data.dataloader.RandomFaultTolerantSampler attribute) restore() (MolecularDiffusion.modules.models.syncogen.models.ema.ExponentialMovingAverage method) restore_model_and_sample() (MolecularDiffusion.modules.models.syncogen.core.Diffusion method) resume() (MolecularDiffusion.core.engine.Engine method) RetAugmentationLinearAttention (class in MolecularDiffusion.modules.models.apo2mol.attn) return_step_output (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory attribute) reverse_schedule() (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousDiffusionInterpolant method) reverse_tensor() (in module MolecularDiffusion.modules.tasks.diffusion) reweight_factor() (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows method) rigid_alignment() (in module MolecularDiffusion.modules.models.loqi.interpolant) RING_SIZES (in module MolecularDiffusion.runmodes.analyze.druglike) rms_norm() (MolecularDiffusion.modules.models.goflow.ops.VecLayerNorm method) rmsd_align() (in module MolecularDiffusion.modules.models.etflow.flow) rmsd_loss() (in module MolecularDiffusion.modules.models.goflow.flow) rmsd_threshold (MolecularDiffusion.runmodes.generate.tasks_conformer.ConformerFactory attribute) (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator attribute) root (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataModule attribute) (MolecularDiffusion.data.component.diffdec_data.DiffDecDataModule attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataModule attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataModule attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataModule attribute) (MolecularDiffusion.data.component.graph3d_dataset.Graph3DDataset attribute) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataModule attribute) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataModule attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) root_path (MolecularDiffusion.runmodes.train.data.DataModule attribute) rotate() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Rotation method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Rotation method) rotate_inv() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Rotation method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Rotation method) rotate_inv_rescale_cache (MolecularDiffusion.modules.layers.equiformer_v2.so3.CoefficientMappingModule attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.CoefficientMappingModule attribute) rotation_augmentation() (in module MolecularDiffusion.modules.models.ditmc.flow_matching) rotation_axis() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca) rotation_axis_np() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca_np) rotation_to_wigner() (in module MolecularDiffusion.modules.layers.esen.common.rotation) RotationToWignerDMatrix() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Rotation method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Rotation method) row_index (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRRecord attribute) rpe_qk (MolecularDiffusion.modules.layers.e3x.modules.SelfAttention attribute) rpe_v (MolecularDiffusion.modules.layers.e3x.modules.SelfAttention attribute) rtol (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTSGenerator attribute) run() (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecScaffoldGenerator method) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeGenerator method) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolGenerator method) (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator method) (MolecularDiffusion.modules.tasks.pocket_generator.PocketGenerator method) (MolecularDiffusion.runmodes.generate.tasks_conformer.ConformerFactory method) (MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize.GCDMOptimizeFactory method) (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory method) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator method) run_ema_update_cpu() (in module MolecularDiffusion.modules.models.tabasco.callbacks.ema) run_featurize() (in module MolecularDiffusion.runmodes.analyze.featurize) run_postbuster() (in module MolecularDiffusion.utils.geom_metrics) run_processing() (in module MolecularDiffusion.runmodes.analyze.xyz2mol) runner() (in module MolecularDiffusion.cli.predict) (in module MolecularDiffusion.runmodes.analyze.compute_metrics) RunResult (class in MolecularDiffusion.runmodes.generate.sweep) rxn_indices (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) rxn_indices_to_onehot() (in module MolecularDiffusion.modules.models.syncogen.api.ops.graph_ops) rxn_onehot (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) rxn_onehot_dim (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) rxn_onehot_to_indices() (in module MolecularDiffusion.modules.models.syncogen.api.ops.graph_ops) rxn_onehot_to_tuple() (in module MolecularDiffusion.modules.models.syncogen.api.ops.graph_ops) rxn_pad (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph attribute) rxn_tuple (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) rxn_tuple_to_onehot() (in module MolecularDiffusion.modules.models.syncogen.api.ops.graph_ops) S s (MolecularDiffusion.modules.models.loqi.interpolant.CosineSchedule attribute) s2_act (MolecularDiffusion.modules.layers.equiformer_v2.activation.SeparableS2Activation attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.SeparableS2Activation attribute) (MolecularDiffusion.modules.layers.esen.nn.activation.SeparableS2Activation attribute) S2Activation (class in MolecularDiffusion.modules.layers.equiformer_v2.activation) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.activation) (class in MolecularDiffusion.modules.layers.esen.nn.activation) s2v (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) s_message_dim (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) s_V (in module MolecularDiffusion.modules.models.ligandiff.dropout) (in module MolecularDiffusion.modules.models.ligandiff.gvp) (in module MolecularDiffusion.modules.models.ligandiff.layer_norm) SA() (in module MolecularDiffusion.modules.tasks.metrics) sactivation (MolecularDiffusion.modules.models.goflow.outputs.GatedEquivariantBlock attribute) safe_norm() (in module MolecularDiffusion.modules.models.gcdm.gcp_utils) SAGPoolNet (class in MolecularDiffusion.modules.models.apo2mol.uni_transformer) sample() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) (MolecularDiffusion.modules.models.difflinker.linker_size.DistributionNodes method) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffpharma.distributions.DistributionNodes method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.DistributionNodes method) (MolecularDiffusion.modules.models.ditmc.flow_matching.FlowMatching method) (MolecularDiffusion.modules.models.ditmc.priors.GaussianPrior method) (MolecularDiffusion.modules.models.ditmc.priors.HarmonicPrior method) (MolecularDiffusion.modules.models.en_diffusion.DistributionNodes method) (MolecularDiffusion.modules.models.en_diffusion.DistributionProperty method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows method) (MolecularDiffusion.modules.models.etflow.flow.HarmonicSampler method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnLatentDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB method) (MolecularDiffusion.modules.models.syncogen.core.Diffusion method) (MolecularDiffusion.modules.models.tabasco.flow.utils.HistogramTimeDistribution method) (MolecularDiffusion.modules.models.tabasco.flow_model.FlowMatchingModel method) (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) (MolecularDiffusion.modules.models.tabasco.sample.guided_sampling.GuidedSampling method) (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask method) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask method) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTask method) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDTask method) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.LigandPocketSizePrior method) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeNodeDistribution method) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTask method) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTask method) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask method) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask method) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask method) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTask method) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTask method) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.IPDiffDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.KGDiffDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.PocketSizePrior method) (MolecularDiffusion.modules.tasks.diffusion_ldm.DiagonalGaussianDistribution method) (MolecularDiffusion.modules.tasks.diffusion_ldm.FlowMatchingInterpolant method) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask method) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask method) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask method) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask method) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQINodeDistribution method) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask method) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask method) (MolecularDiffusion.modules.tasks.diffusion_pmdm.LigandSizeDistribution method) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask method) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenSizePrior method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoNodeDistribution method) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETask method) sample_around_xh_target() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) sample_atom_num() (in module MolecularDiffusion.modules.models.kgdiff.atom_num) sample_batch() (MolecularDiffusion.modules.models.en_diffusion.DistributionProperty method) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB method) sample_categorical() (in module MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.utils) sample_center_gravity_zero_gaussian_batch() (in module MolecularDiffusion.modules.models.oareactdiff.graph_tools) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion static method) sample_center_gravity_zero_gaussian_with_mask() (in module MolecularDiffusion.modules.models.difflinker.utils) (in module MolecularDiffusion.modules.models.jodo.utils) (in module MolecularDiffusion.utils.geom_utils) sample_chain() (MolecularDiffusion.modules.models.difflinker.edm.EDM method) (MolecularDiffusion.modules.models.difflinker.edm.InpaintingEDM method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnLatentDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) sample_chain_guide() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) sample_cmd() (in module MolecularDiffusion.cli.data) sample_com_rand_pos() (in module MolecularDiffusion.modules.models.nextmol.dgt) sample_combined_position_feature_noise() (in module MolecularDiffusion.modules.models.jodo.utils) (MolecularDiffusion.modules.models.difflinker.edm.EDM method) (MolecularDiffusion.modules.models.difflinker.edm.InpaintingEDM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) sample_conditional() (MolecularDiffusion.modules.models.diffpharma.distributions.DistributionNodes method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.DistributionNodes method) sample_conditional_path() (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField method) (MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field.CTMCVectorField method) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField method) sample_conditonal() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask method) sample_conformer (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataset attribute) sample_db() (in module MolecularDiffusion.runmodes.data.ase_ops) sample_ddim() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) sample_ddim_step() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) sample_diffusion() (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.ipdiff.score_model.IPDiffScorePosNet3D method) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D method) sample_discrete_features() (in module MolecularDiffusion.modules.models.midi.diffusion_utils) sample_edges() (in module MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.utils) sample_every_n_epochs (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) sample_for_volume() (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeNodeDistribution method) sample_gamma_schedule() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) sample_gamma_schedule_type (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion attribute) sample_gaussian() (in module MolecularDiffusion.modules.models.oareactdiff.graph_tools) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM static method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion static method) sample_gaussian_with_mask() (in module MolecularDiffusion.modules.models.difflinker.utils) (in module MolecularDiffusion.modules.models.jodo.utils) (in module MolecularDiffusion.utils.geom_utils) sample_given_pocket() (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.ConditionalDDPM method) sample_guidance() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) sample_guidance_conitional() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask method) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask method) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask method) sample_hybrid_guidance() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) sample_input (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_conformer.ConformerFactory attribute) sample_joint() (MolecularDiffusion.modules.models.diffpharma.distributions.DistributionNodes method) sample_limit_dist() (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel method) sample_molecular_surface_with_radius() (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) sample_molecular_surface_with_radius_fibonacci() (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) (in module MolecularDiffusion.utils.shepherd_utils) sample_n_nodes() (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager method) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenSizePrior method) sample_noise() (MolecularDiffusion.modules.models.tabasco.flow.interpolate.CenteredMetricInterpolant method) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.DiscreteInterpolant method) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.Interpolant method) sample_normal() (MolecularDiffusion.modules.models.difflinker.edm.EDM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion method) sample_normal_zero_com() (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.ConditionalDDPM method) sample_p_xh_given_z0() (MolecularDiffusion.modules.models.difflinker.edm.InpaintingEDM method) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnLatentDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion method) sample_p_xh_given_z0_only_ligandDiff() (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) sample_p_xh_given_z0_only_linker() (MolecularDiffusion.modules.models.difflinker.edm.EDM method) sample_p_zs_given_zt() (MolecularDiffusion.modules.models.difflinker.edm.InpaintingEDM method) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion method) sample_p_zs_given_zt_guidance_cfg() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) sample_p_zs_given_zt_guidance_cfg_gg() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) sample_p_zs_given_zt_guidance_v0() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) sample_p_zs_given_zt_guidance_v1() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) sample_p_zs_given_zt_guidance_v2() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) sample_p_zs_given_zt_ip() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) sample_p_zs_given_zt_only_ligandDiff() (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) sample_p_zs_given_zt_only_linker() (MolecularDiffusion.modules.models.difflinker.edm.EDM method) sample_p_zs_given_zt_op() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) sample_p_zs_given_zt_op_ft() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) sample_p_zs_given_zt_silvr() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) sample_p_zs_given_zt_ssgd() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) sample_p_zt_given_zs() (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion method) sample_pool_limit (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory attribute) sample_q_xh_given_z0_and_x() (MolecularDiffusion.modules.models.difflinker.edm.InpaintingEDM method) sample_q_zs_given_zt_and_x() (MolecularDiffusion.modules.models.difflinker.edm.InpaintingEDM method) sample_schedule (MolecularDiffusion.modules.models.tabasco.flow_model.FlowMatchingModel attribute) sample_sigma_schedule() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) sample_sigma_schedule_type (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion attribute) sample_smiles() (in module MolecularDiffusion.modules.models.nextmol.mollama) sample_symmetric_edge_feature_noise() (in module MolecularDiffusion.modules.models.jodo.utils) sample_time() (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D method) (MolecularDiffusion.modules.models.loqi.interpolant.Interpolant method) sample_time_dist (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask attribute) sample_time_method (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) sample_timestep_biased() (in module MolecularDiffusion.data.component.pharmacophore) sample_uniform_rotation() (in module MolecularDiffusion.modules.models.tabasco.data.transforms) sample_zs_from_zt_and_pred() (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel method) SampleNoiseSchedule (class in MolecularDiffusion.modules.models.tabasco.sample.noise_schedule) sampler_kwargs (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMPocketGenerator attribute) (MolecularDiffusion.runmodes.generate.tasks_conformer.ConformerFactory attribute) SAMPLES_PER_ATOM (in module MolecularDiffusion.runmodes.analyze.similarity3d) sampling_eps (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) sampling_mode (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) sampling_noise_removal (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) sampling_steps (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) sanitize_smiles() (in module MolecularDiffusion.runmodes.analyze.xyz2mol) sanitized_config_dict() (MolecularDiffusion.core.engine.Engine method) save() (MolecularDiffusion.core.engine.Engine method) save_as_sdf() (in module MolecularDiffusion.modules.models.syncogen.utils.rdkit) save_ema_model() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) save_every_iteration (MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize.GCDMOptimizeFactory attribute) save_every_val_epoch (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) save_features() (in module MolecularDiffusion.runmodes.data.featurization) save_modalities (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) save_molecules() (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator method) save_original_optimizer_state (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) save_original_optimizer_state() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) save_pickle() (MolecularDiffusion.data.component.dataset.GraphDataset method) (MolecularDiffusion.data.component.dataset.PointCloudDataset method) (MolecularDiffusion.data.component.graph3d_dataset.Graph3DDataset method) save_pkl (MolecularDiffusion.runmodes.train.data.DataModule attribute) save_reconstruction (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) save_reference (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecScaffoldGenerator attribute) save_safetensors (in module MolecularDiffusion.runmodes.data.featurization) save_shepherd_outputs() (in module MolecularDiffusion.utils.geom_utils) save_top_k (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) save_xyz_file() (in module MolecularDiffusion.utils.geom_utils) save_xyz_file_atomic_numbers() (in module MolecularDiffusion.utils.geom_utils) save_xyz_tmp() (in module MolecularDiffusion.utils.geom_analyzer) save_xyzrender_figures (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeGenerator attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) SaveGeneratedMolsCallback (class in MolecularDiffusion.modules.models.tabasco.callbacks.save_molecules) SBSchedule (class in MolecularDiffusion.modules.models.reactot.schedule) sc_mlp (MolecularDiffusion.modules.models.ditmc.embedding.DiTNodeEmbed attribute) scaffold_smarts (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) scalar (MolecularDiffusion.modules.models.gcdm.gcp_utils.ScalarVector property) scalar_act (MolecularDiffusion.modules.layers.equiformer_v2.activation.GateActivation attribute) (MolecularDiffusion.modules.layers.equiformer_v2.activation.SeparableS2Activation attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.GateActivation attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.SeparableS2Activation attribute) (MolecularDiffusion.modules.layers.esen.nn.activation.GateActivation attribute) (MolecularDiffusion.modules.layers.esen.nn.activation.SeparableS2Activation attribute) scalar_activation (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) scalar_dropout (MolecularDiffusion.modules.models.gcdm.gcp_utils.GCPDropout attribute) scalar_embedding (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.tabasco_gvp.gvp_backbone.GVPBackbone attribute) scalar_gate (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) scalar_hidden_dim (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) scalar_mlp (MolecularDiffusion.modules.layers.esen.esen_block.SpectralAtomwise attribute) scalar_MLP (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2DecompositionEdgeBlock attribute) scalar_net (MolecularDiffusion.modules.models.goflow.outputs.GatedEquivariantBlock attribute) scalar_node_projection_gcp (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) scalar_nonlinearity (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2Block attribute) (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2DecompositionEdgeBlock attribute) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) scalar_norm (MolecularDiffusion.modules.models.diffsmol.common.GVPLayerNorm attribute) (MolecularDiffusion.modules.models.gcdm.gcp_utils.GCPLayerNorm attribute) scalar_size (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) scalarization() (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet method) scalarize() (in module MolecularDiffusion.modules.models.gcdm.gcp_utils) ScalarVector (class in MolecularDiffusion.modules.models.gcdm.gcp_utils) scale (MolecularDiffusion.modules.models.chefnmr.embedders.Attention attribute) (MolecularDiffusion.modules.models.chefnmr.layers.Attention attribute) (MolecularDiffusion.modules.models.jodo.layers.CoorsNorm attribute) scale() (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates method) scale_atom_features_x1 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) scale_bond_features_x1 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) scale_dist_features (MolecularDiffusion.modules.models.loqi.fn_model.MegaFNV3Conf attribute) scale_edge (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet attribute) SCALE_FACTOR (in module MolecularDiffusion.runmodes.analyze.compute_metrics) (in module MolecularDiffusion.runmodes.data.augmentation) (in module MolecularDiffusion.runmodes.train.eval) (in module MolecularDiffusion.utils.geom_analyzer) (in module MolecularDiffusion.utils.geom_metrics) scale_factor (MolecularDiffusion.modules.layers.equiformer_v2.activation.ScaledSigmoid attribute) (MolecularDiffusion.modules.layers.equiformer_v2.activation.ScaledSiLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2.activation.ScaledSmoothLeakyReLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantDegreeLayerScale attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.ScaledSigmoid attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.ScaledSiLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.ScaledSmoothLeakyReLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantDegreeLayerScale attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantDegreeLayerScale attribute) (MolecularDiffusion.modules.models.ligandiff.egnn.ScaledSiLU attribute) scale_node_features_x3 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) scale_node_features_x4 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) scale_noise (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) scale_noise_by_log_num_atoms (MolecularDiffusion.modules.models.tabasco.flow.interpolate.CenteredMetricInterpolant attribute) scale_noise_factor (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) scale_schedule() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) scale_vector_features_x4 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) scale_with_hops (MolecularDiffusion.modules.models.ditmc.embedding.RadialSphericalEdgeEmbedding attribute) ScaledScatter (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) ScaledSigmoid (class in MolecularDiffusion.modules.layers.equiformer_v2.activation) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.activation) ScaledSiLU (class in MolecularDiffusion.modules.layers.equiformer_v2.activation) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.activation) (class in MolecularDiffusion.modules.models.ligandiff.egnn) ScaledSmoothLeakyReLU (class in MolecularDiffusion.modules.layers.equiformer_v2.activation) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.activation) ScaledSwiGLU (class in MolecularDiffusion.modules.layers.equiformer_v2.activation) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.activation) scales (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) scaling (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet attribute) (MolecularDiffusion.modules.models.goflow.ops.CosineCutoff attribute) schedule (MolecularDiffusion.modules.models.jodo.noise_schedule.NoiseScheduleVP attribute) (MolecularDiffusion.modules.models.nextmol.scheduler.NoiseScheduleVPV2 attribute) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute), [1] schedule_type (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant attribute) schedule_types (MolecularDiffusion.modules.models.flowmol.interpolant_scheduler.InterpolantScheduler attribute) scheduler (MolecularDiffusion.core.engine.Engine attribute) scheduler_choice (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) scheduler_choice_kwargs (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) scheduler_config (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) SchNetProteinEncoder (class in MolecularDiffusion.modules.models.pmdm.encoders) score (MolecularDiffusion.modules.tasks.elucidation_generator.Candidate attribute), [1] score_model (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask attribute) score_model_args (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) score_pose() (in module MolecularDiffusion.runmodes.analyze.docking) score_reference() (in module MolecularDiffusion.runmodes.analyze.docking) score_type (MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.p2.PathPlanning attribute) ScorePosNet3D (class in MolecularDiffusion.modules.models.apo2mol.score_model) (class in MolecularDiffusion.modules.models.diffsmol.score_model) (class in MolecularDiffusion.modules.models.kgdiff.score_model) SCORES_THRESHOLD (in module MolecularDiffusion.runmodes.analyze.compute_metrics) (in module MolecularDiffusion.utils.geom_metrics) scprop (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) SDEMetricInterpolant (class in MolecularDiffusion.modules.models.tabasco.flow.interpolate) sdf_output_path (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask attribute) sdf_per_molecule (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) sdf_to_coordinates() (in module MolecularDiffusion.modules.models.syncogen.utils.rdkit) SE3Norm (class in MolecularDiffusion.modules.layers.conv) (class in MolecularDiffusion.modules.models.midi.layers) (class in MolecularDiffusion.modules.models.syncogen.models.layers) search() (MolecularDiffusion.core.core.Registry class method) seed (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecScaffoldGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolGenerator attribute) (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.pocket_generator.PocketGenerator attribute) (MolecularDiffusion.runmodes.generate.tasks_conformer.ConformerFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize.GCDMOptimizeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) seed_everything() (in module MolecularDiffusion.utils.torch) seed_numpy (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTSGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTSGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTSGenerator attribute) (MolecularDiffusion.modules.tasks.pocket_generator.PocketGenerator attribute) seed_prior() (MolecularDiffusion.modules.tasks.diffusion_nextmol.Graph3DBatchToNextMolAdapter method) segment_mean() (in module MolecularDiffusion.modules.layers.e3x.indexed) select_conformer_key() (in module MolecularDiffusion.modules.models.syncogen.utils.file_readers) select_fragment() (in module MolecularDiffusion.utils.substituent_builder) selected_gcp (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig property) self_attn (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) (MolecularDiffusion.modules.models.diffspectra.specformer.TSTEncoderLayer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.XEyTransformerLayer attribute) self_cond (MolecularDiffusion.modules.models.ditmc.graphs.LatentGraph attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.EquiInvDynamics attribute) (MolecularDiffusion.modules.models.syncogen.models.semla.SemlaGenerator attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.EquiInvDynamics attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask attribute) self_condition (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.FlowMatchingInterpolant attribute) self_condition_prob (MolecularDiffusion.modules.tasks.diffusion_ldm.FlowMatchingInterpolant attribute) self_conditioning (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) self_conditioning_bool (MolecularDiffusion.modules.models.ditmc.embedding.DiTNodeEmbed attribute) (MolecularDiffusion.modules.models.ditmc.flow_matching.FlowMatching attribute) self_conditioning_prob (MolecularDiffusion.modules.models.ditmc.flow_matching.FlowMatching attribute) self_message (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPLayerConfig attribute) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPMessagePassing attribute) SelfAttention (class in MolecularDiffusion.modules.layers.e3x.modules) SelfConditioningResidualLayer (class in MolecularDiffusion.modules.models.flowmol_graph3d.self_conditioning) SemlaGenerator (class in MolecularDiffusion.modules.models.syncogen.models.semla) SemlaPharmGenerator (class in MolecularDiffusion.modules.models.syncogen.models.semla_pharm) senders (MolecularDiffusion.modules.models.ditmc.graphs.CondGraph attribute) (MolecularDiffusion.modules.models.ditmc.graphs.LatentGraph attribute) (MolecularDiffusion.modules.models.ditmc.graphs.PriorGraph attribute) sep_vecj (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) SeparableFCTP (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) SeparableS2Activation (class in MolecularDiffusion.modules.layers.equiformer_v2.activation) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.activation) (class in MolecularDiffusion.modules.layers.esen.nn.activation) separate_mol_updaters (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) separator (in module MolecularDiffusion.utils.pretty) series_decomp (class in MolecularDiffusion.modules.models.diffspectra.specformer_layers) set_atomic_charges() (in module MolecularDiffusion.utils.xyz2mol.converter) set_atomic_radicals() (in module MolecularDiffusion.utils.xyz2mol.converter) set_coordinates() (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates method) set_data_stats() (MolecularDiffusion.modules.models.tabasco.flow_model.FlowMatchingModel method) (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) set_embedding() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Embedding method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Embedding method) set_epoch() (MolecularDiffusion.core.meter.Meter method) set_extra_state() (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTask method) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask method) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask method) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask method) set_inf (MolecularDiffusion.modules.models.jodo.layers.TransMixLayer attribute) set_lmax_mmax() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Embedding method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Embedding method) set_mask() (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates method) set_mol_coordinates() (in module MolecularDiffusion.modules.models.syncogen.utils.rdkit) set_normalizer() (MolecularDiffusion.modules.models.en_diffusion.DistributionProperty method) set_rank() (MolecularDiffusion.utils.io.RankState class method) set_weights (MolecularDiffusion.modules.models.syncogen.models.semla.CoordNorm attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.CoordNorm attribute) set_wigner() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Rotation method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Rotation method) SetNorm (class in MolecularDiffusion.modules.models.syncogen.models.layers) setup() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule method) sha256_file() (in module MolecularDiffusion.modules.models.chefnmr.sidecar) shadow_params (MolecularDiffusion.modules.models.syncogen.models.ema.ExponentialMovingAverage attribute) shape (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates property) shape_cache_path (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolTaskFactory attribute) shape_dim (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask attribute) shape_emb (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeGenerator attribute) shape_emb_layer (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer attribute) shape_from_atoms() (in module MolecularDiffusion.modules.models.diffsmol.shape_utils) shape_in (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer attribute) shape_latent_dim (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) shape_measure() (in module MolecularDiffusion.utils.shape_measure) shape_scalar_layer (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer attribute) shape_tanimoto() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap) shape_tanimoto_batched() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap) shape_tanimoto_esp() (in module MolecularDiffusion.utils.shepherd_score.score.electrostatic_scoring) shape_tanimoto_esp_np() (in module MolecularDiffusion.utils.shepherd_score.score.electrostatic_scoring_np) shape_tanimoto_full() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap) shape_tanimoto_np() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap_np) shape_volume (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeGenerator attribute) share_atom_edge_embedding (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) ShepherdPharmacophores (class in MolecularDiffusion.modules.models.syncogen.api.atomics.pharmacophores) shift (MolecularDiffusion.modules.models.apo2mol.common.ShiftedSoftplus attribute) (MolecularDiffusion.modules.models.diffsmol.common.ShiftedSoftplus attribute) (MolecularDiffusion.modules.models.kgdiff.common.ShiftedSoftplus attribute) (MolecularDiffusion.modules.models.pmdm.common.ShiftedSoftplus attribute) shift_t_mlp_pos (MolecularDiffusion.modules.models.ipdiff.score_model.IPDiffScorePosNet3D attribute) shifted_softplus() (in module MolecularDiffusion.modules.layers.functional) (in module MolecularDiffusion.modules.models.goflow.ops) ShiftedSoftplus (class in MolecularDiffusion.modules.models.apo2mol.common) (class in MolecularDiffusion.modules.models.diffsmol.common) (class in MolecularDiffusion.modules.models.kgdiff.common) (class in MolecularDiffusion.modules.models.pmdm.common) SHIPPED_GLOBALS (in module MolecularDiffusion.modules.models.ditmc.build) SHIPPED_VARIANTS (in module MolecularDiffusion.modules.models.ditmc.build) short_cut (MolecularDiffusion.modules.layers.common.MLP attribute) shortcut (MolecularDiffusion.modules.layers.vn.vn_layers.ResnetBlockFC attribute) (MolecularDiffusion.modules.layers.vn.vn_layers.VNResnetBlockFC attribute) shortest_hops (MolecularDiffusion.modules.models.ditmc.graphs.LatentGraph attribute) shortest_hops_from_adjacency() (in module MolecularDiffusion.modules.models.ditmc.graph_features) show_schedule() (MolecularDiffusion.modules.models.en_diffusion.GammaNetwork method) shuffle_train (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) sid (MolecularDiffusion.modules.layers.atomic_data.AtomicData attribute) sigma (MolecularDiffusion.modules.models.ditmc.flow_matching.FlowMatching attribute) (MolecularDiffusion.modules.models.ditmc.priors.GaussianPrior attribute) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) sigma() (MolecularDiffusion.modules.models.difflinker.edm.EDM method) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) (MolecularDiffusion.modules.models.oareactdiff.schedule.DiffSchedule method) sigma_and_alpha_t_given_s() (MolecularDiffusion.modules.models.difflinker.edm.EDM method) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) (MolecularDiffusion.modules.models.oareactdiff.schedule.DiffSchedule method) sigma_data (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) sigma_frame_gate (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) sigma_in_network() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) sigma_max (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.linear.LinearNoise attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.loglinear.LogLinearNoise attribute) (MolecularDiffusion.modules.tasks.ssl3d.CoordDenoiseObjective attribute) sigma_min (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion attribute) (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.linear.LinearNoise attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.loglinear.LogLinearNoise attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory attribute) (MolecularDiffusion.modules.tasks.ssl3d.CoordDenoiseObjective attribute) sigma_schedule (MolecularDiffusion.modules.tasks.ssl3d.CoordDenoiseObjective attribute) sigmas (MolecularDiffusion.modules.models.syncogen.diffusion.noise.geometric.GeometricNoise attribute) SigmoidSmearing (class in MolecularDiffusion.modules.models.shepherd_arch.ocp_compat) SignalToNoiseTimeFactor (class in MolecularDiffusion.modules.models.tabasco.flow.time_factor) signed_volume() (in module MolecularDiffusion.modules.models.etflow.flow) silent (MolecularDiffusion.core.meter.Meter attribute) SiLU (in module MolecularDiffusion.modules.models.pmdm.encoders) silu() (in module MolecularDiffusion.modules.layers.e3x.activations) SiLUSmearing (class in MolecularDiffusion.modules.models.shepherd_arch.ocp_compat) SimLow2High (class in MolecularDiffusion.modules.layers.gfmdiff.blocks) simple_idx_match_check() (in module MolecularDiffusion.data.component.pointcloud) (in module MolecularDiffusion.utils.smilify), [1] SimplePositionalEmbedding (class in MolecularDiffusion.modules.models.syncogen.models.layers) SimpleReadout (class in MolecularDiffusion.modules.models.ditmc.readout) sin_embedding (MolecularDiffusion.modules.layers.conv.EquivariantBlock attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.BAPNet attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.EquivariantBlock attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantBlock attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.EquivariantBlock attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) SinCosPosEncoding (in module MolecularDiffusion.modules.models.diffspectra.specformer_layers) single_bond_only() (in module MolecularDiffusion.utils.geom_analyzer) single_frag_only (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) SinusoidalPosEmb (class in MolecularDiffusion.modules.models.apo2mol.score_model) (class in MolecularDiffusion.modules.models.diffsmol.common) (class in MolecularDiffusion.modules.models.en_diffusion) SinusoidalPositionalEmbedding (class in MolecularDiffusion.modules.models.syncogen.models.layers) SinusoidalPositionEmbedding (class in MolecularDiffusion.modules.layers.common) SinusoidEncoding (class in MolecularDiffusion.modules.layers.tabasco.positional_encoder) SinusoidsEmbeddingNew (class in MolecularDiffusion.modules.layers.common) (class in MolecularDiffusion.modules.models.difflinker.egnn) (class in MolecularDiffusion.modules.models.diffpharma.egnn) (class in MolecularDiffusion.modules.models.diffsbdd.egnn) (class in MolecularDiffusion.modules.models.geoldm.egnn) (class in MolecularDiffusion.modules.models.ipdiff.bapnet) size_cmd() (in module MolecularDiffusion.cli.data) size_distribution (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM attribute) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion property) size_distribution_path (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTaskFactory attribute) size_emb (MolecularDiffusion.modules.models.syncogen.models.semla.SemlaGenerator attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator attribute) size_gnn_checkpoint (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) size_histogram (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute) size_predictor (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask attribute) size_prior (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask attribute) size_repr() (in module MolecularDiffusion.modules.layers.atomic_data) SizeGNN (class in MolecularDiffusion.modules.models.difflinker.size_gnn) SKELETON_BUILDERS (in module MolecularDiffusion.utils.geom_constraint) sleep_every_N (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) sleep_time (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) slerp_identity_to_q() (in module MolecularDiffusion.modules.models.apo2mol.residue_ops) smart_open() (in module MolecularDiffusion.utils.file) SMARTS_FEATURES_FDEF (in module MolecularDiffusion.utils.shepherd_utils) smiles (MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly.FragmentInstance attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRRecord attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraRecord attribute) (MolecularDiffusion.modules.tasks.elucidation_generator.Candidate attribute), [1] smiles_list (MolecularDiffusion.data.component.dataset.LazyChunkedDataset attribute) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset attribute) smilfy_xtb() (in module MolecularDiffusion.utils.smilify) smilify_openbabel() (in module MolecularDiffusion.runmodes.data.preparation) (in module MolecularDiffusion.utils.smilify) smilify_structure() (in module MolecularDiffusion.runmodes.data.preparation) smilify_wrapper() (in module MolecularDiffusion.utils.geom_metrics) smilify_xyz2mol() (in module MolecularDiffusion.runmodes.data.preparation) (in module MolecularDiffusion.utils.smilify) smooth_lddt_loss() (in module MolecularDiffusion.modules.models.chefnmr.utils) SmoothLDDTLoss (class in MolecularDiffusion.modules.models.syncogen.diffusion.loss.smooth_lddt) SmoothLeakyReLU (class in MolecularDiffusion.modules.layers.equiformer_v2.activation) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.activation) (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) SNNDense (class in MolecularDiffusion.modules.models.goflow.outputs) SNR() (MolecularDiffusion.modules.models.difflinker.edm.EDM method) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM static method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion static method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) snr() (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousDiffusionInterpolant method) SNR() (MolecularDiffusion.modules.models.oareactdiff.schedule.DiffSchedule static method) SNR_CLAMP_MAX (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) so2_conv_1 (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.esen.esen_block.Edgewise attribute) so2_conv_2 (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.esen.esen_block.Edgewise attribute) SO2_Convolution (class in MolecularDiffusion.modules.layers.equiformer_v2.so2_ops) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops) (class in MolecularDiffusion.modules.layers.esen.nn.so2_layers) SO2_Linear (class in MolecularDiffusion.modules.layers.equiformer_v2.so2_ops) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops) (class in MolecularDiffusion.modules.layers.esen.nn.so2_layers) SO2_m_Conv (class in MolecularDiffusion.modules.layers.esen.nn.so2_layers) so2_m_conv (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Convolution attribute) SO2_m_Convolution (class in MolecularDiffusion.modules.layers.equiformer_v2.so2_ops) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops) so2_m_fc (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Linear attribute) SO2EquivariantGraphAttention (class in MolecularDiffusion.modules.layers.equiformer_v2.transformer_block) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block) SO3_Embedding (class in MolecularDiffusion.modules.layers.equiformer_v2.so3) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.so3) so3_equivariant (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) SO3_Grid (class in MolecularDiffusion.modules.layers.equiformer_v2.so3) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.so3) (class in MolecularDiffusion.modules.layers.esen.common.so3) SO3_grid (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.esen.esen_block.Edgewise attribute) (MolecularDiffusion.modules.layers.esen.esen_block.GridAtomwise attribute) (MolecularDiffusion.modules.layers.esen.esen_block.SpectralAtomwise attribute) (MolecularDiffusion.modules.layers.esen.nn.activation.S2Activation attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) so3_grid (MolecularDiffusion.modules.models.tabasco_equiformer.equiformer_backbone.EquiformerV2TabascoBackbone attribute) SO3_Linear (class in MolecularDiffusion.modules.layers.equiformer_v2.so3) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.so3) (class in MolecularDiffusion.modules.layers.esen.nn.so3_layers) so3_linear_1 (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.esen.esen_block.SpectralAtomwise attribute) (MolecularDiffusion.modules.models.esen.eSEN_VelocityFFN attribute) so3_linear_2 (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.esen.esen_block.SpectralAtomwise attribute) (MolecularDiffusion.modules.models.esen.eSEN_VelocityFFN attribute) SO3_LinearV2 (class in MolecularDiffusion.modules.layers.equiformer_v2.so3) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.so3) SO3_Rotation (class in MolecularDiffusion.modules.layers.equiformer_v2.so3) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.so3) SO3_rotation (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) SO3DiTLayer (class in MolecularDiffusion.modules.models.ditmc.dit) SOAPFeaturizer (class in MolecularDiffusion.runmodes.analyze.featurize) soft_edge (MolecularDiffusion.modules.models.pmdm.encoders.EGNNSparseLayer attribute) softmax_inf (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) softplus() (in module MolecularDiffusion.modules.models.en_diffusion) (MolecularDiffusion.modules.models.difflinker.edm.EDM static method) solve_eot() (in module MolecularDiffusion.modules.models.equifm.eot) solver (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTSGenerator attribute) solver_type (MolecularDiffusion.modules.models.loqi.interpolant.Interpolant attribute) sort_irreps_even_first() (in module MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) source_key (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTSGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTSGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTSGenerator attribute) (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.ts_generator.TSGenerator attribute) source_required_msg (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) SP_regularizer (class in MolecularDiffusion.callbacks.train_helper) sp_regularizer (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) space_indices() (in module MolecularDiffusion.modules.models.reactot.schedule) space_size (MolecularDiffusion.modules.tasks.diffusion_kgdiff.PocketSizePrior attribute) spacegroup_embedder (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT attribute) spatial_cut_off (MolecularDiffusion.modules.models.diffspectra.dmt.DMT attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.Cond_DGT_concat attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.DGT_concat attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) spearmanr() (in module MolecularDiffusion.modules.tasks.metrics) SpecFormer (class in MolecularDiffusion.modules.models.diffspectra.specformer) specformer_kwargs (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) spectra_index (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) spectra_sidecar_path (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) spectra_source (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) spectra_version (MolecularDiffusion.modules.models.diffspectra.dmt.DMT attribute) (MolecularDiffusion.modules.models.diffspectra.specformer.SpecFormer attribute) (MolecularDiffusion.modules.models.diffspectra.specformer.TSTiEncoder attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) SpectralAtomwise (class in MolecularDiffusion.modules.layers.esen.esen_block) SpectraTokenizerConv1D (class in MolecularDiffusion.modules.models.chefnmr.embedders) SpectraTokenizerPatch1D (class in MolecularDiffusion.modules.models.chefnmr.embedders) sph_feature_size (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.esen.eSEN_dynamics attribute) sphere_channels (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_m_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_m_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.esen.esen_block.Edgewise attribute) (MolecularDiffusion.modules.layers.esen.esen_block.eSEN_Block attribute) (MolecularDiffusion.modules.layers.esen.esen_block.GridAtomwise attribute) (MolecularDiffusion.modules.layers.esen.esen_block.SpectralAtomwise attribute) (MolecularDiffusion.modules.layers.esen.nn.embedding.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_Linear attribute) (MolecularDiffusion.modules.layers.esen.nn.so2_layers.SO2_m_Conv attribute) (MolecularDiffusion.modules.models.equiformer_v2_backbone.EquiformerV2Backbone attribute) (MolecularDiffusion.modules.models.equiformer_v2_dynamics.EquiformerV2_dynamics attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.esen.MLP_EFS_Head attribute) (MolecularDiffusion.modules.models.esen.MLP_Energy_Head attribute) (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) (MolecularDiffusion.modules.models.tabasco_equiformer.equiformer_backbone.EquiformerV2TabascoBackbone attribute) sphere_channels_all (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) sphere_embedding (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) sphere_embedding_type (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) spherical_harmonics() (in module MolecularDiffusion.modules.layers.e3x.so3) SphericalBesselBasis (class in MolecularDiffusion.modules.layers.esen.nn.radial) sphharm_norm (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2SymmetricTensorHead attribute), [1] spin (MolecularDiffusion.modules.layers.atomic_data.AtomicData attribute) split (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDTask attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTask attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTSGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.IPDiffDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.KGDiffDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask attribute) (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) split_cmd() (in module MolecularDiffusion.cli.data) split_db() (in module MolecularDiffusion.runmodes.data.ase_ops) split_degree() (in module MolecularDiffusion.modules.models.goflow.gotennet) split_feature_axis() (in module MolecularDiffusion.modules.models.en_diffusion) split_features() (in module MolecularDiffusion.modules.models.difflinker.utils) split_file (MolecularDiffusion.data.component.goflow_data.GoFlowDataModule attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTSGenerator attribute) split_frame() (in module MolecularDiffusion.modules.models.en_diffusion) split_losses_by_time() (in module MolecularDiffusion.modules.models.tabasco.utils.metric_utils) split_path (MolecularDiffusion.data.component.goflow_data.GoFlowDataModule attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTSGenerator attribute) split_reset_hook (MolecularDiffusion.runmodes.train.eval.TaskEvalConfig attribute) split_z() (in module MolecularDiffusion.modules.models.en_diffusion) sqrd (MolecularDiffusion.modules.layers.tabasco.losses.InterDistancesLoss attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.bond_length.BondLengthLoss attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.pairwise_distance.PairwiseDistanceLoss attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.loss.smooth_lddt.SmoothLDDTLoss attribute) sqrt (MolecularDiffusion.modules.models.loqi.interpolant.CosineSchedule attribute) sqrt_alphas_cumprod (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) sqrt_one_minus_alphas_cumprod (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) sqrt_recip_alphas_cumprod (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) sqrt_recipm1_alphas_cumprod (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) square_time_weight (MolecularDiffusion.modules.models.syncogen.diffusion.loss.base.LossBase attribute) SquaredSignalToNoiseTimeFactor (class in MolecularDiffusion.modules.models.tabasco.flow.time_factor) SquareSampleNoiseSchedule (class in MolecularDiffusion.modules.models.tabasco.sample.noise_schedule) SquareTimeFactor (class in MolecularDiffusion.modules.models.tabasco.flow.time_factor) SSL3D (class in MolecularDiffusion.modules.tasks.ssl3d) SSL3DFeaturizer (class in MolecularDiffusion.runmodes.analyze.featurize) SSL3DObjective (class in MolecularDiffusion.modules.tasks.ssl3d) stack() (in module MolecularDiffusion.utils.comm) (in module MolecularDiffusion.utils.torch) start (MolecularDiffusion.modules.models.apo2mol.common.GaussianSmearing attribute) (MolecularDiffusion.modules.models.diffsmol.common.GaussianSmearing attribute) (MolecularDiffusion.modules.models.kgdiff.common.GaussianSmearing attribute) start_time (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) state_dict() (MolecularDiffusion.modules.models.syncogen.data.dataloader.FaultTolerantDistributedSampler method) (MolecularDiffusion.modules.models.syncogen.data.dataloader.RandomFaultTolerantSampler method) (MolecularDiffusion.modules.models.syncogen.models.ema.ExponentialMovingAverage method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer method) std (MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf.GaussianRadialBasisLayer attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf.GaussianRadialBasisLayer attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.DiagonalGaussianDistribution attribute) std() (MolecularDiffusion.callbacks.train_helper.Queue method) std_balance_degrees (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.esen.nn.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) std_bwd (MolecularDiffusion.modules.models.reactot.schedule.SBSchedule attribute), [1] std_fwd (MolecularDiffusion.modules.models.reactot.schedule.SBSchedule attribute), [1] std_init_max (MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf.GaussianRadialBasisLayer attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf.GaussianRadialBasisLayer attribute) std_init_min (MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf.GaussianRadialBasisLayer attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf.GaussianRadialBasisLayer attribute) std_mean (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) std_sb (MolecularDiffusion.modules.models.reactot.schedule.SBSchedule attribute), [1] stderr (MolecularDiffusion.utils.io.CaptureStdIO attribute) stdout (MolecularDiffusion.utils.io.CaptureStdIO attribute) stds (MolecularDiffusion.modules.models.jodo.layers.CondGaussianLayer attribute) (MolecularDiffusion.modules.models.jodo.layers.GaussianLayer attribute) stdv (in module MolecularDiffusion.utils.geom_analyzer) steer_interpolant (MolecularDiffusion.modules.models.tabasco.sample.guided_sampling.GuidedSampling attribute) step() (MolecularDiffusion.core.meter.Meter method) (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField method) (MolecularDiffusion.modules.models.flowmol_graph3d.ctmc_vector_field.CTMCVectorField method) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField method) (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousDiffusionInterpolant method) (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant method) (MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.base.DiscreteStrategyBase method) (MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.mdlm.MDLM method) (MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.p2.PathPlanning method) (MolecularDiffusion.modules.models.syncogen.diffusion.sampling.integrators.base.IntegratorBase method) (MolecularDiffusion.modules.models.syncogen.diffusion.sampling.integrators.euler.EulerIntegrator method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer method) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.CenteredMetricInterpolant method) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.DiscreteInterpolant method) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.Interpolant method) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.SDEMetricInterpolant method) step_scale (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion attribute) stereo_scores() (in module MolecularDiffusion.runmodes.analyze.conformer_metrics) stochasticity (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) stop (MolecularDiffusion.modules.models.apo2mol.common.GaussianSmearing attribute) (MolecularDiffusion.modules.models.diffsmol.common.GaussianSmearing attribute) (MolecularDiffusion.modules.models.kgdiff.common.GaussianSmearing attribute) stop_inpainting_at_time_x1_bonds (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) stop_inpainting_at_time_x1_pos (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) stop_inpainting_at_time_x1_x (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) stop_inpainting_at_time_x4 (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) store() (MolecularDiffusion.modules.models.syncogen.models.ema.ExponentialMovingAverage method) store_attn (MolecularDiffusion.modules.models.diffspectra.specformer.TSTEncoderLayer attribute) str2act() (in module MolecularDiffusion.modules.models.goflow.ops) str2basis() (in module MolecularDiffusion.modules.models.goflow.ops) str_atom() (in module MolecularDiffusion.utils.xyz2mol.converter) (MolecularDiffusion.data.component.pointcloud.PointCloud_Mol class method) stream (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) stride (MolecularDiffusion.modules.models.chefnmr.embedders.SpectraTokenizerPatch1D attribute) (MolecularDiffusion.modules.models.diffspectra.specformer.SpecFormer attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) structural_guidance() (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory method) subsample_noise_schedule() (in module MolecularDiffusion.modules.models.shepherd_arch.inference.noise) subset() (MolecularDiffusion.modules.models.syncogen.api.atomics.pharmacophores.ShepherdPharmacophores method) subspace_dimensionality() (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnHierarchicalVAE method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) SUBSTITUENT_GEOMETRIES (in module MolecularDiffusion.utils.substituent_geometries) sum_except_batch() (in module MolecularDiffusion.modules.models.difflinker.utils) (in module MolecularDiffusion.modules.models.en_diffusion) (in module MolecularDiffusion.modules.models.oareactdiff.graph_tools) (MolecularDiffusion.modules.models.difflinker.edm.EDM static method) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM static method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion static method) supported_schedule_types (MolecularDiffusion.modules.models.flowmol.interpolant_scheduler.InterpolantScheduler attribute) supports_guidance (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) swap_ema_weights() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer method) swap_model_weights() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) swap_tensors() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer method) swapping_react_prod (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffTS1xDataset attribute) SwiGLU (class in MolecularDiffusion.modules.layers.equiformer_v2.activation) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.activation) (class in MolecularDiffusion.modules.layers.tabasco.common) (class in MolecularDiffusion.modules.models.loqi.fn_model) swiglu_correction_fn() (in module MolecularDiffusion.modules.models.loqi.fn_model) swiglu_ffn() (in module MolecularDiffusion.modules.models.loqi.fn_model) swiglu_ffn_edge() (in module MolecularDiffusion.modules.models.loqi.fn_model) Swish (class in MolecularDiffusion.modules.models.apo2mol.common) swish (class in MolecularDiffusion.modules.models.goflow.ops) (in module MolecularDiffusion.modules.layers.e3x.activations) swish() (in module MolecularDiffusion.modules.models.oareactdiff.leftnet) switch_main_parameter_weights() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer method) switch_parity_of_pos() (in module MolecularDiffusion.modules.models.etflow.flow) symbol2num (in module MolecularDiffusion.utils.geom_analyzer) symbols (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRRecord attribute) (MolecularDiffusion.utils.smilify.Molecule attribute) sync_on_compute (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularUniqueness attribute) sync_twoup (MolecularDiffusion.modules.models.apo2mol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) synchronize() (in module MolecularDiffusion.utils.comm) synchronize_sigmas (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion attribute) SyncogenDataManager (class in MolecularDiffusion.modules.models.syncogen.data.dataloader) SyncogenDataModule (class in MolecularDiffusion.modules.models.syncogen.datamodule) SyncogenDataset (class in MolecularDiffusion.modules.models.syncogen.data.dataloader) SyncogenDiffusionTask (class in MolecularDiffusion.modules.tasks.diffusion_syncogen) SyncogenSizePrior (class in MolecularDiffusion.modules.tasks.diffusion_syncogen) T T (MolecularDiffusion.modules.models.difflinker.edm.EDM attribute) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM attribute) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.jodo.noise_schedule.NoiseScheduleVP attribute) (MolecularDiffusion.modules.models.ligandiff.edm.EDM attribute) (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) t (MolecularDiffusion.modules.models.midi.placeholder.PlaceHolder attribute) T (MolecularDiffusion.modules.models.nextmol.scheduler.NoiseScheduleVPV2 attribute) (MolecularDiffusion.modules.models.noisemodel.NoiseModel attribute) (MolecularDiffusion.modules.models.oareactdiff.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute), [1] t (MolecularDiffusion.modules.models.tabasco.flow.path.FlowPath attribute) T (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTask attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.JodoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask property) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTask attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTask attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTask attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask attribute) T() (in module MolecularDiffusion.modules.models.equifm.paths) t_cond (MolecularDiffusion.modules.tasks.diffusion_nextmol.Graph3DBatchToNextMolAdapter attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) t_embedder (MolecularDiffusion.modules.models.chefnmr.score_models.DiffusionModuleTransformer attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT attribute) t_embedding (MolecularDiffusion.modules.tasks.ssl3d.SSL3D attribute) T_hat() (in module MolecularDiffusion.modules.models.equifm.paths) t_int (MolecularDiffusion.modules.models.midi.placeholder.PlaceHolder attribute) t_max (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) t_threshold (MolecularDiffusion.modules.models.syncogen.diffusion.loss.base.LossBase attribute) tabasco_model (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.TabascoEGNNDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.TabascoEquiformerDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.TabascoGVPDiffusionTask attribute) TabascoDiffusionTask (class in MolecularDiffusion.modules.tasks.diffusion_tabasco) TabascoEGNNDiffusionTask (class in MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn) TabascoEquiformerDiffusionTask (class in MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer) TabascoGVPDiffusionTask (class in MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp) TabascoNodeDistribution (class in MolecularDiffusion.modules.tasks.diffusion_tabasco) table (MolecularDiffusion.core.core.Registry attribute) tag (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffint.DiffIntPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.DiffSBDDPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.GoFlowTSGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.IPDiffPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.KGDiffPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.OAReactDiffTSGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMConstrainedGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMPocketGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ReactOTTSGenerator attribute) (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.pocket_generator.PocketGenerator attribute) (MolecularDiffusion.modules.tasks.ts_generator.TSGenerator attribute) tags (MolecularDiffusion.modules.layers.atomic_data.AtomicData attribute) (MolecularDiffusion.runmodes.train.logger.Logger attribute) tags_wandb (MolecularDiffusion.core.engine.Engine attribute) tanh (MolecularDiffusion.modules.layers.conv.EquivariantUpdate attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.PosUpdate attribute) (MolecularDiffusion.modules.models.apo2mol.pminet.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.difflinker.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.diffpharma.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.diffsbdd.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.geoldm.egnn.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.ipdiff.bapnet.EquivariantUpdate attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) tanimoto_func() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring) tanimoto_func_np() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring_np) target() (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPredictionPointCloud method) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative method) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction method) (MolecularDiffusion.modules.tasks.ssl3d.SSL3D method) (MolecularDiffusion.modules.tasks.task.Task method) target_fields (MolecularDiffusion.runmodes.train.data.DataModule attribute) target_values (MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize.GCDMOptimizeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) targets (MolecularDiffusion.data.component.dataset.LazyChunkedDataset property) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset property) Task (class in MolecularDiffusion.modules.tasks.task) task (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.diffusion_apo2mol.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecScaffoldGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolGenerator attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) (MolecularDiffusion.modules.tasks.pocket_generator.PocketGenerator attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) (MolecularDiffusion.runmodes.generate.tasks_conformer.ConformerFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_gcdm_optimize.GCDMOptimizeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) (MolecularDiffusion.runmodes.train.tasks_equiformer.ModelTaskFactory attribute) task_name (MolecularDiffusion.modules.layers.atomic_data.AtomicData property) task_names (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gcdm.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gfmdiff.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_painn.ModelTaskFactory attribute) TASK_REGISTRY (in module MolecularDiffusion.runmodes.train.eval) task_type (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataModule attribute) (MolecularDiffusion.data.component.diffdec_data.DiffDecDataModule attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataModule attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataModule attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataModule attribute) (MolecularDiffusion.data.component.goflow_data.GoFlowDataModule attribute) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataModule attribute) (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataModule attribute) (MolecularDiffusion.modules.models.syncogen.datamodule.SyncogenDataModule attribute) (MolecularDiffusion.modules.tasks.diffusion_apo2mol.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRElucidationTask attribute) (MolecularDiffusion.modules.tasks.diffusion_chefnmr.ChefNMRTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffdec.DiffDecTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffpharma.DiffPharmaTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTask attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTask attribute) (MolecularDiffusion.modules.tasks.diffusion_etflow.ETFlowTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_goflow.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ipdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_kgdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff.LigandDiffTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ligandiff_multi.LigandDiffMultiTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.MidiDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTask attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.TabascoEGNNDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.TabascoEquiformerDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.TabascoGVPDiffusionTask attribute) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative attribute) (MolecularDiffusion.modules.tasks.vae_geoldm.GeoLDMVAETaskFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_equiformer.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gcdm.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gfmdiff.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_painn.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_transformer.ModelTaskFactory attribute) task_wrapper() (in module MolecularDiffusion.utils.pretty) TaskEvalConfig (class in MolecularDiffusion.runmodes.train.eval) tasks (MolecularDiffusion.data.component.dataset.GraphDataset property) (MolecularDiffusion.data.component.dataset.LazyChunkedDataset property) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset property) (MolecularDiffusion.data.component.dataset.PointCloudDataset property) (MolecularDiffusion.data.component.graph3d_dataset.Graph3DDataset property) temb (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) temb_proj (MolecularDiffusion.modules.models.pmdm.epsnet.PMDMEpsNet attribute) temperature (MolecularDiffusion.modules.models.syncogen.diffusion.sampling.discrete_strategies.p2.PathPlanning attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolGenerator attribute) Tensor (class in MolecularDiffusion.modules.layers.e3x.modules) tensor (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates attribute) tensor_init (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet attribute) tensor_lecun_normal_() (in module MolecularDiffusion.modules.layers.e3x.initializers) tensor_obj_to_points() (MolecularDiffusion.modules.models.tabasco.chem.convert.MoleculeConverter method) tensor_or_int_to_tensor() (in module MolecularDiffusion.modules.layers.atomic_data) tensor_product_mask() (in module MolecularDiffusion.modules.layers.e3x.initializers) tensor_size (MolecularDiffusion.modules.models.goflow.ops.TensorInit property) TensorDictCollator (class in MolecularDiffusion.modules.models.tabasco.data.utils) TensorDictToPointCloudAdapter (class in MolecularDiffusion.modules.tasks.diffusion_tabasco) TensorInit (class in MolecularDiffusion.modules.models.goflow.ops) TensorProductRescale (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) test_dataloader() (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule method) test_file (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataModule attribute) (MolecularDiffusion.data.component.diffdec_data.DiffDecDataModule attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataModule attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataModule attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataModule attribute) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataModule attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataModule attribute) test_set (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataModule attribute) (MolecularDiffusion.data.component.diffdec_data.DiffDecDataModule attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataModule attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataModule attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataModule attribute) (MolecularDiffusion.data.component.goflow_data.GoFlowDataModule attribute) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataModule attribute) (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataModule attribute) (MolecularDiffusion.modules.models.syncogen.datamodule.SyncogenDataModule attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) test_size (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) test_step() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) tf_layers (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) (MolecularDiffusion.modules.models.midi.transformer_model.GraphTransformer attribute) thread (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) threshold_cfg() (in module MolecularDiffusion.modules.models.diffsmol.score_model) threshold_p (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolTaskFactory attribute) threshold_type (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolTaskFactory attribute) time (MolecularDiffusion.core.meter.Meter attribute) time() (in module MolecularDiffusion.utils.pretty) time_alpha_factor (MolecularDiffusion.modules.models.tabasco.flow_model.FlowMatchingModel attribute) time_conditioning (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) time_dim (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) time_emb (MolecularDiffusion.modules.models.jodo.layers.CondCoorsNorm attribute) time_emb_dim (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) time_emb_mode (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) time_embedding (MolecularDiffusion.modules.models.ditmc.dit.GenerativeModel attribute) (MolecularDiffusion.modules.models.goflow.gotennet.GotenNet attribute) (MolecularDiffusion.modules.models.painn_dynamics.PaiNNDynamics attribute) time_embedding_dim (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField attribute) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) time_encoding (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) (MolecularDiffusion.modules.models.transformer_dynamics.TransformerDynamics attribute) time_factor (MolecularDiffusion.modules.layers.tabasco.losses.InterDistancesLoss attribute) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.Interpolant attribute) TIME_HIGH (in module MolecularDiffusion.modules.tasks.diffusion_etflow) TIME_LOW (in module MolecularDiffusion.modules.tasks.diffusion_etflow) time_mlp (MolecularDiffusion.modules.models.jodo.layers.CondGaussianLayer attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.CondEquiUpdate attribute) (MolecularDiffusion.modules.models.jodo.mol_gnn.MultiCondEquiUpdate attribute) (MolecularDiffusion.modules.models.nextmol.dgt.DGTDiffusion attribute) time_scaled_loss (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) time_type (MolecularDiffusion.modules.models.loqi.interpolant.Interpolant attribute) time_weighted (MolecularDiffusion.modules.models.syncogen.diffusion.loss.base.LossBase attribute) TimeEmbedding (class in MolecularDiffusion.modules.models.ditmc.embedding) TimeFourierEncoding (class in MolecularDiffusion.modules.layers.tabasco.positional_encoder) TIMEOUT (in module MolecularDiffusion.utils.smilify) TimeoutException timestep_embedding() (MolecularDiffusion.modules.models.chefnmr.layers.TimestepEmbedder static method) (MolecularDiffusion.modules.models.ldm.denoisers.dit.TimestepEmbedder static method) (MolecularDiffusion.modules.models.loqi.fn_model.TimestepEmbedder static method) (MolecularDiffusion.modules.models.syncogen.models.layers.TimestepEmbedding static method) TimestepEmbedder (class in MolecularDiffusion.modules.models.chefnmr.layers) (class in MolecularDiffusion.modules.models.ldm.denoisers.dit) (class in MolecularDiffusion.modules.models.loqi.fn_model) TimestepEmbedding (class in MolecularDiffusion.modules.models.goflow.gotennet) (class in MolecularDiffusion.modules.models.syncogen.models.layers) timesteps (MolecularDiffusion.modules.models.difflinker.noise.PredefinedNoiseSchedule attribute) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.PredefinedNoiseSchedule attribute) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.PredefinedNoiseSchedule attribute) (MolecularDiffusion.modules.models.en_diffusion.PredefinedNoiseSchedule attribute) (MolecularDiffusion.modules.models.ligandiff.noise.PredefinedNoiseSchedule attribute) (MolecularDiffusion.modules.models.loqi.interpolant.Interpolant attribute) (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) (MolecularDiffusion.modules.models.oareactdiff.schedule.PredefinedNoiseSchedule attribute) (MolecularDiffusion.modules.models.reactot.schedule.SBSchedule attribute), [1] (MolecularDiffusion.modules.tasks.diffusion_loqi.LoQIConformerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) tln (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) to() (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates method) (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph method) to_2tuple (in module MolecularDiffusion.modules.models.chefnmr.layers) to_ase() (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) to_ase_single() (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) to_dense_bonds() (in module MolecularDiffusion.modules.models.syncogen.data.utils) to_dense_coords() (in module MolecularDiffusion.modules.models.syncogen.data.utils) to_dense_edge_attr() (in module MolecularDiffusion.modules.models.jodo.utils) to_dense_graph() (in module MolecularDiffusion.modules.models.syncogen.data.utils) to_dense_pharmacophores() (in module MolecularDiffusion.modules.models.syncogen.data.utils) to_dgl (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) to_dict() (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) to_edge_logits (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) to_feats_out (MolecularDiffusion.modules.layers.gvp.gvp.GVP attribute) to_grid() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Embedding method) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Grid method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Embedding method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Grid method) (MolecularDiffusion.modules.layers.esen.common.so3.SO3_Grid method) to_k (MolecularDiffusion.modules.models.apo2mol.attn.RetAugmentationLinearAttention attribute) to_mol() (MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly.RDKitMoleculeAssembly method) to_numpy() (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates method) to_out (MolecularDiffusion.modules.models.chefnmr.embedders.Attention attribute) to_pc (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) to_pointcloud (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.TabascoEGNNDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.TabascoEquiformerDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.TabascoGVPDiffusionTask attribute) to_qkv (MolecularDiffusion.modules.models.chefnmr.embedders.Attention attribute) to_smiles() (MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly.RDKitMoleculeAssembly method) to_tensor() (MolecularDiffusion.modules.models.tabasco.chem.convert.MoleculeConverter method) to_tensordict (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.TabascoEGNNDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.TabascoEquiformerDiffusionTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.TabascoGVPDiffusionTask attribute) to_torch() (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates method) to_torch_const() (in module MolecularDiffusion.modules.models.apo2mol.score_model) (in module MolecularDiffusion.modules.models.diffsmol.score_model) (in module MolecularDiffusion.modules.models.kgdiff.score_model) to_v (MolecularDiffusion.modules.models.apo2mol.attn.RetAugmentationLinearAttention attribute) token_dims (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) token_drop() (MolecularDiffusion.modules.models.ldm.denoisers.dit.LabelEmbedder method) token_embeddings (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField attribute) top_k (MolecularDiffusion.modules.tasks.elucidation_generator.ElucidationGenerator attribute) topk_prompt (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) TorchMD_ET_dynamics (class in MolecularDiffusion.modules.models.etflow.torchmd) TorchMDDynamics (class in MolecularDiffusion.modules.models.etflow.torchmd) total_charge (MolecularDiffusion.utils.smilify.Molecule attribute) total_loss_weights (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) total_N (MolecularDiffusion.modules.models.jodo.noise_schedule.NoiseScheduleVP attribute) (MolecularDiffusion.modules.models.nextmol.scheduler.NoiseScheduleVPV2 attribute) total_noise() (MolecularDiffusion.modules.models.syncogen.diffusion.noise.base.NoiseBase method) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.brownian.BrownianBridgeNoise method) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.cosine.CosineNoise method) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.cosine.CosineSqrNoise method) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.geometric.GeometricNoise method) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.linear.LinearNoise method) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.loglinear.LogLinearNoise method) tp (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.TensorProductRescale attribute) train() (in module MolecularDiffusion.cli.main) (in module MolecularDiffusion.cli.train) (MolecularDiffusion.core.engine.Engine method) (MolecularDiffusion.modules.models.ipdiff.bapnet.BAPNet method) (MolecularDiffusion.molcraftdiff.MolCraftDiff method) train_dataloader() (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule method) train_file (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataModule attribute) (MolecularDiffusion.data.component.diffdec_data.DiffDecDataModule attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataModule attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataModule attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataModule attribute) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataModule attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataModule attribute) train_length_probs (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenSizePrior attribute) train_length_values (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.SyncogenSizePrior attribute) train_main() (in module MolecularDiffusion.cli.train) train_pkl (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) train_ratio (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) train_rot_align (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) train_set (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataModule attribute) (MolecularDiffusion.data.component.diffdec_data.DiffDecDataModule attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataModule attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataModule attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataModule attribute) (MolecularDiffusion.data.component.goflow_data.GoFlowDataModule attribute) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataModule attribute) (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataModule attribute) (MolecularDiffusion.modules.models.syncogen.datamodule.SyncogenDataModule attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsbdd.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_loqi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_nextmol.NextMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_pmdm.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_egnn.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_equiformer.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco_gvp.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gcdm.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_gfmdiff.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_painn.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) train_sigma_args (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion attribute) train_sigma_distribution() (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion method) train_sigma_distribution_type (MolecularDiffusion.modules.models.chefnmr.diffusion.AtomDiffusion attribute) train_size (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) TRAIN_SMILES (in module MolecularDiffusion.modules.models.syncogen.constants.constants) trainable (MolecularDiffusion.modules.layers.esen.nn.gaussian_embedding.GaussianFeatureEmbedding attribute) (MolecularDiffusion.modules.models.esen.GaussianFeatureEmbedding attribute) (MolecularDiffusion.modules.models.etflow.torchmd.ExpNormalSmearing attribute) (MolecularDiffusion.modules.models.goflow.ops.ExpNormalSmearing attribute) trainable_ae (MolecularDiffusion.modules.models.geoldm.diffusion.EnLatentDiffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) trainable_rbf (MolecularDiffusion.modules.models.etflow.torchmd.TorchMD_ET_dynamics attribute) trained (MolecularDiffusion.modules.models.chefnmr.unknown.Channel attribute), [1] training_step() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) Trans_Layer (class in MolecularDiffusion.modules.models.jodo.layers) trans_name (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_jodo.ModelTaskFactory attribute) TransBlockV2 (class in MolecularDiffusion.modules.layers.equiformer_v2.transformer_block) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block) transform (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset attribute) (MolecularDiffusion.data.component.graph3d_dataset.Graph3DDataset attribute) Transformer (class in MolecularDiffusion.modules.layers.tabasco.transformer) transformer (MolecularDiffusion.modules.models.ldm.decoders.transformer.TransformerDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.transformer.TransformerEncoder attribute) (MolecularDiffusion.modules.models.transformer_dynamics.TransformerDynamics attribute) transformer_config (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) TransformerBlock (class in MolecularDiffusion.modules.layers.tabasco.transformer) TransformerDecoder (class in MolecularDiffusion.modules.models.ldm.decoders.transformer) TransformerDynamics (class in MolecularDiffusion.modules.models.transformer_dynamics) TransformerEncoder (class in MolecularDiffusion.modules.models.chefnmr.embedders) (class in MolecularDiffusion.modules.models.ldm.encoders.transformer) TransformerModule (class in MolecularDiffusion.modules.layers.tabasco.transformer_module) Transition (class in MolecularDiffusion.modules.layers.tabasco.transition) transition (MolecularDiffusion.modules.tasks.diffusion_midi.ModelTaskFactory attribute) translate_to_origine() (in module MolecularDiffusion.utils.geom_constraint) (in module MolecularDiffusion.utils.geom_utils) TransMixLayer (class in MolecularDiffusion.modules.models.jodo.layers) Transpose (class in MolecularDiffusion.modules.models.diffspectra.specformer_layers) Tree (class in MolecularDiffusion.core.core) tri_dim (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer attribute) TriTransLayer (class in MolecularDiffusion.modules.layers.gfmdiff.blocks) TRUNCATED_NORMAL_STDDEV (in module MolecularDiffusion.modules.layers.e3x.initializers) truncation (MolecularDiffusion.utils.pretty.PrettyPrinter attribute) ts_guess (MolecularDiffusion.modules.models.reactot.en_sb.EnSB attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) TS_IDX (in module MolecularDiffusion.modules.models.reactot.en_sb) TS_INDEX (in module MolecularDiffusion.data.component.oareactdiff_data) ts_pos (MolecularDiffusion.data.component.reaction_data.Reaction attribute), [1] TSGenerator (class in MolecularDiffusion.modules.tasks.ts_generator) TSTEncoder (class in MolecularDiffusion.modules.models.diffspectra.specformer) TSTEncoderLayer (class in MolecularDiffusion.modules.models.diffspectra.specformer) TSTiEncoder (class in MolecularDiffusion.modules.models.diffspectra.specformer) tversky_func() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring) tversky_func_np() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring_np) type_grad_weight (MolecularDiffusion.modules.tasks.diffusion_kgdiff.KGDiffPocketGenerator attribute) type_head (MolecularDiffusion.modules.tasks.ssl3d.MaskedAtomTypeObjective attribute) types (MolecularDiffusion.modules.tasks.diffusion_nextmol.MoleculeFeatureCache attribute) U UFFBoundGuidance (class in MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance) UMAFeaturizer (class in MolecularDiffusion.runmodes.analyze.featurize) unconditional_generation() (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory method) uniform (MolecularDiffusion.modules.models.tabasco.flow.utils.HistogramTimeDistribution attribute) uniform() (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates class method) uniform_simplex_prior() (in module MolecularDiffusion.modules.models.flowmol.priors) UniTransformerO2TwoUpdateGeneral (class in MolecularDiffusion.modules.models.apo2mol.uni_transformer) (class in MolecularDiffusion.modules.models.diffsmol.uni_transformer) (class in MolecularDiffusion.modules.models.kgdiff.uni_transformer) unmasked_bbs (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) unmasked_rxns (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph property) unnormalize() (MolecularDiffusion.modules.models.difflinker.edm.EDM method) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) (MolecularDiffusion.modules.models.oareactdiff.normalizer.Normalizer method) unnormalize_z() (MolecularDiffusion.modules.models.difflinker.edm.EDM method) (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) (MolecularDiffusion.modules.models.diffsbdd.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnLatentDiffusion method) (MolecularDiffusion.modules.models.geoldm.diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.models.ligandiff.edm.EDM method) (MolecularDiffusion.modules.models.oareactdiff.normalizer.Normalizer method) UNREACHABLE_HOPS (in module MolecularDiffusion.modules.models.ditmc.embedding) (in module MolecularDiffusion.modules.models.ditmc.graph_features) unsorted_segment_sum() (in module MolecularDiffusion.modules.layers.conv) (in module MolecularDiffusion.modules.models.apo2mol.pminet) (in module MolecularDiffusion.modules.models.difflinker.egnn) (in module MolecularDiffusion.modules.models.diffpharma.egnn) (in module MolecularDiffusion.modules.models.diffsbdd.egnn) (in module MolecularDiffusion.modules.models.geoldm.egnn) (in module MolecularDiffusion.modules.models.ipdiff.bapnet) (in module MolecularDiffusion.modules.models.oareactdiff.leftnet) UNSPECIFIED_EDGE_TYPE (in module MolecularDiffusion.modules.models.etflow.flow) unsqueeze_like() (in module MolecularDiffusion.modules.models.etflow.flow) unsqueeze_xdim() (in module MolecularDiffusion.modules.models.reactot.schedule) unwrap_forward() (MolecularDiffusion.modules.models.egcl.EGNN_dynamics method) (MolecularDiffusion.modules.models.egt.EGT_dynamics method) (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics method) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_decoder_QM9 method) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_dynamics_QM9 method) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_encoder_QM9 method) (MolecularDiffusion.modules.models.gfmdiff.dynamics.GFMDiffDynamics method) (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN method) (MolecularDiffusion.modules.models.painn_dynamics.PaiNNDynamics method) update (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) update() (MolecularDiffusion.core.meter.Meter method) (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention method) (MolecularDiffusion.modules.models.goflow.gotennet.GATA method) (MolecularDiffusion.modules.models.ligandiff.conv_layer.GVPMessagePassing method) (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiMessage method) (MolecularDiffusion.modules.models.syncogen.models.ema.ExponentialMovingAverage method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.AtomFractionMetric method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.AtomTypeDistribution method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularConnectivity method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularDiversity method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularLipinski method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularLogP method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularNovelty method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularQEDValue method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularUniqueness method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularValidity method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.PoseBustersValidity method) (MolecularDiffusion.modules.models.tabasco.utils.metrics.PoseCheckStrainEnergy method) update_atom_graph() (MolecularDiffusion.modules.models.syncogen.api.rdkit.assembly.RDKitMoleculeAssembly method) update_average() (MolecularDiffusion.callbacks.train_helper.EMA method) update_device() (MolecularDiffusion.modules.models.flowmol.interpolant_scheduler.InterpolantScheduler method) update_edge_w_distance (MolecularDiffusion.modules.layers.gvp.gvp.EdgeUpdate attribute) (MolecularDiffusion.modules.models.flowmol.vector_field.EdgeUpdate attribute) update_info (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) update_lambda() (MolecularDiffusion.callbacks.train_helper.SP_regularizer method) update_layer_norm (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) update_layers (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) update_model_average() (MolecularDiffusion.callbacks.train_helper.EMA method) update_mol_coordinates() (in module MolecularDiffusion.utils.shepherd_utils) update_net (MolecularDiffusion.modules.models.etflow.torchmd.GatedEquivariantBlock attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.GatedEquivariantBlock attribute) update_node_positions (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPInteractions attribute) (MolecularDiffusion.modules.models.painn_backbone.EquivNetHParams attribute) update_pocket_coords (MolecularDiffusion.modules.models.diffpharma.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.diffsbdd.dynamics.EGNNDynamics attribute) (MolecularDiffusion.modules.models.oareactdiff.dynamics.BaseDynamics attribute) (MolecularDiffusion.modules.tasks.diffusion_oareactdiff.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_reactot.ModelTaskFactory attribute) update_position (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) update_positions_with_vector_sum (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPInteractions attribute) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) update_weight() (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant method) updates (MolecularDiffusion.modules.models.painn_backbone.EquivNet attribute) upstream_int8_edge_mask (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTask attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.DiffLinkerTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_difflinker.PointCloudToDiffLinkerBatch attribute) use_adapter_module (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.equiformer_v2_dynamics.EquiformerV2_dynamics attribute) (MolecularDiffusion.modules.models.esen.eSEN_dynamics attribute) use_amp (MolecularDiffusion.modules.layers.esen.nn.utils.HeadInterface property) (MolecularDiffusion.modules.layers.graph_module.HeadInterface property) use_atom_edge_embedding (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.input_block.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) use_attn_renorm (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) use_batchnorm (MolecularDiffusion.modules.layers.vn.vn_layers.VNLinearLeakyReLU attribute) use_bias (MolecularDiffusion.modules.layers.e3x.modules.Dense attribute) (MolecularDiffusion.modules.models.ditmc.layers.EquivariantLayerNorm attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.TensorProductRescale attribute) use_by_ind (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) use_c_mask_token (MolecularDiffusion.modules.models.chefnmr.embedders.NMRSpectraEmbedder attribute) use_classifier_guide (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) use_cnmr (MolecularDiffusion.modules.models.chefnmr.embedders.NMRSpectraEmbedder attribute) use_compat (MolecularDiffusion.modules.models.syncogen.core.Diffusion attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) use_cross_product (MolecularDiffusion.modules.models.loqi.fn_model.XEGNNK attribute) use_dst_feats (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) use_envelope (MolecularDiffusion.modules.layers.esen.esen_block.Edgewise attribute) (MolecularDiffusion.modules.layers.esen.esen_block.eSEN_Block attribute) (MolecularDiffusion.modules.layers.esen.nn.embedding.EdgeDegreeEmbedding attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.runmodes.train.tasks_esen.ModelTaskFactory attribute) use_eot (MolecularDiffusion.modules.models.equifm.cnflows.Cnflows attribute) (MolecularDiffusion.modules.tasks.diffusion_equifm.EquiFMTaskFactory attribute) use_gate_act (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) use_gcp_dropout (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPLayerConfig attribute) use_gcp_norm (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPLayerConfig attribute) (MolecularDiffusion.modules.models.gcdm.gcp_utils.GCPLayerNorm attribute) use_grid_mlp (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) use_h_mask_token (MolecularDiffusion.modules.models.chefnmr.embedders.NMRSpectraEmbedder attribute) use_hnmr (MolecularDiffusion.modules.models.chefnmr.embedders.NMRSpectraEmbedder attribute) use_holo_reference (MolecularDiffusion.modules.tasks.diffusion_apo2mol.Apo2MolPocketGenerator attribute) use_m_share_rad (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) use_noised_conditioning (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) use_ohe (MolecularDiffusion.data.component.feature.NodeFeaturizer attribute) use_ohe_feature (MolecularDiffusion.runmodes.train.data.DataModule attribute) use_pbc (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) use_pbc_single (MolecularDiffusion.modules.models.esen.eSEN_Backbone attribute) use_posebuster (MolecularDiffusion.core.lightning_callbacks.generative_eval_callback.GenerativeEvalCallback attribute) use_residual_message_gcp (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPLayerConfig attribute) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPMessagePassing attribute) use_residue (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) use_rotary (MolecularDiffusion.modules.models.loqi.fn_model.DiTeBlock attribute) use_row_data_features (MolecularDiffusion.runmodes.train.data.DataModule attribute) use_s2_act_attn (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) use_scalar_message_attention (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPLayerConfig attribute) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPMessagePassing attribute) use_scale (MolecularDiffusion.modules.models.ditmc.layers.EquivariantLayerNorm attribute) use_sep_s2_act (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) use_shape_vec_mul (MolecularDiffusion.modules.models.diffsmol.uni_transformer.BaseGVPAttLayer attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) use_source_target_embedding (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2SymmetricTensorHead attribute) use_stored_split (MolecularDiffusion.runmodes.train.data.DataModule attribute) used_spectra_type (MolecularDiffusion.modules.models.diffspectra.specformer.TSTiEncoder attribute) uv (MolecularDiffusion.modules.tasks.diffusion_diffspectra.DiffSpectraRecord attribute) V v (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.ligandiff.gvp.GVP attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) v_a_proj (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer attribute) v_add (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer attribute) v_e_proj (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer attribute) v_inference (MolecularDiffusion.modules.models.apo2mol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.kgdiff.score_model.ScorePosNet3D attribute) v_message_dim (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) v_mode (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) v_net_type (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) v_proj (MolecularDiffusion.modules.layers.gfmdiff.blocks.NodeTransformerLayer attribute) (MolecularDiffusion.modules.layers.gfmdiff.blocks.TriTransLayer attribute) (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) VAB_2nd_order() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap) VAB_2nd_order_batched() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap) VAB_2nd_order_cosine() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap) VAB_2nd_order_cosine_mask() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap) VAB_2nd_order_cosine_mask_batch() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap) VAB_2nd_order_cosine_np() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap_np) VAB_2nd_order_esp() (in module MolecularDiffusion.utils.shepherd_score.score.electrostatic_scoring) VAB_2nd_order_esp_np() (in module MolecularDiffusion.utils.shepherd_score.score.electrostatic_scoring_np) VAB_2nd_order_full() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap) VAB_2nd_order_mask() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap) VAB_2nd_order_mask_batch() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap) VAB_2nd_order_np() (in module MolecularDiffusion.utils.shepherd_score.score.gaussian_overlap_np) vae_ckpt (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) vae_config (MolecularDiffusion.modules.tasks.diffusion_geoldm.GeoLDMTaskFactory attribute) VAETask (class in MolecularDiffusion.modules.tasks.diffusion_ldm) VAETaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_ldm) val_dataloader() (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule method) val_file (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataModule attribute) (MolecularDiffusion.data.component.diffdec_data.DiffDecDataModule attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataModule attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataModule attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataModule attribute) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataModule attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataModule attribute) valence_electrons (in module MolecularDiffusion.utils.xyz2mol.converter) valenceelectrons (MolecularDiffusion.utils.xyz2mol.elements.ElementData attribute) valences_not_too_large() (in module MolecularDiffusion.utils.xyz2mol.converter) valencies (MolecularDiffusion.data.component.graph3d_dataset.Graph3DStats attribute) valid_pkl (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) valid_seed (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) valid_set (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.data.component.apo2mol_data.Apo2MolDataModule attribute) (MolecularDiffusion.data.component.diffdec_data.DiffDecDataModule attribute) (MolecularDiffusion.data.component.diffint_data.DiffIntDataModule attribute) (MolecularDiffusion.data.component.diffpharma_data.DiffPharmaDataModule attribute) (MolecularDiffusion.data.component.diffsbdd_data.DiffSBDDDataModule attribute) (MolecularDiffusion.data.component.goflow_data.GoFlowDataModule attribute) (MolecularDiffusion.data.component.kgdiff_data.KGDiffDataModule attribute) (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.data.component.pmdm_data.PMDMDataModule attribute) (MolecularDiffusion.modules.models.syncogen.datamodule.SyncogenDataModule attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) valid_valencies (in module MolecularDiffusion.utils.geom_constant) validate() (MolecularDiffusion.data.component.reaction_data.ReactionSide method) (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) validate_original_weights (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA attribute) validation_interval (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) validation_size (MolecularDiffusion.modules.models.syncogen.data.dataloader.SyncogenDataManager attribute) validation_step() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) validity_filter (MolecularDiffusion.modules.tasks.diffusion_pmdm.PMDMPocketGenerator attribute) value (MolecularDiffusion.modules.layers.e3x.modules.SelfAttention attribute) values() (MolecularDiffusion.modules.layers.atomic_data.AtomicData method) variadic_accuracy() (in module MolecularDiffusion.modules.tasks.metrics) variadic_arange() (in module MolecularDiffusion.modules.layers.functional) variadic_area_under_prc() (in module MolecularDiffusion.modules.tasks.metrics) variadic_area_under_roc() (in module MolecularDiffusion.modules.tasks.metrics) variadic_cross_entropy() (in module MolecularDiffusion.modules.layers.functional) variadic_log_softmax() (in module MolecularDiffusion.modules.layers.functional) variadic_max() (in module MolecularDiffusion.modules.layers.functional) variadic_mean() (in module MolecularDiffusion.modules.layers.functional) variadic_meshgrid() (in module MolecularDiffusion.modules.layers.functional) variadic_randperm() (in module MolecularDiffusion.modules.layers.functional) variadic_sample() (in module MolecularDiffusion.modules.layers.functional) variadic_softmax() (in module MolecularDiffusion.modules.layers.functional) variadic_sort() (in module MolecularDiffusion.modules.layers.functional) variadic_sum() (in module MolecularDiffusion.modules.layers.functional) variadic_to_padded() (in module MolecularDiffusion.modules.layers.functional) variadic_top_precision() (in module MolecularDiffusion.modules.tasks.metrics) variadic_topk() (in module MolecularDiffusion.modules.layers.functional) VariadicOption (class in MolecularDiffusion.cli.data) variant (MolecularDiffusion.modules.models.ditmc.dit.GenerativeModel attribute) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTask attribute) (MolecularDiffusion.modules.tasks.diffusion_ditmc.DiTMCTaskFactory attribute) VARIANTS (in module MolecularDiffusion.modules.models.ditmc.build) vec (MolecularDiffusion.modules.models.oareactdiff.leftnet.LEFTNet attribute) vec1_proj (MolecularDiffusion.modules.models.etflow.torchmd.GatedEquivariantBlock attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.GatedEquivariantBlock attribute) vec2_proj (MolecularDiffusion.modules.models.etflow.torchmd.GatedEquivariantBlock attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.GatedEquivariantBlock attribute) Vec2AttnHeads (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) vec_hidden_dim (MolecularDiffusion.modules.models.diffsmol.score_model.ScorePosNet3D attribute) (MolecularDiffusion.modules.models.diffsmol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) vec_proj (MolecularDiffusion.modules.models.etflow.torchmd.EquivariantMultiHeadAttention attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiUpdate attribute) VecLayerNorm (class in MolecularDiffusion.modules.models.goflow.ops) vector (class in MolecularDiffusion.modules.models.oareactdiff.leftnet) (MolecularDiffusion.modules.models.gcdm.gcp_utils.ScalarVector property) vector_activation (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) vector_dropout (MolecularDiffusion.modules.layers.gvp.gvp.GVPDropout attribute) (MolecularDiffusion.modules.models.gcdm.gcp_utils.GCPDropout attribute) vector_field (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolFlowMatchingTask attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTask attribute) vector_field() (MolecularDiffusion.modules.models.flowmol.vector_field.EndpointVectorField method) (MolecularDiffusion.modules.models.flowmol_graph3d.vector_field.EndpointVectorField static method) (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant method) vector_field_config (MolecularDiffusion.modules.tasks.diffusion_flowmol.FlowMolTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_flowmol_graph3d.FlowMolGraph3DTaskFactory attribute) vector_field_type (MolecularDiffusion.modules.models.loqi.interpolant.ContinuousFlowMatchingInterpolant attribute) vector_frame_residual (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) vector_gate (MolecularDiffusion.modules.models.diffsmol.common.GVP attribute) (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) (MolecularDiffusion.modules.models.ligandiff.gvp.GVP attribute) vector_mask (MolecularDiffusion.modules.models.loqi.self_conditioning.BaseSelfConditioningModule attribute) vector_nonlinearity (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) vector_norm_ (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) vector_output (MolecularDiffusion.modules.models.etflow.torchmd.GatedEquivariantBlock attribute) vector_residual (MolecularDiffusion.modules.models.gcdm.gcp_layers.GCPModuleConfig attribute) vector_size (MolecularDiffusion.modules.layers.gvp.gvp.GVPConv attribute) VectorDropout (class in MolecularDiffusion.modules.models.gcdm.gcp_utils) vectorize() (in module MolecularDiffusion.modules.models.gcdm.gcp_utils) vectors_activation (MolecularDiffusion.modules.layers.gvp.gvp.GVP attribute) vel_SO3_grid (MolecularDiffusion.modules.models.equiformer_v2_dynamics.EquiformerV2_dynamics attribute) verbose (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) verify() (in module MolecularDiffusion.assets) verify_cmd() (in module MolecularDiffusion.cli.zoo) verify_datapoint() (in module MolecularDiffusion.runmodes.data.ase_ops) verify_db() (in module MolecularDiffusion.runmodes.data.graph3d_import) vertices_labels (in module MolecularDiffusion.utils.geom_constant) vn1 (MolecularDiffusion.modules.layers.vn.vn_layers.VNStdFeature attribute) vn2 (MolecularDiffusion.modules.layers.vn.vn_layers.VNStdFeature attribute) vn_lin (MolecularDiffusion.modules.layers.vn.vn_layers.VNStdFeature attribute) VNBatchNorm (class in MolecularDiffusion.modules.layers.vn.vn_layers) VNDGCNNEncoder (class in MolecularDiffusion.modules.models.diffsmol.shape_ae) VNLeakyReLU (class in MolecularDiffusion.modules.layers.vn.vn_layers) VNLinear (class in MolecularDiffusion.modules.layers.vn.vn_layers) VNLinearLeakyReLU (class in MolecularDiffusion.modules.layers.vn.vn_layers) VNMaxPool (class in MolecularDiffusion.modules.layers.vn.vn_layers) vnode_idx (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM attribute) VNResnetBlockFC (class in MolecularDiffusion.modules.layers.vn.vn_layers) VNResnetEncoder (class in MolecularDiffusion.modules.models.diffsmol.shape_ae) VNStdFeature (class in MolecularDiffusion.modules.layers.vn.vn_layers) vocab_dir (MolecularDiffusion.modules.models.syncogen.datamodule.SyncogenDataModule attribute) (MolecularDiffusion.modules.tasks.diffusion_syncogen.ModelTaskFactory attribute) vocab_map() (MolecularDiffusion.modules.tasks.diffusion_loqi.Graph3DToLoQIAdapter method) VOCAB_NUM_BBS (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph attribute) VOCAB_NUM_CENTERS (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph attribute) VOCAB_NUM_RXNS (MolecularDiffusion.modules.models.syncogen.api.graph.graph.BBRxnGraph attribute) volume_bins (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeNodeDistribution attribute) volume_hist (MolecularDiffusion.modules.tasks.diffusion_diffsmol.DiffSMolShapeNodeDistribution attribute) vp_interpolate() (in module MolecularDiffusion.modules.models.equifm.paths) vp_issnr_schedule() (in module MolecularDiffusion.modules.models.en_diffusion) vp_smld_schedule() (in module MolecularDiffusion.modules.models.en_diffusion) vs() (MolecularDiffusion.modules.models.gcdm.gcp_utils.ScalarVector method) W w (MolecularDiffusion.modules.layers.equiformer_v2.activation.ScaledSwiGLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2.activation.SwiGLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.ScaledSwiGLU attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.SwiGLU attribute) W_h (MolecularDiffusion.modules.models.ligandiff.gvp.GVP attribute) W_m (MolecularDiffusion.modules.models.ligandiff.gvp.GVP attribute) W_mu (MolecularDiffusion.modules.models.ligandiff.gvp.GVP attribute) W_P (MolecularDiffusion.modules.models.diffspectra.specformer.TSTiEncoder attribute) w_re (MolecularDiffusion.modules.models.goflow.gotennet.GATA attribute) w_vu (MolecularDiffusion.modules.models.goflow.gotennet.EQFF attribute) WandbLogger (class in MolecularDiffusion.core.logger) warm_up_steps (MolecularDiffusion.callbacks.train_helper.SP_regularizer attribute) weight (MolecularDiffusion.modules.layers.conv.SE3Norm attribute) (MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf.GaussianRadialBasisLayer attribute) (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_LinearV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf.GaussianRadialBasisLayer attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_LinearV2 attribute) (MolecularDiffusion.modules.layers.esen.nn.so3_layers.SO3_Linear attribute) (MolecularDiffusion.modules.models.difflinker.noise.PositiveLinear attribute) (MolecularDiffusion.modules.models.en_diffusion.PositiveLinear attribute) (MolecularDiffusion.modules.models.ligandiff.noise.PositiveLinear attribute) (MolecularDiffusion.modules.models.midi.layers.SE3Norm attribute) (MolecularDiffusion.modules.models.syncogen.diffusion.noise.brownian.BrownianBridgeNoise attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.SE3Norm attribute) (MolecularDiffusion.modules.tasks.ssl3d.SSL3DObjective attribute) weight_decay (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) WEIGHT_FACTOR (in module MolecularDiffusion.utils.geom_constraint) weight_init (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.goflow.ops.Dense attribute) (MolecularDiffusion.modules.models.goflow.outputs.SNNDense attribute) (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.ligandiff.egnn.DenseLayer attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) weight_init_offset (MolecularDiffusion.modules.models.difflinker.noise.PositiveLinear attribute) (MolecularDiffusion.modules.models.en_diffusion.PositiveLinear attribute) (MolecularDiffusion.modules.models.ligandiff.noise.PositiveLinear attribute) weighted_loss_bool (MolecularDiffusion.modules.models.ditmc.flow_matching.FlowMatching attribute) weights (MolecularDiffusion.modules.models.jodo.layers.LearnedSinusodialposEmb attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.GraphNorm attribute) (MolecularDiffusion.modules.models.syncogen.models.layers.SetNorm attribute) Wh (MolecularDiffusion.modules.layers.gvp.gvp.GVP attribute) white_noise_sampling_scale (MolecularDiffusion.modules.models.tabasco.flow.interpolate.SDEMetricInterpolant attribute) wigner_D() (in module MolecularDiffusion.modules.layers.equiformer_v2.wigner) (in module MolecularDiffusion.modules.layers.equiformer_v2_s.wigner) (in module MolecularDiffusion.modules.layers.esen.common.rotation) with_hydrogen (MolecularDiffusion.data.component.dataset.LazyChunkedDataset attribute) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) world_size (MolecularDiffusion.core.engine.Engine attribute) wrap_forward() (MolecularDiffusion.modules.models.egcl.EGNN_dynamics method) (MolecularDiffusion.modules.models.egt.EGT_dynamics method) (MolecularDiffusion.modules.models.gcdm.dynamics.GCDMDynamics method) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_decoder_QM9 method) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_dynamics_QM9 method) (MolecularDiffusion.modules.models.geoldm.networks.EGNN_encoder_QM9 method) (MolecularDiffusion.modules.models.gfmdiff.dynamics.GFMDiffDynamics method) (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN method) (MolecularDiffusion.modules.models.painn_dynamics.PaiNNDynamics method) write_graph3d_db() (in module MolecularDiffusion.runmodes.data.graph3d_import) write_pocket_pdb() (in module MolecularDiffusion.data.component.pmdm_data) (in module MolecularDiffusion.modules.tasks.diffusion_apo2mol) write_xyz() (in module MolecularDiffusion.runmodes.data.augmentation) write_xyz_file() (in module MolecularDiffusion.modules.models.tabasco.chem.utils) Wu (MolecularDiffusion.modules.layers.gvp.gvp.GVP attribute) X x (MolecularDiffusion.data.component.pointcloud.Atom attribute) X (MolecularDiffusion.modules.models.midi.placeholder.Dims attribute) (MolecularDiffusion.modules.models.midi.placeholder.PlaceHolder attribute) x1 (MolecularDiffusion.modules.models.ditmc.graphs.LatentGraph attribute) x1_bond_diffusion (MolecularDiffusion.modules.models.shepherd_arch.model.Model attribute) x2h_layers (MolecularDiffusion.modules.models.apo2mol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) x2h_out_fc (MolecularDiffusion.modules.models.apo2mol.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.apo2mol.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.AttentionLayerO2TwoUpdateNodeGeneral attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.UniTransformerO2TwoUpdateGeneral attribute) x_0 (MolecularDiffusion.modules.models.tabasco.flow.path.FlowPath attribute) x_1 (MolecularDiffusion.modules.models.tabasco.flow.path.FlowPath attribute) X_atomtofrag_out (MolecularDiffusion.modules.models.syncogen.models.semla.SemlaGenerator attribute) (MolecularDiffusion.modules.models.syncogen.models.semla_pharm.SemlaPharmGenerator attribute) x_channels (MolecularDiffusion.modules.models.jodo.layers.EdgeGateTransLayer attribute) (MolecularDiffusion.modules.models.jodo.layers.Trans_Layer attribute) (MolecularDiffusion.modules.models.jodo.layers.TransMixLayer attribute) X_classes (MolecularDiffusion.modules.models.midi.noise_model.DiscreteUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.MarginalUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) x_e_mul1 (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) x_e_mul2 (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) x_embedder (MolecularDiffusion.modules.models.chefnmr.score_models.DiffusionModuleTransformer attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT attribute) x_h_nan_idx (MolecularDiffusion.modules.models.difflinker.utils.FoundNaNException attribute) (MolecularDiffusion.modules.models.ligandiff.utils.FoundNaNException attribute) x_layernorm (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiMessage attribute) (MolecularDiffusion.modules.models.oareactdiff.leftnet.GCLMessage attribute) X_marginals (MolecularDiffusion.modules.models.midi.noise_model.DiscreteUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.MarginalUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) x_norm (MolecularDiffusion.modules.models.loqi.fn_model.XEGNNK attribute) x_out (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) x_proj (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiMessage attribute) x_t (MolecularDiffusion.modules.models.tabasco.flow.path.FlowPath attribute) xedge_layer_norm (MolecularDiffusion.modules.layers.esen.nn.rank2.Rank2SymmetricTensorHead attribute), [1] XEGNNK (class in MolecularDiffusion.modules.models.loqi.fn_model) XEyTransformerLayer (class in MolecularDiffusion.modules.layers.conv) (class in MolecularDiffusion.modules.models.midi.transformer_model) xh_embedding (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) xh_embedding_out (MolecularDiffusion.modules.models.gfmdiff.equignn.EquiGNN attribute) xh_given_zt_and_epsilon() (MolecularDiffusion.modules.models.diffpharma.conditional_ddpm.ConditionalDDPM method) xk_func (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseH2XAttLayer attribute) xq_func (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseH2XAttLayer attribute) xtb_available() (in module MolecularDiffusion.runmodes.analyze.conformer_metrics) xtb_electronic() (in module MolecularDiffusion.cli.analyze) xtb_energy (MolecularDiffusion.runmodes.generate.tasks_conformer.ConformerFactory attribute) Xtoy (class in MolecularDiffusion.modules.layers.conv) (class in MolecularDiffusion.modules.models.midi.layers) (class in MolecularDiffusion.modules.models.syncogen.models.layers) xv_func (MolecularDiffusion.modules.models.apo2mol.uni_transformer.BaseH2XAttLayer attribute) (MolecularDiffusion.modules.models.kgdiff.uni_transformer.BaseH2XAttLayer attribute) xvec_proj (MolecularDiffusion.modules.models.oareactdiff.leftnet.EquiUpdate attribute) xyz2mol() (in module MolecularDiffusion.cli.analyze) (in module MolecularDiffusion.cli.predict) (in module MolecularDiffusion.utils.xyz2mol.converter) xyz2mol_converter() (in module MolecularDiffusion.runmodes.analyze.compare_to_optimized) xyz2mol_openbabel() (in module MolecularDiffusion.runmodes.analyze.compare_to_optimized) xyz_dir (MolecularDiffusion.runmodes.train.data.DataModule attribute) xyz_to_pdb() (in module MolecularDiffusion.utils.geom_metrics) xyz_to_rdkit_mol() (in module MolecularDiffusion.utils.geom_metrics) Y y (MolecularDiffusion.data.component.pointcloud.Atom attribute) (MolecularDiffusion.modules.models.midi.placeholder.Dims attribute) (MolecularDiffusion.modules.models.midi.placeholder.PlaceHolder attribute) y_classes (MolecularDiffusion.modules.models.midi.noise_model.DiscreteUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.MarginalUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) y_e_add (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) y_e_mul (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) y_embedder (MolecularDiffusion.modules.models.chefnmr.score_models.DiffusionModuleTransformer attribute) y_marginals (MolecularDiffusion.modules.models.midi.noise_model.DiscreteUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.MarginalUniformTransition attribute) (MolecularDiffusion.modules.models.midi.noise_model.NoiseModel attribute) y_x_add (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) y_x_mul (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.models.midi.transformer_model.NodeEdgeBlock attribute) YTOL (in module MolecularDiffusion.modules.layers.esen.common.rotation) Z z (MolecularDiffusion.data.component.pointcloud.Atom attribute) (MolecularDiffusion.data.component.reaction_data.Reaction attribute), [1] z_dim (MolecularDiffusion.modules.models.diffsmol.shape_ae.DecoderInner attribute) zero_before (MolecularDiffusion.modules.models.tabasco.flow.time_factor.BaseTimeFactor attribute) zero_charge (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffDataModule attribute) (MolecularDiffusion.data.component.oareactdiff_data.OAReactDiffTS1xDataset attribute) zeros() (MolecularDiffusion.modules.models.syncogen.api.atomics.coordinates.Coordinates class method) zeros_initializer (in module MolecularDiffusion.modules.models.goflow.ops) ZeroSampleNoiseSchedule (class in MolecularDiffusion.modules.models.tabasco.sample.noise_schedule) ZeroTimeFactor (class in MolecularDiffusion.modules.models.tabasco.flow.time_factor) zoo() (in module MolecularDiffusion.cli.zoo)