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) 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.models.ldm.denoisers.dit.Mlp attribute) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.SiLUSmearing attribute) act_fn (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_scalars (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Gate attribute) Activation (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) activation (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) activation_type (MolecularDiffusion.modules.layers.tabasco.transition.Transition attribute) acts (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Activation attribute) adaln_beta (MolecularDiffusion.modules.layers.tabasco.attention.AdaLNAttention attribute) (MolecularDiffusion.modules.layers.tabasco.attention.CrossAdaLNAttention attribute) adaln_gamma (MolecularDiffusion.modules.layers.tabasco.attention.AdaLNAttention attribute) (MolecularDiffusion.modules.layers.tabasco.attention.CrossAdaLNAttention attribute) adaLN_modulation (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiTBlock attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.FinalLayer attribute) AdaLNAttention (class in MolecularDiffusion.modules.layers.tabasco.attention) adapter_module (MolecularDiffusion.modules.models.egcl.EGNN attribute) add() (MolecularDiffusion.callbacks.train_helper.Queue method) (MolecularDiffusion.utils.geom_analyzer.Histogram_cont method) (MolecularDiffusion.utils.geom_analyzer.Histogram_discrete method) add_h_unit() (in module MolecularDiffusion.runmodes.data.augmentation) add_param_group() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer method) add_random_permutation (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional.UnconditionalLMDBDataset attribute) add_random_rotation (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional.UnconditionalLMDBDataset attribute) add_sinusoid_posenc (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule 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) 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.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) aggregation_method (MolecularDiffusion.modules.layers.conv.EquivariantBlock attribute) (MolecularDiffusion.modules.layers.conv.EquivariantUpdate attribute) (MolecularDiffusion.modules.layers.conv.GCL attribute) (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) align_atoms() (in module MolecularDiffusion.runmodes.data.preparation) align_target_with_reference() (in module MolecularDiffusion.utils.geom_constraint) all_parameters() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer method) all_smiles (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional.UnconditionalLMDBDataset attribute) 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.shepherd_arch.equiformer_operations.SmoothLeakyReLU attribute) alpha() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion 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) analyze() (in module MolecularDiffusion.cli.analyze) analyze_and_save() (in module MolecularDiffusion.runmodes.train.eval) analyze_node_distribution() (in module MolecularDiffusion.utils.geom_analyzer) analyze_stability_for_molecules() (in module MolecularDiffusion.utils.geom_analyzer) 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_RELAX (in module MolecularDiffusion.runmodes.train.eval) annotate_cmd() (in module MolecularDiffusion.cli.data) annotate_db() (in module MolecularDiffusion.runmodes.data.preparation) append() (MolecularDiffusion.data.dataloader.DataQueue method) append_gt_array() (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator method) append_pred_array() (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator method) apply_mask() (in module MolecularDiffusion.modules.models.tabasco.utils.tensor_ops) 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) area_under_prc() (in module MolecularDiffusion.modules.tasks.metrics) area_under_roc() (in module MolecularDiffusion.modules.tasks.metrics) artifact_to_mols() (in module MolecularDiffusion.modules.models.tabasco.utils.artifacts) 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) assert_correctly_masked() (in module MolecularDiffusion.utils.geom_utils) assert_mean_zero() (in module MolecularDiffusion.utils.geom_utils) assert_mean_zero_with_mask() (in module MolecularDiffusion.utils.geom_utils) Atom (class in MolecularDiffusion.data.component.pointcloud) atom_center_identification() (in module MolecularDiffusion.data.component.feature) ATOM_COLOR_MAP (in module MolecularDiffusion.modules.models.tabasco.chem.constants) atom_default() (in module MolecularDiffusion.data.component.feature) atom_explicit_property_prediction() (in module MolecularDiffusion.data.component.feature) 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_NAMES (in module MolecularDiffusion.modules.models.tabasco.chem.constants) atom_names (MolecularDiffusion.modules.models.tabasco.utils.metrics.AtomTypeDistribution attribute) 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_topological() (in module MolecularDiffusion.data.component.feature) 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_types() (MolecularDiffusion.data.component.dataset.GraphDataset method) (MolecularDiffusion.data.component.dataset.PointCloudDataset method) 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.feature.NodeFeaturizer attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) AtomFractionMetric (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) ATOMIC_LEVEL_GROUPS (in module MolecularDiffusion.runmodes.analyze.xtb_electronic) atomic_valence (in module MolecularDiffusion.utils.xyz2mol.converter) atomic_valence_electrons (in module MolecularDiffusion.utils.xyz2mol.converter) atomics_interpolant (MolecularDiffusion.modules.models.tabasco.flow_model.FlowMatchingModel attribute) atomics_interpolant_config (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) AtomTypeDistribution (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) attempt_sanitize() (in module MolecularDiffusion.modules.models.tabasco.chem.utils) Attention (class in MolecularDiffusion.modules.layers.tabasco.attention) attention (MolecularDiffusion.modules.layers.conv.GCL attribute) (MolecularDiffusion.modules.layers.tabasco.attention.AttentionBlock attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) AttentionBlock (class in MolecularDiffusion.modules.layers.tabasco.attention) attn (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiTBlock 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.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_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_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) 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_ldm.VAETask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory 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) 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) avg_aggregate_num (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.ScaledScatter attribute) B BASE_ATOM_VOCAB (in module MolecularDiffusion.data.component.dataset) BaseLMDBDataset (class in MolecularDiffusion.modules.models.tabasco.data.components.lmdb_base) BaseModel (class in MolecularDiffusion.modules.models.shepherd_arch.ocp_compat) BaseNoiseSchedule (class in MolecularDiffusion.modules.models.tabasco.sample.noise_schedule) BaseTimeFactor (class in MolecularDiffusion.modules.models.tabasco.flow.time_factor) BasicMolecularMetrics (class in MolecularDiffusion.utils.geom_analyzer) batch_id (MolecularDiffusion.core.meter.Meter attribute) batch_size (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.modules.models.tabasco.data.lmdb_datamodule.LmdbDataModule 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_list() (in module MolecularDiffusion.modules.models.tabasco.data.utils) batch_xtb_electronic() (in module MolecularDiffusion.runmodes.analyze.xtb_electronic) beta (MolecularDiffusion.callbacks.train_helper.EMA attribute) betas (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) bin_width (MolecularDiffusion.modules.models.tabasco.flow.utils.HistogramTimeDistribution attribute) bins (MolecularDiffusion.utils.geom_analyzer.Histogram_cont attribute) (MolecularDiffusion.utils.geom_analyzer.Histogram_discrete 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.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) bond_default() (in module MolecularDiffusion.data.component.feature) bond_dict (in module MolecularDiffusion.utils.geom_analyzer) (in module MolecularDiffusion.utils.smilify) bond_feat_dim (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.BaseModel attribute) bond_length() (in module MolecularDiffusion.data.component.feature) bond_matrix (MolecularDiffusion.utils.smilify.Molecule attribute) bond_pretrain() (in module MolecularDiffusion.data.component.feature) bond_property_prediction() (in module MolecularDiffusion.data.component.feature) bond_type_to_symbol() (in module MolecularDiffusion.utils.geom_stability) bond_types_x1 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) bonds1 (in module MolecularDiffusion.utils.geom_analyzer) bonds2 (in module MolecularDiffusion.utils.geom_analyzer) bonds3 (in module MolecularDiffusion.utils.geom_analyzer) build() (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory method) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative method) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory method) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory method) build_default_noise_schedule() (in module MolecularDiffusion.data.component.pharmacophore) build_molecule() (in module MolecularDiffusion.utils.geom_analyzer) build_xae_molecule() (in module MolecularDiffusion.utils.geom_analyzer) C CalcSpherePoints() (in module MolecularDiffusion.modules.models.shepherd_arch.ocp_compat) calculate_fan_in() (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.TensorProductRescale method) calculate_props() (in module MolecularDiffusion.runmodes.data.preparation) calculate_sa_score() (in module MolecularDiffusion.runmodes.data.preparation) calculate_score() (MolecularDiffusion.modules.models.tabasco.flow.interpolate.SDEMetricInterpolant method) calculateScore() (in module MolecularDiffusion.utils.sascore) call (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) capture_rdkit_log() (in module MolecularDiffusion.utils.io) CaptureStdIO (class in MolecularDiffusion.utils.io) cat() (in module MolecularDiffusion.utils.comm) (in module MolecularDiffusion.utils.torch) categorical (MolecularDiffusion.modules.models.tabasco.flow.utils.HistogramTimeDistribution attribute) cdf_standard_gaussian() (in module MolecularDiffusion.modules.models.en_diffusion) ce_loss (MolecularDiffusion.modules.models.tabasco.flow.interpolate.DiscreteInterpolant attribute) centered (MolecularDiffusion.modules.models.tabasco.flow.interpolate.CenteredMetricInterpolant attribute) 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) cfg_file (MolecularDiffusion.modules.models.tabasco.callbacks.posebusters.PoseBustersCallback attribute) charge_cmd() (in module MolecularDiffusion.cli.data) charge_is_OK() (in module MolecularDiffusion.utils.xyz2mol.converter) charge_types_x1 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset 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.en_diffusion.EnVariationalDiffusion method) check_mask_correct() (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_xyz() (in module MolecularDiffusion.runmodes.analyze.xtb_optimization) checkpoint_path (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) Chem (in module MolecularDiffusion.data.component.dataset) (in module MolecularDiffusion.data.component.pharmacophore) (in module MolecularDiffusion.runmodes.data.ase_ops) (in module MolecularDiffusion.runmodes.data.featurization) (in module MolecularDiffusion.runmodes.data.preparation) chemical_validity() (in module MolecularDiffusion.modules.tasks.metrics) chiral_stereo_check() (in module MolecularDiffusion.utils.xyz2mol.converter) chkpt_path (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) clean_charges() (in module MolecularDiffusion.utils.xyz2mol.converter) clear() (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator method) cli() (in module MolecularDiffusion.cli.main) clip_noise_schedule() (in module MolecularDiffusion.modules.models.en_diffusion) (in module MolecularDiffusion.modules.models.noisemodel) 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.equiformer_v2.so3.SO3_Embedding method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Embedding method) coeff (MolecularDiffusion.modules.models.ldm.encoders.equiformer.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) CoefficientMappingModule (class in MolecularDiffusion.modules.layers.equiformer_v2.so3) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.so3) collate_fn (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) color_pcd_with_electrostatics() (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) comb_input_dim (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) compare() (in module MolecularDiffusion.cli.analyze) compare_graph_topology() (in module MolecularDiffusion.utils.geom_metrics) compile_cmd() (in module MolecularDiffusion.cli.data) compile_to_asedb() (in module MolecularDiffusion.runmodes.data.preparation) complex_idx() (MolecularDiffusion.modules.layers.equiformer_v2.so3.CoefficientMappingModule method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.CoefficientMappingModule method) compute() (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_atom_type_accuracy() (in module MolecularDiffusion.utils.geom_utils) compute_bond_angles_diff() (in module MolecularDiffusion.utils.geom_stability) compute_bond_lengths_diff() (in module MolecularDiffusion.utils.geom_stability) compute_coord_rmsd() (in module MolecularDiffusion.runmodes.analyze.compare_to_optimized) compute_dataset_stats() (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) 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_geom() (MolecularDiffusion.data.component.feature.NodeFeaturizer method) compute_loss() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion 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) compute_loss_distillation() (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_novelty() (MolecularDiffusion.utils.geom_analyzer.BasicMolecularMetrics method) compute_ohe() (MolecularDiffusion.data.component.feature.NodeFeaturizer method) compute_pharm_similarity() (in module MolecularDiffusion.utils.geom_metrics) 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_rmsd() (in module MolecularDiffusion.utils.geom_stability) (in module MolecularDiffusion.utils.geom_utils) compute_shape_similarity() (in module MolecularDiffusion.utils.geom_metrics) compute_statistics() (in module MolecularDiffusion.utils.geom_stability) compute_stats() (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional.UnconditionalLMDBDataset method) compute_torsion_angles_diff() (in module MolecularDiffusion.utils.geom_stability) compute_uniqueness() (MolecularDiffusion.utils.geom_analyzer.BasicMolecularMetrics method) compute_validity() (MolecularDiffusion.utils.geom_analyzer.BasicMolecularMetrics 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.en_diffusion.EnVariationalDiffusion method) compute_xtb_electronic() (in module MolecularDiffusion.runmodes.analyze.xtb_electronic) concat_combine_input (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) ConcatIrrepsTensor (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) condition (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) condition_configs (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) condition_names (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) condition_tensor (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) condition_time (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.egt.EGT_dynamics attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) conditional_generation() (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory method) conditional_grad() (in module MolecularDiffusion.modules.models.shepherd_arch.ocp_compat) Configurable (class in MolecularDiffusion.core.core) configure_optimizers() (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) context_mask_rate (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) context_node_nf (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.egt.EGT_dynamics attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) CONTEXT_SETTINGS (in module MolecularDiffusion.cli.analyze) (in module MolecularDiffusion.cli.main) 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) coord2cosine() (in module MolecularDiffusion.utils.geom_utils) coord2diff() (in module MolecularDiffusion.utils.geom_utils) coord_file (MolecularDiffusion.runmodes.train.data.DataModule attribute) coord_mlp (MolecularDiffusion.modules.layers.conv.EquivariantUpdate attribute) coord_model() (MolecularDiffusion.modules.layers.conv.EquivariantUpdate method) coordinate_mlp (MolecularDiffusion.modules.models.shepherd_arch.egnn.EGNN attribute) coords_interpolant (MolecularDiffusion.modules.models.tabasco.flow_model.FlowMatchingModel attribute) coords_interpolant_config (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) coords_range (MolecularDiffusion.modules.layers.conv.EquivariantUpdate attribute) coords_range_layer (MolecularDiffusion.modules.layers.conv.EquivariantBlock attribute) (MolecularDiffusion.modules.models.egcl.EGNN 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_batch() (MolecularDiffusion.modules.tasks.diffusion_ldm.FlowMatchingInterpolant method) cosine_beta_schedule() (in module MolecularDiffusion.modules.models.en_diffusion) cosine_schedule() (in module MolecularDiffusion.modules.models.noisemodel) 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) cov_radius() (in module MolecularDiffusion.utils.smilify) cpu() (in module MolecularDiffusion.utils.torch) cpu_group (in module MolecularDiffusion.utils.comm) cpu_offload (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA attribute) 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) criterion (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) cross_attention (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) CrossAdaLNAttention (class in MolecularDiffusion.modules.layers.tabasco.attention) CSV_FIELDS (in module MolecularDiffusion.runmodes.data.augmentation) cuda() (in module MolecularDiffusion.utils.torch) current_step (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) custom_weight_init (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule 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.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) (MolecularDiffusion.modules.models.tabasco.sample.noise_schedule.BaseNoiseSchedule attribute) D d_model (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) d_x (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT attribute) data() (in module MolecularDiffusion.cli.data) data_augmentation (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) data_dir (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional.UnconditionalLMDBDataset attribute) (MolecularDiffusion.modules.models.tabasco.data.lmdb_datamodule.LmdbDataModule attribute) data_efficient_collator (MolecularDiffusion.runmodes.train.data.DataModule attribute) data_fraction (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule 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) DataQueue (class in MolecularDiffusion.data.dataloader) dataset_embedder (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT attribute) dataset_kwargs (MolecularDiffusion.modules.models.tabasco.data.lmdb_datamodule.LmdbDataModule attribute) dataset_name (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) dataset_normalizer (MolecularDiffusion.modules.models.tabasco.chem.convert.MoleculeConverter attribute) dataset_smiles_list (MolecularDiffusion.utils.geom_analyzer.BasicMolecularMetrics attribute) dataset_stats (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) DatasetStatsCallback (class in MolecularDiffusion.modules.models.tabasco.callbacks.dataset_stats) db (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_base.BaseLMDBDataset attribute) (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional.UnconditionalLMDBDataset attribute) de (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) debug (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) decay (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) decode() (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask method) decoder (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) degree_angles_ref (in module MolecularDiffusion.utils.geom_constant) 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) density_estimation() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) DepthwiseTensorProduct() (in module MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) detach() (in module MolecularDiffusion.utils.torch) 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.ldm.encoders.equiformer.EquiformerEncoder 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.tabasco.callbacks.ema.EMAOptimizer attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction property) (MolecularDiffusion.modules.tasks.diffusion_ldm.FlowMatchingInterpolant attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask property) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask property) (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator attribute) df (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) DiagonalGaussianDistribution (class in MolecularDiffusion.modules.tasks.diffusion_ldm) dim (MolecularDiffusion.modules.layers.common.SinusoidsEmbeddingNew attribute) (MolecularDiffusion.modules.layers.tabasco.attention.AdaLNAttention attribute) (MolecularDiffusion.modules.layers.tabasco.attention.CrossAdaLNAttention attribute) (MolecularDiffusion.modules.models.en_diffusion.SinusoidalPosEmb attribute) dims (MolecularDiffusion.modules.layers.common.MLP attribute) dir_wandb (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.runmodes.train.logger.Logger attribute) DIRECTIONAL_PTYPES (in module MolecularDiffusion.utils.shepherd_score.score.constants) DiscreteInterpolant (class in MolecularDiffusion.modules.models.tabasco.flow.interpolate) 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) dist_mul_e (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) DIST_RELAX_BOND (in module MolecularDiffusion.runmodes.train.eval) DIST_THRESHOLD (in module MolecularDiffusion.runmodes.train.eval) distance_expansion (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.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) distance_threshold (MolecularDiffusion.modules.layers.tabasco.losses.InterDistancesLoss attribute) distortion_cmd() (in module MolecularDiffusion.cli.data) 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.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) DiTBlock (class in MolecularDiffusion.modules.models.ldm.denoisers.dit) 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.ldm.denoisers.dit.Mlp attribute) drop2 (MolecularDiffusion.modules.models.ldm.denoisers.dit.Mlp 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) dropout (MolecularDiffusion.modules.layers.conv.GCL attribute) (MolecularDiffusion.modules.layers.tabasco.transition.Transition attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) dropout_prob (MolecularDiffusion.modules.models.ldm.denoisers.dit.LabelEmbedder attribute) dropoutE1 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) dropoutE2 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) dropoutE3 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) dropoutX1 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) dropoutX2 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) dropoutX3 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) DropPath (class in MolecularDiffusion.modules.layers.equiformer_v2.drop) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.drop) 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) dx (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) dx_t (MolecularDiffusion.modules.models.tabasco.flow.path.FlowPath attribute) dy (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) dynamics (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.pharmacophore_dynamics.PharmacophoreEnVariationalDiff attribute) dynamics_in_node_nf (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) dynamics_teacher (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) E e_att_mul (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) e_out (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) e_pos1 (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) e_pos2 (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) e_x_mul (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) ECFP (in module MolecularDiffusion.data.component.feature) 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_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) 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.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_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.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) edge_mlp (MolecularDiffusion.modules.layers.conv.GCL attribute) edge_model() (MolecularDiffusion.modules.layers.conv.GCL method) 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_type (MolecularDiffusion.runmodes.train.data.DataModule attribute) EdgeDegreeEmbedding (class in MolecularDiffusion.modules.layers.equiformer_v2.input_block) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.input_block) (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder) EGNN (class in MolecularDiffusion.modules.models.egcl) (class in MolecularDiffusion.modules.models.shepherd_arch.egnn) egnn (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.egt.EGT_dynamics attribute) EGNN_dynamics (class in MolecularDiffusion.modules.models.egcl) EGT_dynamics (class in MolecularDiffusion.modules.models.egt) 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) EMA (class in MolecularDiffusion.callbacks.train_helper) (class in MolecularDiffusion.modules.models.tabasco.callbacks.ema) ema_decay (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory 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) EMAOptimizer (class in MolecularDiffusion.modules.models.tabasco.callbacks.ema) embedding (MolecularDiffusion.modules.models.egcl.EGNN attribute) embedding_out (MolecularDiffusion.modules.models.egcl.EGNN attribute) embedding_table (MolecularDiffusion.modules.models.ldm.denoisers.dit.LabelEmbedder attribute) encode() (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask method) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask method) encoder (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) encoder_config (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) 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) enforce_min_nodes_per_connector() (in module MolecularDiffusion.utils.geom_constraint) enforce_tags() (in module MolecularDiffusion.modules.models.tabasco.utils.rich_utils) Engine (class in MolecularDiffusion.core.engine) engine_wrapper() (in module MolecularDiffusion.cli.eval_predict) (in module MolecularDiffusion.cli.train) ensure_intact() (in module MolecularDiffusion.utils.geom_constraint) EnVariationalDiffusion (class in MolecularDiffusion.modules.models.en_diffusion) epoch (MolecularDiffusion.core.engine.Engine property) epoch2batch (MolecularDiffusion.core.meter.Meter attribute) epoch_id (MolecularDiffusion.core.meter.Meter attribute) 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.models.shepherd_arch.equiformer_operations.EquivariantGraphNorm attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNormV2 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) EquiformerEncoder (class in MolecularDiffusion.modules.models.ldm.encoders.equiformer) EquiformerV2 (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder) EquiformerV2_OC20 (class in MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20) EquivariantBlock (class in MolecularDiffusion.modules.layers.conv) EquivariantDegreeLayerScale (class in MolecularDiffusion.modules.layers.equiformer_v2.layer_norm) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.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) EquivariantLayerNormArray (class in MolecularDiffusion.modules.layers.equiformer_v2.layer_norm) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm) EquivariantLayerNormArraySphericalHarmonics (class in MolecularDiffusion.modules.layers.equiformer_v2.layer_norm) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm) 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) 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) 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) estimate_batch_size() (in module MolecularDiffusion.data.dataloader) EtoX (class in MolecularDiffusion.modules.layers.conv) Etoy (class in MolecularDiffusion.modules.layers.conv) 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_ldm.LDMTask method) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask method) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative method) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction method) (MolecularDiffusion.modules.tasks.task.Task method) (MolecularDiffusion.utils.geom_analyzer.BasicMolecularMetrics method) evaluate_and_save() (in module MolecularDiffusion.cli.train) every_n_steps (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) exclude_variables_from_decoder_heterogeneous_graph (MolecularDiffusion.modules.models.shepherd_arch.model.Model attribute) expand_edge() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Embedding method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Embedding method) explicit_diffusion_variables (MolecularDiffusion.modules.models.shepherd_arch.model.Model attribute) expm1() (in module MolecularDiffusion.modules.models.en_diffusion) ExtendedConnectivityFingerprint() (in module MolecularDiffusion.data.component.feature) 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) extra_norm_values (MolecularDiffusion.modules.models.en_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.shepherd_arch.equiformer_operations.Activation method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.ScaledScatter method) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.SmoothLeakyReLU method) extract() (in module MolecularDiffusion.utils.file) extract_scaffold_and_fingerprints() (in module MolecularDiffusion.runmodes.analyze.xyz2mol) extras() (in module MolecularDiffusion.modules.models.tabasco.utils.utils) F f1_max() (in module MolecularDiffusion.modules.tasks.metrics) FACTOR (MolecularDiffusion.callbacks.train_helper.gradient_clipping attribute) fc (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_m_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.SO2_m_Convolution attribute) fc1 (MolecularDiffusion.modules.models.ldm.denoisers.dit.Mlp attribute) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.SiLUSmearing attribute) fc2 (MolecularDiffusion.modules.models.ldm.denoisers.dit.Mlp 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) fctp_1 (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.FeedForwardNetwork_equiformer attribute) fctp_2 (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.FeedForwardNetwork_equiformer attribute) feature_colors (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmacophore) featurize() (in module MolecularDiffusion.runmodes.data.featurization) (MolecularDiffusion.data.component.feature.NodeFeaturizer method) featurize_all() (MolecularDiffusion.data.component.feature.NodeFeaturizer method) featurize_cmd() (in module MolecularDiffusion.cli.data) FeedForward (class in MolecularDiffusion.modules.layers.tabasco.transition) 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) FeedForwardNetwork_equiformer (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) ff_block (MolecularDiffusion.modules.layers.tabasco.transformer.TransformerBlock attribute) ffn (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.TransBlockV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.TransBlockV2 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_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) 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_layer (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT attribute) FinalLayer (class in MolecularDiffusion.modules.models.ldm.denoisers.dit) 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_project_root() (in module MolecularDiffusion.molcraftdiff) find_subgraph_centroids() (in module MolecularDiffusion.utils.geom_constraint) first_iteration (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) flatten() (MolecularDiffusion.core.core.Tree method) flow_matching_config (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) FlowMatchingInterpolant (class in MolecularDiffusion.modules.tasks.diffusion_ldm) FlowMatchingModel (class in MolecularDiffusion.modules.models.tabasco.flow_model) FlowPath (class in MolecularDiffusion.modules.models.tabasco.flow.path) fm_num_timesteps (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask property) forbidden_atom (MolecularDiffusion.runmodes.train.data.DataModule attribute) foreach (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) formal_charge_diffusion (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) format() (in module MolecularDiffusion.utils.pretty) forward() (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.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.tabasco.attention.AdaLNAttention method) (MolecularDiffusion.modules.layers.tabasco.attention.Attention method) (MolecularDiffusion.modules.layers.tabasco.attention.AttentionBlock method) (MolecularDiffusion.modules.layers.tabasco.attention.CrossAdaLNAttention method) (MolecularDiffusion.modules.layers.tabasco.common.SwiGLU method) (MolecularDiffusion.modules.layers.tabasco.losses.InterDistancesLoss method) (MolecularDiffusion.modules.layers.tabasco.positional_encoder.PositionalEncoding method) (MolecularDiffusion.modules.layers.tabasco.positional_encoder.SinusoidEncoding method) (MolecularDiffusion.modules.layers.tabasco.positional_encoder.TimeFourierEncoding method) (MolecularDiffusion.modules.layers.tabasco.transformer.Transformer method) (MolecularDiffusion.modules.layers.tabasco.transformer.TransformerBlock method) (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule method) (MolecularDiffusion.modules.layers.tabasco.transition.FeedForward method) (MolecularDiffusion.modules.layers.tabasco.transition.Transition 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.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.pharmacophore_dynamics.PharmacophoreEnVariationalDiff method) (MolecularDiffusion.modules.models.pharmacophore_dynamics.PharmacophoreModelWrapper 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.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.tasks.diffusion.GeomMolecularGenerative method) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask method) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask 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) 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_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) 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) frequencies (MolecularDiffusion.modules.layers.common.SinusoidsEmbeddingNew attribute) frequency_embedding_dim (MolecularDiffusion.modules.models.ldm.denoisers.dit.TimestepEmbedder attribute) from_arrays() (MolecularDiffusion.data.component.pointcloud.PointCloud_Mol class method) from_batch() (MolecularDiffusion.modules.models.tabasco.chem.convert.MoleculeConverter method) from_grid() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Grid method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Grid method) from_tensor() (MolecularDiffusion.modules.models.tabasco.chem.convert.MoleculeConverter method) from_xyz() (MolecularDiffusion.data.component.pointcloud.PointCloud_Mol class method) 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) G ga (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.TransBlockV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.TransBlockV2 attribute) gamma (MolecularDiffusion.modules.models.en_diffusion.PredefinedNoiseSchedule attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) gamma_0 (MolecularDiffusion.modules.models.en_diffusion.GammaNetwork attribute) gamma_1 (MolecularDiffusion.modules.models.en_diffusion.GammaNetwork attribute) gamma_tilde() (MolecularDiffusion.modules.models.en_diffusion.GammaNetwork method) GammaNetwork (class in MolecularDiffusion.modules.models.en_diffusion) 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) GateActivation (class in MolecularDiffusion.modules.layers.equiformer_v2.activation) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.activation) gaussian() (in module MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf) (in module MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf) gaussian_entropy() (in module MolecularDiffusion.modules.models.en_diffusion) gaussian_KL() (in module MolecularDiffusion.modules.models.en_diffusion) gaussian_KL_for_dimension() (in module MolecularDiffusion.modules.models.en_diffusion) GaussianRadialBasisLayer (class in MolecularDiffusion.modules.layers.equiformer_v2.gaussian_rbf) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.gaussian_rbf) GaussianSmearing (class in MolecularDiffusion.modules.models.ldm.encoders.equiformer) (class in MolecularDiffusion.modules.models.shepherd_arch.egnn) (class in MolecularDiffusion.modules.models.shepherd_arch.ocp_compat) GCL (class in MolecularDiffusion.modules.layers.conv) 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_from_intermediate_time() (in module MolecularDiffusion.modules.models.shepherd_arch.inference.sampler) generate_graph() (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) GenerativeFactory (class in MolecularDiffusion.runmodes.generate.tasks_generate) geom_feature (MolecularDiffusion.data.component.feature.NodeFeaturizer attribute) GEOM_FEATURES (MolecularDiffusion.data.component.feature.NodeFeaturizer attribute) geom_predictor() (in module MolecularDiffusion.utils.geom_analyzer) GeomMolecularGenerative (class in MolecularDiffusion.modules.tasks.diffusion) get() (MolecularDiffusion.core.core.Registry class method) get_adj_matrix() (MolecularDiffusion.modules.models.egcl.EGNN_dynamics method) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction method) get_alpha_bar() (MolecularDiffusion.modules.models.noisemodel.NoiseModel method) get_alpha_sigma_t() (MolecularDiffusion.modules.models.noisemodel.NoiseModel method) get_asset_path() (in module MolecularDiffusion.runmodes.data.preparation) get_atom_coords() (in module MolecularDiffusion.utils.shepherd_score.generate_point_cloud) 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_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_coord() (MolecularDiffusion.data.component.pointcloud.Atom method) (MolecularDiffusion.data.component.pointcloud.PointCloud_Mol method) get_cpu_count() (in module MolecularDiffusion.utils.comm) get_cutoffs() (in module MolecularDiffusion.utils.geom_analyzer) (in module MolecularDiffusion.utils.smilify) get_data_dict() (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional.UnconditionalLMDBDataset method) get_dataset_stats() (MolecularDiffusion.modules.models.tabasco.data.lmdb_datamodule.LmdbDataModule method) get_default_valencies() (in module MolecularDiffusion.utils.geom_stability) 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_from_grid_mat() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Grid method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Grid method) get_group() (in module MolecularDiffusion.utils.comm) get_index_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.PointCloudDataset 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) 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_loss_weight() (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) 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_metric_value() (in module MolecularDiffusion.modules.models.tabasco.utils.utils) get_metrics() (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator method) 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_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) 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_pharm_combo_score() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring) (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring_np) get_pharmacophores() (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_property() (MolecularDiffusion.data.component.dataset.GraphDataset method) (MolecularDiffusion.data.component.dataset.PointCloudDataset method) get_proto_mol() (in module MolecularDiffusion.utils.xyz2mol.converter) get_rank() (in module MolecularDiffusion.utils.comm) (MolecularDiffusion.utils.io.RankState class method) get_rotate_inv_rescale() (MolecularDiffusion.modules.layers.equiformer_v2.so3.CoefficientMappingModule method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.CoefficientMappingModule method) 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_sigma_bar() (MolecularDiffusion.modules.models.noisemodel.NoiseModel method) get_simple_valencies() (in module MolecularDiffusion.utils.geom_stability) get_stats() (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional.UnconditionalLMDBDataset method) get_tabasco_stats() (MolecularDiffusion.data.component.dataset.PointCloudDataset method) get_target_count() (in module MolecularDiffusion.runmodes.data.augmentation) get_to_grid_mat() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Grid method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Grid method) get_UA() (in module MolecularDiffusion.utils.xyz2mol.converter) get_UA_pairs() (in module MolecularDiffusion.utils.xyz2mol.converter) 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_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_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_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) 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) gradient_clip_algorithm (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) graph_collate() (in module MolecularDiffusion.data.dataloader) 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) GraphTransformer (class in MolecularDiffusion.modules.models.egt) 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.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) gt_arrays_list (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator attribute) guess_bond_matrix() (in module MolecularDiffusion.utils.smilify) GuidanceModelPrediction (class in MolecularDiffusion.modules.tasks.diffusion) GuidedSampling (class in MolecularDiffusion.modules.models.tabasco.sample.guided_sampling) H hard() (MolecularDiffusion.callbacks.train_helper.SP_regularizer method) hard_relax() (MolecularDiffusion.callbacks.train_helper.SP_regularizer method) HARTREE_TO_EV (in module MolecularDiffusion.runmodes.analyze.xtb_electronic) head_indices (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.AttnHeads2Vec 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) hidden_dim (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) hidden_dims (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) hidden_mlp_dims (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) hidden_nf (MolecularDiffusion.modules.layers.conv.EquivariantBlock attribute) (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) hidden_size (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory 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_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) hybiridization_map (in module MolecularDiffusion.data.component.dataset) hybrid_guidance() (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory method) I ignore_zeros (MolecularDiffusion.utils.geom_analyzer.Histogram_cont attribute) implementation (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) 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_E (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) in_edge_nf (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) in_features (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.models.en_diffusion.PositiveLinear attribute) in_node_nf (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.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) in_saving_ema_model_context (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) include_charge (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) include_charges (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) include_cosine (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.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) (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_base.BaseLMDBDataset attribute) inflate_batch_array() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) 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) 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.ldm.denoisers.dit.DiT 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) 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) 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) instantiate_callbacks() (in module MolecularDiffusion.modules.models.tabasco.utils.instantiators) instantiate_loggers() (in module MolecularDiffusion.modules.models.tabasco.utils.instantiators) int_atom() (in module MolecularDiffusion.utils.xyz2mol.converter) inter_distances() (MolecularDiffusion.modules.layers.tabasco.losses.InterDistancesLoss method) interdist_loss (MolecularDiffusion.modules.models.tabasco.flow_model.FlowMatchingModel attribute) InterDistancesLoss (class in MolecularDiffusion.modules.layers.tabasco.losses) 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) Interpolant (class in MolecularDiffusion.modules.models.tabasco.flow.interpolate) interpolant (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask attribute) interpolant_config (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTaskFactory attribute) InterpolantGuidance (class in MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance) inv_sublayers (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) inverse_mapping (MolecularDiffusion.modules.models.noisemodel.NoiseModel attribute) InverseTimeFactor (class in MolecularDiffusion.modules.models.tabasco.flow.time_factor) ir_mul_list (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.ConcatIrrepsTensor 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) is_clean() (in module MolecularDiffusion.runmodes.data.ase_ops) is_cosymlib_available (in module MolecularDiffusion.utils.geom_metrics) is_fully_connected() (in module MolecularDiffusion.utils.geom_analyzer) (in module MolecularDiffusion.utils.geom_metrics) 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) items (MolecularDiffusion.callbacks.train_helper.Queue attribute) iter_files() (in module MolecularDiffusion.runmodes.data.preparation) J join() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer method) joint_SO3_grid (MolecularDiffusion.modules.models.shepherd_arch.model.Model attribute) K k (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) kabsch_align() (in module MolecularDiffusion.utils.geom_metrics) key (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.en_diffusion.DistributionNodes attribute) (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_base.BaseLMDBDataset attribute) (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional.UnconditionalLMDBDataset attribute) kl() (MolecularDiffusion.modules.tasks.diffusion_ldm.DiagonalGaussianDistribution method) kl_prior() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) kwargs (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) L l1 (MolecularDiffusion.modules.models.en_diffusion.GammaNetwork attribute) l2 (MolecularDiffusion.modules.models.en_diffusion.GammaNetwork attribute) l3 (MolecularDiffusion.modules.models.en_diffusion.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_update_step (MolecularDiffusion.callbacks.train_helper.SP_regularizer attribute) lambda_update_value (MolecularDiffusion.callbacks.train_helper.SP_regularizer attribute) largest_component() (in module MolecularDiffusion.modules.models.tabasco.chem.utils) last_layer (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) lat_resolution (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Grid attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Grid attribute) latent_dim (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) lattice_head (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.decoders.transformer.TransformerDecoder attribute) layers (MolecularDiffusion.modules.layers.common.MLP attribute) (MolecularDiffusion.modules.layers.tabasco.transformer.Transformer attribute) LDMTask (class in MolecularDiffusion.modules.tasks.diffusion_ldm) LDMTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_ldm) lg (in module MolecularDiffusion.utils.smilify) lightning_module (MolecularDiffusion.modules.models.tabasco.sample.guided_sampling.GuidedSampling attribute) LightningTabasco (class in MolecularDiffusion.modules.models.tabasco.lightning_tabasco) limit_samples (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_base.BaseLMDBDataset attribute) lin (MolecularDiffusion.modules.layers.conv.EtoX attribute) (MolecularDiffusion.modules.layers.conv.Etoy attribute) (MolecularDiffusion.modules.layers.conv.Xtoy attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.SeparableFCTP attribute) lin_dist1 (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) lin_norm_pos1 (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) lin_norm_pos2 (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) line (in module MolecularDiffusion.utils.pretty) linE1 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) linE2 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) linear (MolecularDiffusion.modules.models.ldm.denoisers.dit.FinalLayer attribute) linear() (MolecularDiffusion.callbacks.train_helper.SP_regularizer method) linear_embed (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) linear_list (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Linear attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Linear attribute) LinearRS (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) LinearSigmoidSmearing (class in MolecularDiffusion.modules.models.shepherd_arch.ocp_compat) linX1 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) linX2 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) literal_eval() (in module MolecularDiffusion.utils.io) 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) 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.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) lmdb_dir (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_base.BaseLMDBDataset attribute) (MolecularDiffusion.modules.models.tabasco.data.lmdb_datamodule.LmdbDataModule attribute) lmdb_path (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_base.BaseLMDBDataset attribute) LmdbDataModule (class in MolecularDiffusion.modules.models.tabasco.data.lmdb_datamodule) load() (MolecularDiffusion.core.engine.Engine method) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule method) (MolecularDiffusion.runmodes.train.data.DataModule method) load_checkpoint_weights() (in module MolecularDiffusion.cli.eval_predict) 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) load_file_list_from_dir() (in module MolecularDiffusion.runmodes.analyze.xyz2mol) load_from_checkpoint() (MolecularDiffusion.core.engine.Engine class method) 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_npy() (MolecularDiffusion.data.component.dataset.GraphDataset method) (MolecularDiffusion.data.component.dataset.PointCloudDataset method) load_pickle() (MolecularDiffusion.data.component.dataset.GraphDataset method) (MolecularDiffusion.data.component.dataset.PointCloudDataset method) load_pkl (MolecularDiffusion.runmodes.train.data.DataModule attribute) load_smiles() (MolecularDiffusion.data.component.dataset.GraphDataset method) load_state_dict() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer method) load_valency_table() (in module MolecularDiffusion.utils.geom_stability) load_weights() (in module MolecularDiffusion.cli.train) load_xyz() (MolecularDiffusion.data.component.dataset.GraphDataset method) (MolecularDiffusion.data.component.dataset.PointCloudDataset method) 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.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.data.lmdb_datamodule) (in module MolecularDiffusion.modules.models.tabasco.utils.instantiators) (in module MolecularDiffusion.modules.models.tabasco.utils.metric_utils) (in module MolecularDiffusion.modules.models.tabasco.utils.metrics) (in module MolecularDiffusion.modules.models.tabasco.utils.rich_utils) (in module MolecularDiffusion.modules.models.tabasco.utils.utils) (in module MolecularDiffusion.utils.pretty) log() (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_config() (MolecularDiffusion.core.logger.LoggerBase method) (MolecularDiffusion.core.logger.LoggingLogger method) (MolecularDiffusion.core.logger.WandbLogger method) (MolecularDiffusion.core.meter.Meter method) log_constants_p_x_given_z0() (MolecularDiffusion.modules.models.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) (in module MolecularDiffusion.modules.models.tabasco.utils.utils) log_info() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) log_interval (MolecularDiffusion.core.meter.Meter attribute) (MolecularDiffusion.runmodes.train.logger.Logger attribute) log_prob() (MolecularDiffusion.modules.models.en_diffusion.DistributionNodes method) log_pxh_given_z0_without_constants() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) log_pxh_given_z0_without_constants_pyG() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) 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.core.engine) (in module MolecularDiffusion.core.meter) (in module MolecularDiffusion.data.component.dataset) (in module MolecularDiffusion.data.component.pharmacophore) (in module MolecularDiffusion.data.dataset) (in module MolecularDiffusion.modules.models.en_diffusion) (in module MolecularDiffusion.modules.models.pharmacophore_dynamics) (in module MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional) (in module MolecularDiffusion.modules.models.tabasco.data.transforms) (in module MolecularDiffusion.modules.tasks.diffusion) (in module MolecularDiffusion.modules.tasks.pharmacophore) (in module MolecularDiffusion.molcraftdiff) (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.preparation) (in module MolecularDiffusion.runmodes.generate.tasks_generate) (in module MolecularDiffusion.runmodes.train.tasks_egcl) (in module MolecularDiffusion.runmodes.train.tasks_egt) (in module MolecularDiffusion.utils.file) (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) logP() (in module MolecularDiffusion.modules.tasks.metrics) logvar (MolecularDiffusion.modules.tasks.diffusion_ldm.DiagonalGaussianDistribution attribute) long_array() (in module MolecularDiffusion.utils.pretty) loss_from_bounds() (MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance.UFFBoundGuidance method) loss_param (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) loss_type (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative attribute) loss_weight (MolecularDiffusion.modules.models.tabasco.flow.interpolate.Interpolant attribute) loss_weighting (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) loss_weights (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory 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.models.en_diffusion.DistributionNodes 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.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.models.shepherd_arch.equiformer_v2_encoder.EdgeDegreeEmbedding 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) mae_eval (MolecularDiffusion.runmodes.train.eval.TaskEvalConfig attribute) main() (in module MolecularDiffusion.cli.main) (in module MolecularDiffusion.molcraftdiff) (in module MolecularDiffusion.runmodes.analyze.xyz2mol) make_configurable() (in module MolecularDiffusion.core.core) 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.models.noisemodel.NoiseModel 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.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) mask_and_zero_com() (in module MolecularDiffusion.modules.models.tabasco.utils.tensor_ops) mask_indices_cache (MolecularDiffusion.modules.layers.equiformer_v2.so3.CoefficientMappingModule attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.CoefficientMappingModule attribute) mask_value (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) masked_mean() (in module MolecularDiffusion.modules.layers.functional) masked_softmax() (in module MolecularDiffusion.modules.layers.conv) matthews_corrcoef() (in module MolecularDiffusion.modules.tasks.metrics) max_atom (MolecularDiffusion.runmodes.train.data.DataModule 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_lmax (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork attribute) max_mol_size (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) max_n_nodes (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask 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.ldm.encoders.equiformer.EquiformerEncoder attribute) max_node_types_x4 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) 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.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_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_SEED_VALUE (in module MolecularDiffusion.utils.torch) max_value (MolecularDiffusion.modules.models.tabasco.flow.time_factor.BaseTimeFactor attribute) 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_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) merge_cmd() (in module MolecularDiffusion.cli.data) merge_dbs() (in module MolecularDiffusion.runmodes.data.ase_ops) message_mlp (MolecularDiffusion.modules.models.shepherd_arch.egnn.EGNN attribute) message_mlp_embedding_dim (MolecularDiffusion.modules.models.shepherd_arch.egnn.EGNN attribute) Meter (class in MolecularDiffusion.core.meter) meter (MolecularDiffusion.core.engine.Engine attribute) metric (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) MIN_SEED_VALUE (in module MolecularDiffusion.utils.torch) min_t (MolecularDiffusion.modules.tasks.diffusion_ldm.FlowMatchingInterpolant attribute) min_value (MolecularDiffusion.modules.models.tabasco.flow.time_factor.BaseTimeFactor attribute) MLP (class in MolecularDiffusion.modules.layers.common) Mlp (class in MolecularDiffusion.modules.models.ldm.denoisers.dit) mlp (MolecularDiffusion.modules.layers.conv.PositionsMLP attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiTBlock attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.TimestepEmbedder attribute) (MolecularDiffusion.modules.models.shepherd_arch.egnn.MultiLayerPerceptron 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_dropout (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) mlp_final (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) mlp_in_E (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) mlp_in_pos (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) mlp_in_X (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) mlp_in_y (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) mlp_out_E (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) mlp_out_pos (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) mlp_out_X (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) 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) 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) modality_weights (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative attribute) mode (MolecularDiffusion.modules.models.tabasco.utils.metrics.PoseCheckStrainEnergy 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.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_ldm.LDMTask property) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask property) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) model_class (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) ModelTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_tabasco) (class in MolecularDiffusion.runmodes.train.tasks_egcl) (class in MolecularDiffusion.runmodes.train.tasks_egt) modulate() (in module MolecularDiffusion.modules.models.ldm.denoisers.dit) module MolecularDiffusion 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.core MolecularDiffusion.core.core MolecularDiffusion.core.engine MolecularDiffusion.core.logger MolecularDiffusion.core.meter MolecularDiffusion.data MolecularDiffusion.data.component MolecularDiffusion.data.component.dataset MolecularDiffusion.data.component.feature MolecularDiffusion.data.component.pharmacophore MolecularDiffusion.data.component.pointcloud MolecularDiffusion.data.dataloader MolecularDiffusion.data.dataset MolecularDiffusion.data.valency_tables MolecularDiffusion.modules.layers.common MolecularDiffusion.modules.layers.conv 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.functional 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.models MolecularDiffusion.modules.models.egcl MolecularDiffusion.modules.models.egt MolecularDiffusion.modules.models.en_diffusion 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.noisemodel MolecularDiffusion.modules.models.pharmacophore_dynamics 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.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.components MolecularDiffusion.modules.models.tabasco.data.components.lmdb_base MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional MolecularDiffusion.modules.models.tabasco.data.lmdb_datamodule 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.artifacts MolecularDiffusion.modules.models.tabasco.utils.instantiators MolecularDiffusion.modules.models.tabasco.utils.metric_utils MolecularDiffusion.modules.models.tabasco.utils.metrics MolecularDiffusion.modules.models.tabasco.utils.pylogger MolecularDiffusion.modules.models.tabasco.utils.rich_utils MolecularDiffusion.modules.models.tabasco.utils.tensor_ops MolecularDiffusion.modules.models.tabasco.utils.utils MolecularDiffusion.modules.tasks MolecularDiffusion.modules.tasks.diffusion MolecularDiffusion.modules.tasks.diffusion_ldm MolecularDiffusion.modules.tasks.diffusion_tabasco MolecularDiffusion.modules.tasks.metrics MolecularDiffusion.modules.tasks.pharmacophore MolecularDiffusion.modules.tasks.regression MolecularDiffusion.modules.tasks.task MolecularDiffusion.molcraftdiff MolecularDiffusion.runmodes MolecularDiffusion.runmodes.analyze MolecularDiffusion.runmodes.analyze.compare_to_optimized MolecularDiffusion.runmodes.analyze.compute_metrics 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.preparation MolecularDiffusion.runmodes.generate 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.trainer MolecularDiffusion.utils MolecularDiffusion.utils.comm 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.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.torch MolecularDiffusion.utils.xyz2mol MolecularDiffusion.utils.xyz2mol.converter MolecularDiffusion.utils.xyz2mol.elements module (in module MolecularDiffusion.core.engine) (in module MolecularDiffusion.utils.sascore) ModuleListInfo (class in MolecularDiffusion.modules.layers.equiformer_v2.module_list) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.module_list) 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.data.components.lmdb_unconditional.UnconditionalLMDBDataset attribute) (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco attribute) (MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance.UFFBoundGuidance attribute) mol_idx (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) mol_metrics (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco attribute) mol_num_atoms_list (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional.UnconditionalLMDBDataset attribute) mol_size (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) mol_to_atom_array() (MolecularDiffusion.modules.models.tabasco.chem.convert.MoleculeConverter method) 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.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.core module MolecularDiffusion.core.core module MolecularDiffusion.core.engine module MolecularDiffusion.core.logger module MolecularDiffusion.core.meter module MolecularDiffusion.data module MolecularDiffusion.data.component module MolecularDiffusion.data.component.dataset module MolecularDiffusion.data.component.feature module MolecularDiffusion.data.component.pharmacophore module MolecularDiffusion.data.component.pointcloud module MolecularDiffusion.data.dataloader module MolecularDiffusion.data.dataset module MolecularDiffusion.data.valency_tables module MolecularDiffusion.modules.layers.common module MolecularDiffusion.modules.layers.conv 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.functional 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.models module MolecularDiffusion.modules.models.egcl module MolecularDiffusion.modules.models.egt module MolecularDiffusion.modules.models.en_diffusion 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.noisemodel module MolecularDiffusion.modules.models.pharmacophore_dynamics 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.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.components module MolecularDiffusion.modules.models.tabasco.data.components.lmdb_base module MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional module MolecularDiffusion.modules.models.tabasco.data.lmdb_datamodule 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.artifacts module MolecularDiffusion.modules.models.tabasco.utils.instantiators 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.rich_utils module MolecularDiffusion.modules.models.tabasco.utils.tensor_ops module MolecularDiffusion.modules.models.tabasco.utils.utils module MolecularDiffusion.modules.tasks module MolecularDiffusion.modules.tasks.diffusion module MolecularDiffusion.modules.tasks.diffusion_ldm module MolecularDiffusion.modules.tasks.diffusion_tabasco module MolecularDiffusion.modules.tasks.metrics module MolecularDiffusion.modules.tasks.pharmacophore module MolecularDiffusion.modules.tasks.regression module MolecularDiffusion.modules.tasks.task module MolecularDiffusion.molcraftdiff module MolecularDiffusion.runmodes module MolecularDiffusion.runmodes.analyze module MolecularDiffusion.runmodes.analyze.compare_to_optimized module MolecularDiffusion.runmodes.analyze.compute_metrics 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.preparation module MolecularDiffusion.runmodes.generate 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.trainer module MolecularDiffusion.utils module MolecularDiffusion.utils.comm 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.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.torch module MolecularDiffusion.utils.xyz2mol module MolecularDiffusion.utils.xyz2mol.converter module MolecularDiffusion.utils.xyz2mol.elements 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) MoleculeMetricsCallback (class in MolecularDiffusion.modules.models.tabasco.callbacks.molecule_metrics) MoleculeReconstructionEvaluator (class in MolecularDiffusion.utils.geom_utils) 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) 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) MultiLayerPerceptron (class in MolecularDiffusion.modules.models.shepherd_arch.egnn) multinomial() (in module MolecularDiffusion.modules.layers.functional) multivectors (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) N n_adapter_context (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) n_atom_types (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) n_calls (MolecularDiffusion.callbacks.train_helper.SP_regularizer attribute) n_concat_context (MolecularDiffusion.modules.models.egcl.EGNN attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) n_dim_data (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) n_dims (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.modules.models.egt.EGT_dynamics attribute) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) n_frames (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) n_frequencies (MolecularDiffusion.modules.layers.common.SinusoidsEmbeddingNew attribute) n_head (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) n_layers (MolecularDiffusion.modules.layers.conv.EquivariantBlock 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) n_neigh (MolecularDiffusion.runmodes.train.data.DataModule attribute) n_node_dist (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask property) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoNodeDistribution attribute) n_nodes (MolecularDiffusion.modules.models.en_diffusion.DistributionNodes attribute) n_steps (MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance.UFFBoundGuidance 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.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) natoms_file (MolecularDiffusion.runmodes.train.data.DataModule attribute) ndim_extra (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) needs_generative (MolecularDiffusion.runmodes.train.eval.TaskEvalConfig attribute) negative_target_values (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) net (MolecularDiffusion.modules.layers.equiformer_v2.radial_function.RadialFunction attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.radial_function.RadialFunction attribute) (MolecularDiffusion.modules.layers.tabasco.transition.FeedForward attribute) (MolecularDiffusion.modules.models.tabasco.flow_model.FlowMatchingModel 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) nhead (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT attribute) 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.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) node_dist_model (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask property) node_feature_choice (MolecularDiffusion.runmodes.train.data.DataModule attribute) node_mlp (MolecularDiffusion.modules.layers.conv.GCL 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) node_output_embedding (MolecularDiffusion.modules.models.shepherd_arch.egnn.EGNN attribute) node_output_embedding_dim (MolecularDiffusion.modules.models.shepherd_arch.egnn.EGNN attribute) NodeEdgeBlock (class in MolecularDiffusion.modules.layers.conv) NodeFeaturizer (class in MolecularDiffusion.data.component.feature) noise_scale (MolecularDiffusion.modules.models.tabasco.flow.interpolate.CenteredMetricInterpolant attribute) noise_schedule_dict (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) NoiseModel (class in MolecularDiffusion.modules.models.noisemodel) 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.ldm.denoisers.dit.Mlp attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder 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) norm1 (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiTBlock attribute) norm2 (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiTBlock attribute) norm_1 (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.TransBlockV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.TransBlockV2 attribute) norm_2 (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.TransBlockV2 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.TransBlockV2 attribute) norm_biases (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) norm_constant (MolecularDiffusion.modules.layers.conv.EquivariantBlock attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) norm_diff (MolecularDiffusion.modules.layers.conv.EquivariantBlock attribute) (MolecularDiffusion.modules.models.egcl.EGNN attribute) norm_eps (MolecularDiffusion.modules.layers.tabasco.attention.AdaLNAttention attribute) (MolecularDiffusion.modules.layers.tabasco.attention.CrossAdaLNAttention attribute) norm_final (MolecularDiffusion.modules.models.ldm.denoisers.dit.FinalLayer attribute) norm_l0 (MolecularDiffusion.modules.layers.equiformer_v2.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute) norm_pos1 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer 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.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) norm_values (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) 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.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.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.egcl.EGNN attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) normalize() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) (MolecularDiffusion.utils.geom_analyzer.Histogram_discrete method) normalize_condition (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) normalize_distance_vectors (MolecularDiffusion.modules.models.shepherd_arch.egnn.EGNN 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) normalized_shape (MolecularDiffusion.modules.layers.conv.SE3Norm attribute) normalizer (MolecularDiffusion.modules.models.en_diffusion.DistributionProperty attribute) normE1 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) normE2 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) normX1 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) normX2 (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) nu_arr (MolecularDiffusion.modules.models.noisemodel.NoiseModel attribute) num2symbol (in module MolecularDiffusion.utils.geom_analyzer) num_atom_type (MolecularDiffusion.data.component.dataset.GraphDataset property) (MolecularDiffusion.data.component.dataset.PointCloudDataset 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) num_atoms (MolecularDiffusion.data.component.dataset.GraphDataset property) (MolecularDiffusion.data.component.dataset.PointCloudDataset property) (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.BaseModel 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) num_bins (MolecularDiffusion.modules.models.en_diffusion.DistributionProperty 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) num_class (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) num_classes (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.ldm.denoisers.dit.LabelEmbedder 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_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.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) num_epochs (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) num_generate (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) num_heads (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.tabasco.attention.AdaLNAttention attribute) (MolecularDiffusion.modules.layers.tabasco.attention.CrossAdaLNAttention attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Vec2AttnHeads attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) num_irreps (MolecularDiffusion.modules.layers.equiformer_v2.drop.EquivariantDropout attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.drop.EquivariantDropout 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.ldm.decoders.transformer.TransformerDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.transformer.TransformerEncoder 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) num_mlp_layer (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) num_output (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.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_points_x2 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) num_points_x3 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) num_random_augmentations (MolecularDiffusion.modules.models.tabasco.flow_model.FlowMatchingModel 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_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.tabasco.callbacks.molecule_metrics.MoleculeMetricsCallback attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.posebusters.PoseBustersCallback attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.save_molecules.SaveGeneratedMolsCallback attribute) 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.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) num_sublayers (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) num_targets (MolecularDiffusion.modules.models.shepherd_arch.ocp_compat.BaseModel attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) num_timesteps (MolecularDiffusion.modules.tasks.diffusion_ldm.FlowMatchingInterpolant attribute) num_trajectories (MolecularDiffusion.modules.models.tabasco.callbacks.save_molecules.SaveGeneratedMolsCallback attribute) num_worker (MolecularDiffusion.core.engine.Engine attribute) num_workers (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.modules.models.tabasco.data.lmdb_datamodule.LmdbDataModule attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) numBridgeheadsAndSpiro() (in module MolecularDiffusion.utils.sascore) O o3d (in module MolecularDiffusion.data.component.pharmacophore) (in module MolecularDiffusion.utils.shepherd_utils) on_before_optimizer_step() (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) on_fit_start() (MolecularDiffusion.modules.models.tabasco.callbacks.dataset_stats.DatasetStatsCallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) on_load_checkpoint() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) on_save_checkpoint() (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) on_test_end() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) on_test_start() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) on_validation_end() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) on_validation_epoch_end() (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.modules.models.tabasco.callbacks.ema.EMA method) one_hot() (in module MolecularDiffusion.modules.layers.functional) onehot() (in module MolecularDiffusion.data.component.feature) 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) OptimSchedulerFactory (class in MolecularDiffusion.runmodes.train.trainer) original_smiles (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularNovelty 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.ldm.encoders.equiformer.EquiformerEncoder attribute) out (MolecularDiffusion.modules.layers.conv.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) 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) out_dim_y (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) out_features (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.models.en_diffusion.PositiveLinear 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_path (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) P p (MolecularDiffusion.callbacks.train_helper.SP_regularizer attribute) P_ALPHAS (in module MolecularDiffusion.utils.geom_metrics) (in module MolecularDiffusion.utils.shepherd_score.score.constants) 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_data() (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction method) padded_to_variadic() (in module MolecularDiffusion.modules.layers.functional) parameters (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) parametrization (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) params (MolecularDiffusion.modules.models.pharmacophore_dynamics.PharmacophoreModelWrapper attribute) (MolecularDiffusion.modules.models.shepherd_arch.model.Model attribute) parser (in module MolecularDiffusion.runmodes.analyze.compare_to_optimized) (in module MolecularDiffusion.runmodes.analyze.compute_metrics) (in module MolecularDiffusion.runmodes.analyze.xtb_optimization) path (in module MolecularDiffusion.utils.sascore) pattern_of_smarts() (in module MolecularDiffusion.utils.shepherd_score.pharm_utils.pharmacophore) pca_align() (in module MolecularDiffusion.utils.geom_metrics) 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) pharmacophore_collate_fn() (in module MolecularDiffusion.data.component.pharmacophore) 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) phi() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) phi_distillation() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) phi_pyg() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) pin_memory (MolecularDiffusion.core.engine.Engine attribute) pkl_files (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) 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) 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) PointCloudDataset (class in MolecularDiffusion.data.component.dataset) 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.en_diffusion) (in module MolecularDiffusion.modules.models.noisemodel) pop() (MolecularDiffusion.data.dataloader.DataQueue method) pos_att_mul (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) pos_embedder (MolecularDiffusion.modules.models.ldm.encoders.transformer.TransformerEncoder attribute) pos_head (MolecularDiffusion.modules.models.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.decoders.transformer.TransformerDecoder attribute) pos_x_mul (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) 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_encoding() (in module MolecularDiffusion.modules.models.shepherd_arch.utils) PositionalEncoding (class in MolecularDiffusion.modules.layers.tabasco.positional_encoder) positions (MolecularDiffusion.utils.smilify.Molecule attribute) PositionsMLP (class in MolecularDiffusion.modules.layers.conv) PositiveLinear (class in MolecularDiffusion.modules.models.en_diffusion) post_quant_conv (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) pre_filter (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_base.BaseLMDBDataset attribute) pre_softmax (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) precision (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) pred_arrays_list (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator attribute) PredefinedNoiseSchedule (class in MolecularDiffusion.modules.models.en_diffusion) predict() (in module MolecularDiffusion.cli.eval_predict) (in module MolecularDiffusion.cli.main) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative method) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction method) (MolecularDiffusion.modules.tasks.task.Task method) (MolecularDiffusion.molcraftdiff.MolCraftDiff method) predict_and_target() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask method) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask method) (MolecularDiffusion.modules.tasks.task.Task method) predict_main() (in module MolecularDiffusion.cli.predict) 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) prepare() (in module MolecularDiffusion.cli.data) prepare_context() (in module MolecularDiffusion.utils.diffusion_utils) prepare_context_pyG() (in module MolecularDiffusion.utils.diffusion_utils) prepare_data() (MolecularDiffusion.modules.models.tabasco.data.lmdb_datamodule.LmdbDataModule method) preprocess() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask method) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative method) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction 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) print_config_tree() (in module MolecularDiffusion.modules.models.tabasco.utils.rich_utils) prior_noise_scale (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) prob (MolecularDiffusion.modules.models.en_diffusion.DistributionNodes attribute) probe_radius (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) probs (MolecularDiffusion.modules.models.tabasco.flow.utils.HistogramTimeDistribution attribute) 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) 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.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_wandb (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.runmodes.train.logger.Logger attribute) prop_dist_model (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask 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_generate.GenerativeFactory attribute) property_prediction() (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory method) ProperyPrediction (class in MolecularDiffusion.modules.tasks.regression) 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) Q q (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) QED() (in module MolecularDiffusion.modules.tasks.metrics) 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) 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) Queue (class in MolecularDiffusion.callbacks.train_helper) queue (MolecularDiffusion.data.dataloader.DataQueue attribute) R r2() (in module MolecularDiffusion.modules.tasks.metrics) 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.models.shepherd_arch.equiformer_v2_encoder.EdgeDegreeEmbedding attribute) RadialFunction (class in MolecularDiffusion.modules.layers.equiformer_v2.radial_function) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.radial_function) radius (MolecularDiffusion.runmodes.train.data.DataModule attribute) random_permute (MolecularDiffusion.modules.layers.tabasco.positional_encoder.SinusoidEncoding attribute) (MolecularDiffusion.modules.layers.tabasco.positional_encoder.TimeFourierEncoding attribute) random_rotation() (in module MolecularDiffusion.modules.models.tabasco.data.transforms) (in module MolecularDiffusion.utils.geom_utils) random_rotation_matrix() (in module MolecularDiffusion.utils.geom_utils) range (MolecularDiffusion.utils.geom_analyzer.Histogram_cont attribute) rank (MolecularDiffusion.utils.io.RankState attribute) 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) ratio (MolecularDiffusion.utils.geom_analyzer.BasicMolecularMetrics attribute) RatioSampleNoiseSchedule (class in MolecularDiffusion.modules.models.tabasco.sample.noise_schedule) rdEHTTools (in module MolecularDiffusion.utils.xyz2mol.converter) rdkit_mol (MolecularDiffusion.utils.smilify.Molecule attribute) read_fragment_scores() (in module MolecularDiffusion.runmodes.data.preparation) read_xyz() (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.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) rebuild_ema_params (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer 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) reconstruct() (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask method) records (MolecularDiffusion.core.meter.Meter attribute) recursive_module_to_device() (in module MolecularDiffusion.utils.torch) reduce (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNorm attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.EquivariantGraphNormV2 attribute) reduce() (in module MolecularDiffusion.utils.comm) reference_indices (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) reference_mol (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) register() (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) regress_to_center (MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance.UFFBoundGuidance attribute) regularizer (MolecularDiffusion.callbacks.train_helper.SP_regularizer attribute) remap_values() (in module MolecularDiffusion.modules.models.shepherd_arch.model) remove_h_unit() (in module MolecularDiffusion.runmodes.data.augmentation) remove_hydrogens (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional.UnconditionalLMDBDataset attribute) remove_mean() (in module MolecularDiffusion.utils.geom_utils) remove_mean_pyG() (in module MolecularDiffusion.utils.molgraph_utils) remove_mean_with_mask() (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) 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) reorder_to_smiles_order (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional.UnconditionalLMDBDataset attribute) rescale (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.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.models.en_diffusion.PositiveLinear method) resume() (MolecularDiffusion.core.engine.Engine method) reverse_tensor() (in module MolecularDiffusion.modules.tasks.diffusion) rmsd_threshold (MolecularDiffusion.utils.geom_utils.MoleculeReconstructionEvaluator attribute) root (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule 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_axis() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca) rotation_axis_np() (in module MolecularDiffusion.utils.shepherd_score.alignment.utils.pca_np) RotationToWignerDMatrix() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Rotation method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Rotation method) run() (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory method) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator method) run_compare_analysis() (in module MolecularDiffusion.runmodes.analyze.compare_to_optimized) run_ema_update_cpu() (in module MolecularDiffusion.modules.models.tabasco.callbacks.ema) 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) (in module MolecularDiffusion.utils.geom_metrics) S s2_act (MolecularDiffusion.modules.layers.equiformer_v2.activation.SeparableS2Activation attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.activation.SeparableS2Activation attribute) S2Activation (class in MolecularDiffusion.modules.layers.equiformer_v2.activation) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.activation) SA() (in module MolecularDiffusion.modules.tasks.metrics) sample() (MolecularDiffusion.modules.models.en_diffusion.DistributionNodes method) (MolecularDiffusion.modules.models.en_diffusion.DistributionProperty method) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion 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_ldm.DiagonalGaussianDistribution method) (MolecularDiffusion.modules.tasks.diffusion_ldm.FlowMatchingInterpolant method) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoNodeDistribution method) sample_around_xh_target() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) sample_batch() (MolecularDiffusion.modules.models.en_diffusion.DistributionProperty method) sample_center_gravity_zero_gaussian_with_mask() (in module MolecularDiffusion.utils.geom_utils) sample_chain() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) sample_chain_guide() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) sample_cmd() (in module MolecularDiffusion.cli.data) sample_combined_position_feature_noise() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) sample_conditonal() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) 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_gaussian_with_mask() (in module MolecularDiffusion.utils.geom_utils) sample_guidance() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) sample_guidance_conitional() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) sample_hybrid_guidance() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative 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_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.en_diffusion.EnVariationalDiffusion method) sample_p_xh_given_z0() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) sample_p_zs_given_zt() (MolecularDiffusion.modules.models.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_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_ssgd() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) sample_schedule (MolecularDiffusion.modules.models.tabasco.flow_model.FlowMatchingModel attribute) sample_timestep_biased() (in module MolecularDiffusion.data.component.pharmacophore) sample_uniform_rotation() (in module MolecularDiffusion.modules.models.tabasco.data.transforms) SampleNoiseSchedule (class in MolecularDiffusion.modules.models.tabasco.sample.noise_schedule) sampling_mode (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) sanitize_smiles() (in module MolecularDiffusion.runmodes.analyze.xyz2mol) sanitized_config_dict() (MolecularDiffusion.core.engine.Engine method) save() (MolecularDiffusion.core.engine.Engine method) save_ema_model() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) 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) 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_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) SaveGeneratedMolsCallback (class in MolecularDiffusion.modules.models.tabasco.callbacks.save_molecules) scaffold_smarts (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) 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) scale_atom_features_x1 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) scale_bond_features_x1 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset 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) scale_node_features_x3 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) scale_node_features_x4 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset attribute) scale_noise_by_log_num_atoms (MolecularDiffusion.modules.models.tabasco.flow.interpolate.CenteredMetricInterpolant attribute) scale_schedule() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) scale_vector_features_x4 (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataset 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) 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) scheduler (MolecularDiffusion.core.engine.Engine attribute) scheduler_choice (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) scheduler_choice_kwargs (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) SCORES_THRESHOLD (in module MolecularDiffusion.runmodes.analyze.compute_metrics) (in module MolecularDiffusion.utils.geom_metrics) SDEMetricInterpolant (class in MolecularDiffusion.modules.models.tabasco.flow.interpolate) SE3Norm (class in MolecularDiffusion.modules.layers.conv) search() (MolecularDiffusion.core.core.Registry class method) seed (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) seed_everything() (in module MolecularDiffusion.utils.torch) self_attn (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer attribute) self_condition (MolecularDiffusion.modules.tasks.diffusion_ldm.FlowMatchingInterpolant attribute) self_condition_prob (MolecularDiffusion.modules.tasks.diffusion_ldm.FlowMatchingInterpolant 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) separator (in module MolecularDiffusion.utils.pretty) set_atomic_charges() (in module MolecularDiffusion.utils.xyz2mol.converter) set_atomic_radicals() (in module MolecularDiffusion.utils.xyz2mol.converter) 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_lmax_mmax() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Embedding method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Embedding method) set_normalizer() (MolecularDiffusion.modules.models.en_diffusion.DistributionProperty method) set_rank() (MolecularDiffusion.utils.io.RankState class method) set_wigner() (MolecularDiffusion.modules.layers.equiformer_v2.so3.SO3_Rotation method) (MolecularDiffusion.modules.layers.equiformer_v2_s.so3.SO3_Rotation method) setup() (MolecularDiffusion.modules.models.tabasco.data.lmdb_datamodule.LmdbDataModule method) 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) 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) shifted_softplus() (in module MolecularDiffusion.modules.layers.functional) short_cut (MolecularDiffusion.modules.layers.common.MLP attribute) show_schedule() (MolecularDiffusion.modules.models.en_diffusion.GammaNetwork method) sigma() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) sigma_and_alpha_t_given_s() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) SigmoidSmearing (class in MolecularDiffusion.modules.models.shepherd_arch.ocp_compat) SignalToNoiseTimeFactor (class in MolecularDiffusion.modules.models.tabasco.flow.time_factor) silent (MolecularDiffusion.core.meter.Meter attribute) SiLUSmearing (class in MolecularDiffusion.modules.models.shepherd_arch.ocp_compat) simple_idx_match_check() (in module MolecularDiffusion.data.component.pointcloud) (in module MolecularDiffusion.utils.smilify), [1] sin_embedding (MolecularDiffusion.modules.layers.conv.EquivariantBlock attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) single_bond_only() (in module MolecularDiffusion.utils.geom_analyzer) single_sample (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_base.BaseLMDBDataset attribute) SinusoidalPosEmb (class in MolecularDiffusion.modules.models.en_diffusion) SinusoidalPositionEmbedding (class in MolecularDiffusion.modules.layers.common) SinusoidEncoding (class in MolecularDiffusion.modules.layers.tabasco.positional_encoder) SinusoidsEmbeddingNew (class in MolecularDiffusion.modules.layers.common) size_cmd() (in module MolecularDiffusion.cli.data) smart_open() (in module MolecularDiffusion.utils.file) SMARTS_FEATURES_FDEF (in module MolecularDiffusion.utils.shepherd_utils) 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) 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) SNR() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion 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) so2_conv_2 (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) SO2_Convolution (class in MolecularDiffusion.modules.layers.equiformer_v2.so2_ops) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops) SO2_Linear (class in MolecularDiffusion.modules.layers.equiformer_v2.so2_ops) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops) so2_m_conv (MolecularDiffusion.modules.layers.equiformer_v2.so2_ops.SO2_Convolution attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.so2_ops.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) 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_Grid (class in MolecularDiffusion.modules.layers.equiformer_v2.so3) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.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.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_Linear (class in MolecularDiffusion.modules.layers.equiformer_v2.so3) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.so3) so3_linear_1 (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork attribute) so3_linear_2 (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.FeedForwardNetwork attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.FeedForwardNetwork 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) softplus() (in module MolecularDiffusion.modules.models.en_diffusion) sort_irreps_even_first() (in module MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) SP_regularizer (class in MolecularDiffusion.callbacks.train_helper) sp_regularizer (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) spacegroup_embedder (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT attribute) spearmanr() (in module MolecularDiffusion.modules.tasks.metrics) 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.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) 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) split (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_base.BaseLMDBDataset attribute) (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional.UnconditionalLMDBDataset attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask attribute) split_cmd() (in module MolecularDiffusion.cli.data) split_db() (in module MolecularDiffusion.runmodes.data.ase_ops) split_losses_by_time() (in module MolecularDiffusion.modules.models.tabasco.utils.metric_utils) split_reset_hook (MolecularDiffusion.runmodes.train.eval.TaskEvalConfig attribute) sqrd (MolecularDiffusion.modules.layers.tabasco.losses.InterDistancesLoss 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) stack() (in module MolecularDiffusion.utils.comm) (in module MolecularDiffusion.utils.torch) start_time (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) state_dict() (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) 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) stderr (MolecularDiffusion.utils.io.CaptureStdIO attribute) stdout (MolecularDiffusion.utils.io.CaptureStdIO 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.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) 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) 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) structural_guidance() (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory method) subsample_noise_schedule() (in module MolecularDiffusion.modules.models.shepherd_arch.inference.noise) subspace_dimensionality() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction method) sum_except_batch() (in module MolecularDiffusion.modules.models.en_diffusion) 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) 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) switch_main_parameter_weights() (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer method) symbol2num (in module MolecularDiffusion.utils.geom_analyzer) symbols (MolecularDiffusion.utils.smilify.Molecule attribute) sync_on_compute (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularUniqueness attribute) synchronize() (in module MolecularDiffusion.utils.comm) T T (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.models.noisemodel.NoiseModel attribute) t (MolecularDiffusion.modules.models.tabasco.flow.path.FlowPath attribute) T (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask property) t_embedder (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT attribute) t_max (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) tabasco_model (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) TabascoDiffusionTask (class in MolecularDiffusion.modules.tasks.diffusion_tabasco) TabascoNodeDistribution (class in MolecularDiffusion.modules.tasks.diffusion_tabasco) table (MolecularDiffusion.core.core.Registry attribute) tags (MolecularDiffusion.runmodes.train.logger.Logger attribute) tags_wandb (MolecularDiffusion.core.engine.Engine attribute) tanh (MolecularDiffusion.modules.layers.conv.EquivariantUpdate attribute) (MolecularDiffusion.modules.models.egcl.EGNN_dynamics 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.pharmacophore.PharmacophoreGenerative method) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction method) (MolecularDiffusion.modules.tasks.task.Task method) target_fields (MolecularDiffusion.runmodes.train.data.DataModule attribute) target_values (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) Task (class in MolecularDiffusion.modules.tasks.task) task (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) task_names (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) TASK_REGISTRY (in module MolecularDiffusion.runmodes.train.eval) task_type (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule 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_tabasco.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative 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) task_wrapper() (in module MolecularDiffusion.modules.models.tabasco.utils.utils) (in module MolecularDiffusion.utils.pretty) TaskEvalConfig (class in MolecularDiffusion.runmodes.train.eval) tasks (MolecularDiffusion.data.component.dataset.GraphDataset property) (MolecularDiffusion.data.component.dataset.PointCloudDataset property) tensor_obj_to_points() (MolecularDiffusion.modules.models.tabasco.chem.convert.MoleculeConverter method) TensorDictCollator (class in MolecularDiffusion.modules.models.tabasco.data.utils) TensorDictToPointCloudAdapter (class in MolecularDiffusion.modules.tasks.diffusion_tabasco) TensorProductRescale (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) test_data_dir (MolecularDiffusion.modules.models.tabasco.data.lmdb_datamodule.LmdbDataModule attribute) test_dataloader() (MolecularDiffusion.modules.models.tabasco.data.lmdb_datamodule.LmdbDataModule method) test_set (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) test_step() (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) tf_layers (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) thread (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer 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_dim (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) time_encoding (MolecularDiffusion.modules.layers.tabasco.transformer_module.TransformerModule attribute) time_factor (MolecularDiffusion.modules.layers.tabasco.losses.InterDistancesLoss attribute) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.Interpolant attribute) TimeFourierEncoding (class in MolecularDiffusion.modules.layers.tabasco.positional_encoder) TIMEOUT (in module MolecularDiffusion.utils.smilify) TimeoutException timestep_embedding() (MolecularDiffusion.modules.models.ldm.denoisers.dit.TimestepEmbedder static method) TimestepEmbedder (class in MolecularDiffusion.modules.models.ldm.denoisers.dit) timesteps (MolecularDiffusion.modules.models.en_diffusion.PredefinedNoiseSchedule 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) to_pointcloud (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) to_tensor() (MolecularDiffusion.modules.models.tabasco.chem.convert.MoleculeConverter method) to_tensordict (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) token_drop() (MolecularDiffusion.modules.models.ldm.denoisers.dit.LabelEmbedder method) total_charge (MolecularDiffusion.utils.smilify.Molecule attribute) 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.molcraftdiff.MolCraftDiff method) train_dataloader() (MolecularDiffusion.modules.models.tabasco.data.lmdb_datamodule.LmdbDataModule method) train_main() (in module MolecularDiffusion.cli.train) train_ratio (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) train_set (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) training_step() (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) TransBlockV2 (class in MolecularDiffusion.modules.layers.equiformer_v2.transformer_block) (class in MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block) transform (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_base.BaseLMDBDataset 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) 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) TransformerEncoder (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) translate_to_origine() (in module MolecularDiffusion.utils.geom_constraint) (in module MolecularDiffusion.utils.geom_utils) Tree (class in MolecularDiffusion.core.core) truncation (MolecularDiffusion.utils.pretty.PrettyPrinter attribute) tversky_func() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring) tversky_func_np() (in module MolecularDiffusion.utils.shepherd_score.score.pharmacophore_scoring_np) U UFFBoundGuidance (class in MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance) unconditional_generation() (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory method) UnconditionalLMDBDataset (class in MolecularDiffusion.modules.models.tabasco.data.components.lmdb_unconditional) uniform (MolecularDiffusion.modules.models.tabasco.flow.utils.HistogramTimeDistribution attribute) unnormalize() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) unnormalize_z() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) unsorted_segment_sum() (in module MolecularDiffusion.modules.layers.conv) unwrap_forward() (MolecularDiffusion.modules.models.egcl.EGNN_dynamics method) (MolecularDiffusion.modules.models.egt.EGT_dynamics method) update() (MolecularDiffusion.core.meter.Meter 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_average() (MolecularDiffusion.callbacks.train_helper.EMA method) update_data() (MolecularDiffusion.modules.models.tabasco.data.components.lmdb_base.BaseLMDBDataset method) update_lambda() (MolecularDiffusion.callbacks.train_helper.SP_regularizer method) update_model_average() (MolecularDiffusion.callbacks.train_helper.EMA method) update_mol_coordinates() (in module MolecularDiffusion.utils.shepherd_utils) use_adapter_module (MolecularDiffusion.modules.models.egcl.EGNN_dynamics attribute) 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_bias (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.TensorProductRescale 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_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_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_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.ldm.encoders.equiformer.EquiformerEncoder 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_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) V v (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock 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) VAETask (class in MolecularDiffusion.modules.tasks.diffusion_ldm) VAETaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_ldm) val_data_dir (MolecularDiffusion.modules.models.tabasco.data.lmdb_datamodule.LmdbDataModule attribute) val_dataloader() (MolecularDiffusion.modules.models.tabasco.data.lmdb_datamodule.LmdbDataModule method) 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) valid_set (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) valid_valencies (in module MolecularDiffusion.utils.geom_constant) validate_original_weights (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA attribute) validation_interval (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) validation_step() (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco 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) Vec2AttnHeads (class in MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations) verbose (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) verify_datapoint() (in module MolecularDiffusion.runmodes.data.ase_ops) vertices_labels (in module MolecularDiffusion.utils.geom_constant) vp_issnr_schedule() (in module MolecularDiffusion.modules.models.en_diffusion) vp_smld_schedule() (in module MolecularDiffusion.modules.models.en_diffusion) 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) 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.models.en_diffusion.PositiveLinear 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.ldm.decoders.equivariant_feedforward.FeedForwardDecoder attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) weight_init_offset (MolecularDiffusion.modules.models.en_diffusion.PositiveLinear 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) with_hydrogen (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) write_xyz() (in module MolecularDiffusion.runmodes.data.augmentation) write_xyz_file() (in module MolecularDiffusion.modules.models.tabasco.chem.utils) X x (MolecularDiffusion.data.component.pointcloud.Atom attribute) x1_bond_diffusion (MolecularDiffusion.modules.models.shepherd_arch.model.Model attribute) x_0 (MolecularDiffusion.modules.models.tabasco.flow.path.FlowPath attribute) x_1 (MolecularDiffusion.modules.models.tabasco.flow.path.FlowPath attribute) x_e_mul1 (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) x_e_mul2 (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) x_embedder (MolecularDiffusion.modules.models.ldm.denoisers.dit.DiT attribute) x_out (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) x_t (MolecularDiffusion.modules.models.tabasco.flow.path.FlowPath attribute) XEyTransformerLayer (class in MolecularDiffusion.modules.layers.conv) xtb_electronic() (in module MolecularDiffusion.cli.analyze) Xtoy (class in MolecularDiffusion.modules.layers.conv) 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) y_e_add (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) y_e_mul (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) y_x_add (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) y_x_mul (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) Z z (MolecularDiffusion.data.component.pointcloud.Atom attribute) zero_before (MolecularDiffusion.modules.models.tabasco.flow.time_factor.BaseTimeFactor attribute) ZeroSampleNoiseSchedule (class in MolecularDiffusion.modules.models.tabasco.sample.noise_schedule) ZeroTimeFactor (class in MolecularDiffusion.modules.models.tabasco.flow.time_factor)