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_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) 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) ANGSTROM_TO_BOHR (in module MolecularDiffusion.runmodes.analyze.xtb_electronic) 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) 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.LazyChunkedDataset method) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset 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.dataset.LazyChunkedDataset attribute) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset attribute) (MolecularDiffusion.data.component.feature.NodeFeaturizer attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.ModelTaskFactory attribute) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask attribute) (MolecularDiffusion.runmodes.analyze.featurize.SSL3DFeaturizer attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) atom_vocab_size (MolecularDiffusion.modules.tasks.ssl3d.MaskedAtomTypeObjective 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) atoms_to_batch() (in module MolecularDiffusion.runmodes.analyze.ssl3d_embed) 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) BaseFeaturizer (class in MolecularDiffusion.runmodes.analyze.featurize) 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.core.lightning_callbacks.generative_eval_callback.GenerativeEvalCallback attribute) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule attribute) (MolecularDiffusion.runmodes.analyze.featurize.SSL3DFeaturizer 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) BOHR_DEBYE (in module MolecularDiffusion.runmodes.analyze.xtb_electronic) 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_head() (MolecularDiffusion.modules.tasks.ssl3d.CoordDenoiseObjective method) (MolecularDiffusion.modules.tasks.ssl3d.MaskedAtomTypeObjective method) (MolecularDiffusion.modules.tasks.ssl3d.PairwiseDistObjective method) (MolecularDiffusion.modules.tasks.ssl3d.SSL3DObjective method) build_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) (in module MolecularDiffusion.utils.geom_metrics) 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) chunk_dir (MolecularDiffusion.data.component.dataset.LazyChunkedDataset attribute) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) chunk_paths (MolecularDiffusion.data.component.dataset.LazyChunkedDataset attribute) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset attribute) chunk_size (MolecularDiffusion.runmodes.train.data.DataModule attribute) chunk_sizes (MolecularDiffusion.data.component.dataset.LazyChunkedDataset attribute) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset attribute) clean_charges() (in module MolecularDiffusion.utils.xyz2mol.converter) clean_condition_tensor (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) 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) compact (MolecularDiffusion.runmodes.train.data.DataModule 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) (MolecularDiffusion.modules.tasks.ssl3d.CoordDenoiseObjective method) (MolecularDiffusion.modules.tasks.ssl3d.MaskedAtomTypeObjective method) (MolecularDiffusion.modules.tasks.ssl3d.PairwiseDistObjective method) (MolecularDiffusion.modules.tasks.ssl3d.SSL3DObjective method) compute_loss_distillation() (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion method) compute_loss_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_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) config_dict (MolecularDiffusion.runmodes.train.data.DatasetConfigDict attribute) Configurable (class in MolecularDiffusion.core.core) configure_gradient_clipping() (MolecularDiffusion.core.engine_lightning.EngineLightning method) configure_optimizers() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) 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_head (MolecularDiffusion.modules.tasks.ssl3d.CoordDenoiseObjective attribute) coord_mlp (MolecularDiffusion.modules.layers.conv.EquivariantUpdate attribute) coord_model() (MolecularDiffusion.modules.layers.conv.EquivariantUpdate method) CoordDenoiseObjective (class in MolecularDiffusion.modules.tasks.ssl3d) 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() (MolecularDiffusion.modules.tasks.ssl3d.CoordDenoiseObjective method) (MolecularDiffusion.modules.tasks.ssl3d.MaskedAtomTypeObjective method) (MolecularDiffusion.modules.tasks.ssl3d.PairwiseDistObjective method) (MolecularDiffusion.modules.tasks.ssl3d.SSL3DObjective method) corrupt_batch() (MolecularDiffusion.modules.tasks.diffusion_ldm.FlowMatchingInterpolant method) cosine_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) covalent_radii (in module MolecularDiffusion.utils.geom_metrics) 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.utils.geom_metrics) data() (in module MolecularDiffusion.cli.data) data_augmentation (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) data_efficient_collator (MolecularDiffusion.runmodes.train.data.DataModule attribute) data_fraction (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) data_module (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule 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_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) DatasetConfigDict (class in MolecularDiffusion.runmodes.train.data) DatasetStatsCallback (class in MolecularDiffusion.modules.models.tabasco.callbacks.dataset_stats) de (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock attribute) debug (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) decay (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback attribute) (MolecularDiffusion.modules.models.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) DEFAULT_SOAP_SPECIES (in module MolecularDiffusion.runmodes.analyze.featurize) DEFAULT_UMA_CHECKPOINT (in module MolecularDiffusion.runmodes.analyze.uma_embeddings) 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) desc (MolecularDiffusion.runmodes.analyze.featurize.SOAPFeaturizer attribute) 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.modules.tasks.ssl3d.SSL3D property) (MolecularDiffusion.runmodes.analyze.featurize.SSL3DFeaturizer attribute) (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_cutoff (MolecularDiffusion.modules.tasks.ssl3d.PairwiseDistObjective attribute) dist_head (MolecularDiffusion.modules.tasks.ssl3d.PairwiseDistObjective 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) early_stopped (MolecularDiffusion.runmodes.generate.sweep.RunResult 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_radius (MolecularDiffusion.runmodes.analyze.featurize.SSL3DFeaturizer attribute) EDGE_THRESHOLD (in module MolecularDiffusion.runmodes.analyze.compute_metrics) (in module MolecularDiffusion.utils.geom_analyzer) (in module MolecularDiffusion.utils.geom_constraint) (in module MolecularDiffusion.utils.geom_metrics) edge_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 (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback attribute) ema_decay (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) ema_model (MolecularDiffusion.core.engine_lightning.EngineLightning property) (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback attribute) ema_optimizer (MolecularDiffusion.modules.models.tabasco.sample.guided_sampling.GuidedSampling attribute) ema_params (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) ema_update() (in module MolecularDiffusion.modules.models.tabasco.callbacks.ema) EMACallback (class in MolecularDiffusion.core.lightning_callbacks.ema_callback) EMAOptimizer (class in MolecularDiffusion.modules.models.tabasco.callbacks.ema) 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) Engine (class in MolecularDiffusion.core.engine) engine_wrapper() (in module MolecularDiffusion.cli.eval_predict) (in module MolecularDiffusion.cli.train) EngineLightning (class in MolecularDiffusion.core.engine_lightning) 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.ssl3d.SSL3D method) (MolecularDiffusion.modules.tasks.task.Task method) (MolecularDiffusion.utils.geom_analyzer.BasicMolecularMetrics method) evaluate_and_save() (in module MolecularDiffusion.cli.train), [1] every_n_steps (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA attribute) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMAOptimizer attribute) 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) 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.cli.analyze) (in module MolecularDiffusion.runmodes.data.featurization) (MolecularDiffusion.data.component.feature.NodeFeaturizer method) (MolecularDiffusion.runmodes.analyze.featurize.BaseFeaturizer method) (MolecularDiffusion.runmodes.analyze.featurize.SOAPFeaturizer method) (MolecularDiffusion.runmodes.analyze.featurize.SSL3DFeaturizer method) (MolecularDiffusion.runmodes.analyze.featurize.UMAFeaturizer method) featurize_all() (MolecularDiffusion.data.component.feature.NodeFeaturizer method) featurize_cmd() (in module MolecularDiffusion.cli.data) 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.core.engine_lightning.EngineLightning method) (MolecularDiffusion.modules.layers.common.MLP method) (MolecularDiffusion.modules.layers.common.SinusoidalPositionEmbedding method) (MolecularDiffusion.modules.layers.common.SinusoidsEmbeddingNew method) (MolecularDiffusion.modules.layers.conv.EquivariantBlock method) (MolecularDiffusion.modules.layers.conv.EquivariantUpdate method) (MolecularDiffusion.modules.layers.conv.EtoX method) (MolecularDiffusion.modules.layers.conv.Etoy method) (MolecularDiffusion.modules.layers.conv.GCL method) (MolecularDiffusion.modules.layers.conv.NodeEdgeBlock method) (MolecularDiffusion.modules.layers.conv.PositionsMLP method) (MolecularDiffusion.modules.layers.conv.SE3Norm method) (MolecularDiffusion.modules.layers.conv.XEyTransformerLayer method) (MolecularDiffusion.modules.layers.conv.Xtoy method) (MolecularDiffusion.modules.layers.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) (MolecularDiffusion.modules.tasks.ssl3d.SSL3D method) forward_decoder_joint_heterogeneous_graph_encoder() (MolecularDiffusion.modules.models.shepherd_arch.model.Model method) forward_decoder_joint_processing() (MolecularDiffusion.modules.models.shepherd_arch.model.Model method) forward_jump() (in module MolecularDiffusion.modules.models.shepherd_arch.inference.noise) forward_jump_parameters() (in module MolecularDiffusion.modules.models.shepherd_arch.inference.noise) forward_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) generate_sweep() (in module MolecularDiffusion.cli.main) GenerativeEvalCallback (class in MolecularDiffusion.core.lightning_callbacks.generative_eval_callback) 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_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.LazyChunkedDataset method) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset 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_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.LazyChunkedDataset method) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset 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_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_uma_molecule_embeddings() (in module MolecularDiffusion.runmodes.analyze.uma_embeddings) 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.core.engine_lightning.EngineLightning attribute) (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) gradient_clip_mode (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) gradient_clipping (class in MolecularDiffusion.callbacks.train_helper) gradient_clipping_0 (class in MolecularDiffusion.callbacks.train_helper) gradient_interval (MolecularDiffusion.core.engine.Engine attribute) gradnorm_queue (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) 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) GuidanceModelPredictionPointCloud (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) (MolecularDiffusion.modules.tasks.ssl3d.SSL3D 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) 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) install_hint() (in module MolecularDiffusion.optional) 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) k_pairs (MolecularDiffusion.modules.tasks.ssl3d.PairwiseDistObjective 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) 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.analyze.featurize.UMAFeaturizer 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) LazyChunkedDataset (class in MolecularDiffusion.data.component.dataset) LazyChunkedGraphDataset (class in MolecularDiffusion.data.component.dataset) LDMTask (class in MolecularDiffusion.modules.tasks.diffusion_ldm) LDMTaskFactory (class in MolecularDiffusion.modules.tasks.diffusion_ldm) lg (in module MolecularDiffusion.utils.smilify) LIGHTNING_AVAILABLE (in module MolecularDiffusion.cli.train) lightning_module (MolecularDiffusion.modules.models.tabasco.sample.guided_sampling.GuidedSampling attribute) lightning_wrapper() (in module MolecularDiffusion.cli.train) LightningTabasco (class in MolecularDiffusion.modules.models.tabasco.lightning_tabasco) 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 (in module MolecularDiffusion.data.component.dataset) 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_lightning_model() (in module MolecularDiffusion.cli.generate) load_mlps_layer (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) load_model() (in module MolecularDiffusion.cli.generate) (in module MolecularDiffusion.cli.predict) load_molecules_from_xyz() (in module MolecularDiffusion.utils.geom_metrics) load_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_ssl3d_task() (in module MolecularDiffusion.runmodes.analyze.ssl3d_embed) 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.utils.metric_utils) (in module MolecularDiffusion.modules.models.tabasco.utils.metrics) (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) 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.engine_lightning) (in module MolecularDiffusion.core.lightning_callbacks.ema_callback) (in module MolecularDiffusion.core.lightning_callbacks.generative_eval_callback) (in module MolecularDiffusion.core.meter) (in module MolecularDiffusion.data.component.dataset) (in module MolecularDiffusion.data.component.pharmacophore) (in module MolecularDiffusion.data.dataset) (in module MolecularDiffusion.data.lightning_data_module) (in module MolecularDiffusion.modules.models.en_diffusion) (in module MolecularDiffusion.modules.models.pharmacophore_dynamics) (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.data) (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) (in module MolecularDiffusion.runmodes.generate.sweep) 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_rate (MolecularDiffusion.modules.tasks.ssl3d.MaskedAtomTypeObjective attribute) mask_token (MolecularDiffusion.modules.tasks.ssl3d.MaskedAtomTypeObjective 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) MaskedAtomTypeObjective (class in MolecularDiffusion.modules.tasks.ssl3d) 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.core.lightning_callbacks.generative_eval_callback.GenerativeEvalCallback attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction attribute) metric_key (MolecularDiffusion.runmodes.train.eval.TaskEvalConfig attribute) metrics() (in module MolecularDiffusion.cli.analyze) mha (MolecularDiffusion.modules.layers.tabasco.attention.AdaLNAttention attribute) (MolecularDiffusion.modules.layers.tabasco.attention.Attention attribute) (MolecularDiffusion.modules.layers.tabasco.attention.CrossAdaLNAttention attribute) mid_in_indices (MolecularDiffusion.modules.models.shepherd_arch.equiformer_operations.Vec2AttnHeads attribute) 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_hidden_dim (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) (MolecularDiffusion.modules.tasks.ssl3d.SSL3D attribute) model_class (MolecularDiffusion.runmodes.train.tasks_egt.ModelTaskFactory attribute) model_config (MolecularDiffusion.core.engine_lightning.EngineLightning 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.engine_lightning MolecularDiffusion.core.lightning_callbacks MolecularDiffusion.core.lightning_callbacks.ema_callback MolecularDiffusion.core.lightning_callbacks.generative_eval_callback MolecularDiffusion.core.logger MolecularDiffusion.core.meter MolecularDiffusion.data MolecularDiffusion.data.component MolecularDiffusion.data.component.dataset MolecularDiffusion.data.component.feature MolecularDiffusion.data.component.pharmacophore MolecularDiffusion.data.component.pointcloud MolecularDiffusion.data.dataloader MolecularDiffusion.data.dataset MolecularDiffusion.data.lightning_data_module 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.transforms MolecularDiffusion.modules.models.tabasco.data.utils MolecularDiffusion.modules.models.tabasco.flow MolecularDiffusion.modules.models.tabasco.flow.interpolate MolecularDiffusion.modules.models.tabasco.flow.path MolecularDiffusion.modules.models.tabasco.flow.time_factor MolecularDiffusion.modules.models.tabasco.flow.utils MolecularDiffusion.modules.models.tabasco.flow_model MolecularDiffusion.modules.models.tabasco.lightning_tabasco MolecularDiffusion.modules.models.tabasco.sample MolecularDiffusion.modules.models.tabasco.sample.guided_sampling MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance MolecularDiffusion.modules.models.tabasco.sample.noise_schedule MolecularDiffusion.modules.models.tabasco.utils MolecularDiffusion.modules.models.tabasco.utils.metric_utils MolecularDiffusion.modules.models.tabasco.utils.metrics MolecularDiffusion.modules.models.tabasco.utils.pylogger MolecularDiffusion.modules.models.tabasco.utils.tensor_ops MolecularDiffusion.modules.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.ssl3d MolecularDiffusion.modules.tasks.task MolecularDiffusion.molcraftdiff MolecularDiffusion.optional MolecularDiffusion.runmodes MolecularDiffusion.runmodes.analyze MolecularDiffusion.runmodes.analyze.compare_to_optimized MolecularDiffusion.runmodes.analyze.compute_metrics MolecularDiffusion.runmodes.analyze.featurize MolecularDiffusion.runmodes.analyze.ssl3d_embed MolecularDiffusion.runmodes.analyze.uma_embeddings MolecularDiffusion.runmodes.analyze.xtb_electronic MolecularDiffusion.runmodes.analyze.xtb_optimization MolecularDiffusion.runmodes.analyze.xyz2mol MolecularDiffusion.runmodes.data.ase_ops MolecularDiffusion.runmodes.data.augmentation MolecularDiffusion.runmodes.data.featurization MolecularDiffusion.runmodes.data.preparation MolecularDiffusion.runmodes.generate MolecularDiffusion.runmodes.generate.sweep 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.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_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.engine_lightning module MolecularDiffusion.core.lightning_callbacks module MolecularDiffusion.core.lightning_callbacks.ema_callback module MolecularDiffusion.core.lightning_callbacks.generative_eval_callback module MolecularDiffusion.core.logger module MolecularDiffusion.core.meter module MolecularDiffusion.data module MolecularDiffusion.data.component module MolecularDiffusion.data.component.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.lightning_data_module 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.transforms module MolecularDiffusion.modules.models.tabasco.data.utils module MolecularDiffusion.modules.models.tabasco.flow module MolecularDiffusion.modules.models.tabasco.flow.interpolate module MolecularDiffusion.modules.models.tabasco.flow.path module MolecularDiffusion.modules.models.tabasco.flow.time_factor module MolecularDiffusion.modules.models.tabasco.flow.utils module MolecularDiffusion.modules.models.tabasco.flow_model module MolecularDiffusion.modules.models.tabasco.lightning_tabasco module MolecularDiffusion.modules.models.tabasco.sample module MolecularDiffusion.modules.models.tabasco.sample.guided_sampling module MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance module MolecularDiffusion.modules.models.tabasco.sample.noise_schedule module MolecularDiffusion.modules.models.tabasco.utils module MolecularDiffusion.modules.models.tabasco.utils.metric_utils module MolecularDiffusion.modules.models.tabasco.utils.metrics module MolecularDiffusion.modules.models.tabasco.utils.pylogger module MolecularDiffusion.modules.models.tabasco.utils.tensor_ops module MolecularDiffusion.modules.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.ssl3d module MolecularDiffusion.modules.tasks.task module MolecularDiffusion.molcraftdiff module MolecularDiffusion.optional module MolecularDiffusion.runmodes module MolecularDiffusion.runmodes.analyze module MolecularDiffusion.runmodes.analyze.compare_to_optimized module MolecularDiffusion.runmodes.analyze.compute_metrics module MolecularDiffusion.runmodes.analyze.featurize module MolecularDiffusion.runmodes.analyze.ssl3d_embed module MolecularDiffusion.runmodes.analyze.uma_embeddings module MolecularDiffusion.runmodes.analyze.xtb_electronic module MolecularDiffusion.runmodes.analyze.xtb_optimization module MolecularDiffusion.runmodes.analyze.xyz2mol module MolecularDiffusion.runmodes.data.ase_ops module MolecularDiffusion.runmodes.data.augmentation module MolecularDiffusion.runmodes.data.featurization module MolecularDiffusion.runmodes.data.preparation module MolecularDiffusion.runmodes.generate module MolecularDiffusion.runmodes.generate.sweep 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 MolecularDiffusionDataModule (class in MolecularDiffusion.data.lightning_data_module) MolecularDiversity (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) MolecularLipinski (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) MolecularLogP (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) MolecularNovelty (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) MolecularQEDValue (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) MolecularUniqueness (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) MolecularValidity (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) Molecule (class in MolecularDiffusion.utils.smilify) (in module MolecularDiffusion.runmodes.data.preparation) molecule_default() (in module MolecularDiffusion.data.component.feature) MoleculeConverter (class in MolecularDiffusion.modules.models.tabasco.chem.convert) MoleculeMetricsCallback (class in MolecularDiffusion.modules.models.tabasco.callbacks.molecule_metrics) MoleculeReconstructionEvaluator (class in MolecularDiffusion.utils.geom_utils) monitor_metric (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) (MolecularDiffusion.core.lightning_callbacks.generative_eval_callback.GenerativeEvalCallback attribute) mse_loss (MolecularDiffusion.modules.layers.tabasco.losses.InterDistancesLoss attribute) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.CenteredMetricInterpolant attribute) (MolecularDiffusion.modules.models.tabasco.flow.interpolate.SDEMetricInterpolant attribute) 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_atoms (MolecularDiffusion.data.component.dataset.LazyChunkedDataset attribute) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset 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_dist_basis (MolecularDiffusion.modules.tasks.ssl3d.PairwiseDistObjective 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_jobs (MolecularDiffusion.runmodes.analyze.featurize.SOAPFeaturizer 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_samples (MolecularDiffusion.core.lightning_callbacks.generative_eval_callback.GenerativeEvalCallback 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 (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) node_feature_choice (MolecularDiffusion.runmodes.train.data.DataModule attribute) (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) node_feature_dim (MolecularDiffusion.runmodes.train.tasks_egcl.ModelTaskFactory attribute) node_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.LazyChunkedGraphDataset 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.LazyChunkedDataset property) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset 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.data.lightning_data_module.MolecularDiffusionDataModule 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) objectives (MolecularDiffusion.modules.tasks.ssl3d.SSL3D attribute) ok (MolecularDiffusion.runmodes.generate.sweep.RunResult attribute) on_before_optimizer_step() (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) on_fit_start() (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.dataset_stats.DatasetStatsCallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) on_load_checkpoint() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) on_save_checkpoint() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback method) (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) on_test_batch_end() (MolecularDiffusion.core.engine_lightning.EngineLightning method) on_test_end() (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) on_test_epoch_end() (MolecularDiffusion.core.engine_lightning.EngineLightning method) on_test_start() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) on_train_batch_end() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback method) on_train_start() (MolecularDiffusion.core.engine_lightning.EngineLightning method) on_validation_batch_end() (MolecularDiffusion.core.engine_lightning.EngineLightning method) on_validation_end() (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) on_validation_epoch_end() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.core.lightning_callbacks.generative_eval_callback.GenerativeEvalCallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.molecule_metrics.MoleculeMetricsCallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.posebusters.PoseBustersCallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.save_molecules.SaveGeneratedMolsCallback method) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask method) on_validation_epoch_start() (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask method) on_validation_start() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.core.lightning_callbacks.ema_callback.EMACallback method) (MolecularDiffusion.modules.models.tabasco.callbacks.ema.EMA method) one_hot() (in module MolecularDiffusion.modules.layers.functional) 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) optimizer_config (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) OptimSchedulerFactory (class in MolecularDiffusion.runmodes.train.trainer) optional_import_error() (in module MolecularDiffusion.optional) OptionalDependencyError original_smiles (MolecularDiffusion.modules.models.tabasco.utils.metrics.MolecularNovelty attribute) 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_dir (MolecularDiffusion.core.lightning_callbacks.generative_eval_callback.GenerativeEvalCallback 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) PairwiseDistObjective (class in MolecularDiffusion.modules.tasks.ssl3d) 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) persistent_workers (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule attribute) 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) (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule 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) pool_nodes() (in module MolecularDiffusion.runmodes.analyze.ssl3d_embed) pooling (MolecularDiffusion.runmodes.analyze.featurize.SOAPFeaturizer attribute) (MolecularDiffusion.runmodes.analyze.featurize.SSL3DFeaturizer attribute) 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) posebuster_timeout (MolecularDiffusion.core.lightning_callbacks.generative_eval_callback.GenerativeEvalCallback attribute) PoseBusters (in module MolecularDiffusion.utils.geom_metrics) posebusters (MolecularDiffusion.modules.models.tabasco.callbacks.posebusters.PoseBustersCallback attribute) PoseBustersCallback (class in MolecularDiffusion.modules.models.tabasco.callbacks.posebusters) PoseBustersValidity (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) PoseCheckStrainEnergy (class in MolecularDiffusion.modules.models.tabasco.utils.metrics) posenc_dim (MolecularDiffusion.modules.layers.tabasco.positional_encoder.SinusoidEncoding attribute) (MolecularDiffusion.modules.layers.tabasco.positional_encoder.TimeFourierEncoding attribute) positional_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_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.diffusion.GuidanceModelPredictionPointCloud method) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative method) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction method) (MolecularDiffusion.modules.tasks.ssl3d.SSL3D method) (MolecularDiffusion.modules.tasks.task.Task method) (MolecularDiffusion.molcraftdiff.MolCraftDiff method) predict_and_target() (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative method) (MolecularDiffusion.modules.tasks.diffusion_ldm.LDMTask method) (MolecularDiffusion.modules.tasks.diffusion_ldm.VAETask method) (MolecularDiffusion.modules.tasks.diffusion_tabasco.TabascoDiffusionTask method) (MolecularDiffusion.modules.tasks.ssl3d.SSL3D method) (MolecularDiffusion.modules.tasks.task.Task method) predict_dense() (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPredictionPointCloud 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) 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.ssl3d.SSL3D method) (MolecularDiffusion.modules.tasks.task.Task method) preprocess_ref_structure() (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory method) PrettyPrinter (class in MolecularDiffusion.utils.pretty) print() (in module MolecularDiffusion.utils.pretty) prior_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) pybel (in module MolecularDiffusion.utils.geom_metrics) 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) RDLogger (in module MolecularDiffusion.runmodes.analyze.compute_metrics) 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) reason (MolecularDiffusion.runmodes.generate.sweep.RunResult 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_feature_stats (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) reference_freeze_mode (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) reference_indices (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative attribute) reference_mol (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) reference_scaffold (MolecularDiffusion.modules.tasks.diffusion.GeomMolecularGenerative 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_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) require_modules() (in module MolecularDiffusion.optional) 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_featurize() (in module MolecularDiffusion.runmodes.analyze.featurize) run_postbuster() (in module MolecularDiffusion.utils.geom_metrics) run_processing() (in module MolecularDiffusion.runmodes.analyze.xyz2mol) runner() (in module MolecularDiffusion.cli.predict) (in module MolecularDiffusion.runmodes.analyze.compute_metrics) (in module MolecularDiffusion.utils.geom_metrics) RunResult (class in MolecularDiffusion.runmodes.generate.sweep) 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) save_xyzrender_figures (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) 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) scheduler_config (MolecularDiffusion.core.engine_lightning.EngineLightning 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.core.engine_lightning.EngineLightning method) (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule 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) sigma_max (MolecularDiffusion.modules.tasks.ssl3d.CoordDenoiseObjective attribute) sigma_min (MolecularDiffusion.modules.tasks.ssl3d.CoordDenoiseObjective attribute) sigma_schedule (MolecularDiffusion.modules.tasks.ssl3d.CoordDenoiseObjective attribute) 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) 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) sleep_every_N (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) sleep_time (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) smart_open() (in module MolecularDiffusion.utils.file) SMARTS_FEATURES_FDEF (in module MolecularDiffusion.utils.shepherd_utils) smiles_list (MolecularDiffusion.data.component.dataset.LazyChunkedDataset attribute) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset attribute) smilfy_xtb() (in module MolecularDiffusion.utils.smilify) smilify_openbabel() (in module MolecularDiffusion.runmodes.data.preparation) (in module MolecularDiffusion.utils.smilify) smilify_structure() (in module MolecularDiffusion.runmodes.data.preparation) smilify_wrapper() (in module MolecularDiffusion.utils.geom_metrics) smilify_xyz2mol() (in module MolecularDiffusion.runmodes.data.preparation) (in module MolecularDiffusion.utils.smilify) 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) SOAPFeaturizer (class in MolecularDiffusion.runmodes.analyze.featurize) 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.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) SSL3D (class in MolecularDiffusion.modules.tasks.ssl3d) SSL3DFeaturizer (class in MolecularDiffusion.runmodes.analyze.featurize) SSL3DObjective (class in MolecularDiffusion.modules.tasks.ssl3d) stack() (in module MolecularDiffusion.utils.comm) (in module MolecularDiffusion.utils.torch) start_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_embedding (MolecularDiffusion.modules.tasks.ssl3d.SSL3D 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.diffusion.GuidanceModelPredictionPointCloud method) (MolecularDiffusion.modules.tasks.pharmacophore.PharmacophoreGenerative method) (MolecularDiffusion.modules.tasks.regression.ProperyPrediction method) (MolecularDiffusion.modules.tasks.ssl3d.SSL3D method) (MolecularDiffusion.modules.tasks.task.Task method) target_fields (MolecularDiffusion.runmodes.train.data.DataModule attribute) target_values (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory attribute) targets (MolecularDiffusion.data.component.dataset.LazyChunkedDataset property) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset property) Task (class in MolecularDiffusion.modules.tasks.task) task (MolecularDiffusion.core.engine_lightning.EngineLightning attribute) (MolecularDiffusion.modules.tasks.diffusion.GuidanceModelPrediction attribute) (MolecularDiffusion.modules.tasks.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.utils.pretty) TaskEvalConfig (class in MolecularDiffusion.runmodes.train.eval) tasks (MolecularDiffusion.data.component.dataset.GraphDataset property) (MolecularDiffusion.data.component.dataset.LazyChunkedDataset property) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset property) (MolecularDiffusion.data.component.dataset.PointCloudDataset property) 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_dataloader() (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule method) test_set (MolecularDiffusion.core.engine.Engine attribute) (MolecularDiffusion.data.component.pharmacophore.PharmacophoreDataModule attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) test_step() (MolecularDiffusion.core.engine_lightning.EngineLightning method) (MolecularDiffusion.modules.models.tabasco.lightning_tabasco.LightningTabasco method) tf_layers (MolecularDiffusion.modules.models.egt.GraphDiffTransformer attribute) (MolecularDiffusion.modules.models.egt.GraphTransformer attribute) 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.data.lightning_data_module.MolecularDiffusionDataModule 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.core.engine_lightning.EngineLightning method) (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.data.component.dataset.LazyChunkedGraphDataset 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) type_head (MolecularDiffusion.modules.tasks.ssl3d.MaskedAtomTypeObjective attribute) U UFFBoundGuidance (class in MolecularDiffusion.modules.models.tabasco.sample.interpolant_guidance) UMAFeaturizer (class in MolecularDiffusion.runmodes.analyze.featurize) unconditional_generation() (MolecularDiffusion.runmodes.generate.tasks_generate.GenerativeFactory method) uniform (MolecularDiffusion.modules.models.tabasco.flow.utils.HistogramTimeDistribution attribute) 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_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_noised_conditioning (MolecularDiffusion.modules.models.en_diffusion.EnVariationalDiffusion attribute) (MolecularDiffusion.runmodes.generate.tasks_generate.PharmacophoreConditionGenerator attribute) use_ohe (MolecularDiffusion.data.component.feature.NodeFeaturizer attribute) use_ohe_feature (MolecularDiffusion.runmodes.train.data.DataModule attribute) use_pbc (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) use_posebuster (MolecularDiffusion.core.lightning_callbacks.generative_eval_callback.GenerativeEvalCallback attribute) use_row_data_features (MolecularDiffusion.runmodes.train.data.DataModule attribute) use_s2_act_attn (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.transformer_block.SO2EquivariantGraphAttention attribute) (MolecularDiffusion.modules.models.ldm.encoders.equiformer.EquiformerEncoder attribute) (MolecularDiffusion.modules.models.shepherd_arch.equiformer_v2_encoder.EquiformerV2 attribute) use_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_dataloader() (MolecularDiffusion.data.lightning_data_module.MolecularDiffusionDataModule 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.core.engine_lightning.EngineLightning method) (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) (MolecularDiffusion.modules.tasks.ssl3d.SSL3DObjective attribute) weight_decay (MolecularDiffusion.runmodes.train.trainer.OptimSchedulerFactory attribute) WEIGHT_FACTOR (in module MolecularDiffusion.utils.geom_constraint) weight_init (MolecularDiffusion.modules.layers.equiformer_v2.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.layers.equiformer_v2_s.equiformer_v2_oc20.EquiformerV2_OC20 attribute) (MolecularDiffusion.modules.models.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.data.component.dataset.LazyChunkedDataset attribute) (MolecularDiffusion.data.component.dataset.LazyChunkedGraphDataset attribute) (MolecularDiffusion.runmodes.train.data.DataModule attribute) world_size (MolecularDiffusion.core.engine.Engine attribute) wrap_forward() (MolecularDiffusion.modules.models.egcl.EGNN_dynamics method) (MolecularDiffusion.modules.models.egt.EGT_dynamics method) 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)