Index

A

aatype (deepfold.common.protein.Protein attribute) aatype_to_str_sequence() (in module deepfold.common.residue_constants) accept_residue() (bis_protein_structure.DATAGEN.AllResiduesSelector method), [1] accumulate_grad_from_subgraph() (in module diffalign.utils.datasets) add() (in module deepfold.utils.tensor_utils) add_assembly_features() (in module deepfold.data.multimer.input_features) add_hydrogen_index() (gd_dl.lib_pdb_mol2.MOL2_UNIT method) add_particle() (deepfold.eval.cell_lists.CellLists method) add_pdb_headers() (in module deepfold.common.protein) AddAngleDihedral (class in diffalign.utils.transforms) AddEdgeLength (class in diffalign.utils.transforms) AddEdgeName (class in diffalign.utils.transforms) AddHigherOrderEdges (class in diffalign.utils.transforms) AddPlaceHolder (class in diffalign.utils.transforms) affinity_metrics() (in module promptbind.utils.metrics) align() (deepfold.data.tools.kalign.Kalign method) aligned_cols (deepfold.data.search.parsers.TemplateHit attribute) AlignRatioError all_equal() (in module deepfold.utils.iter_utils) all_to_all() (in module deepfold.distributed.model_parallel) AllResiduesSelector (class in bis_protein_structure.DATAGEN) AlphaFold (class in deepfold.modules.alphafold) AlphaFoldConfig (class in deepfold.config) AlphaFoldLoss (class in deepfold.loss) AlphaFoldLRScheduler (class in deepfold.train.lr_scheduler) AlphaFoldSWA (class in deepfold.utils.swa_utils) AmberRelaxation (class in deepfold.relax.relax) angle_norm_weight (deepfold.config.SupervisedChiLossConfig attribute) angle_rad (bis_protein_structure.residue_constants.BondAngle attribute) (deepfold.common.residue_constants.BondAngle attribute) AngleResnet (class in deepfold.modules.angle_resnet) AngleResnetBlock (class in deepfold.modules.angle_resnet) angles_to_sincos() (in module bis_protein_structure.TORSION2) append() (gd_dl.lib_pdb_mol2.Model method) (gd_dl.lib_pdb_mol2.Residue method) append_atom_index() (gd_dl.lib_pdb_mol2.MOL2_UNIT method) append_atom_mol2_type() (gd_dl.lib_pdb_mol2.MOL2_UNIT method) append_coordinates() (gd_dl.lib_pdb_mol2.MOL2_UNIT method) apply() (deepfold.utils.geometry.Rigid method) (deepfold.utils.geometry.Rigid3Array method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array method) (deepfold.utils.geometry.Rotation method) (deepfold.utils.rigid_utils.Rigid method) (deepfold.utils.rigid_utils.Rotation method) apply_inverse_to_point() (deepfold.utils.geometry.Rigid3Array method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array method) (deepfold.utils.geometry.Rot3Array method) (deepfold.utils.geometry.rotation_matrix.Rot3Array method)

apply_rot_fn() (deepfold.utils.geometry.Rigid method) (deepfold.utils.rigid_utils.Rigid method) apply_to_point() (deepfold.utils.geometry.Rigid3Array method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array method) (deepfold.utils.geometry.Rot3Array method) (deepfold.utils.geometry.rotation_matrix.Rot3Array method) apply_trans_fn() (deepfold.utils.geometry.Rigid method) (deepfold.utils.rigid_utils.Rigid method) array_tree_map() (in module deepfold.utils.tensor_utils) assemblies (deepfold.data.pdbx_parsing.PDBxObject attribute) assembly_id (deepfold.data.pdbx_parsing.AssemblyGenerator attribute) AssemblyGenerator (class in deepfold.data.pdbx_parsing) assert_equal_nonterminal_atom_types() (in module deepfold.relax.utils) assert_viewless_tensor() (in module deepfold.distributed.utils) assign() (in module deepfold.utils.import_utils) asym_id_list (deepfold.data.pdbx_parsing.AssemblyGenerator attribute) AsyncGradientClipping (class in deepfold.train.gradient_clipping) atmIndex() (gd_dl.lib_pdb_mol2.Residue method) atmName() (gd_dl.lib_pdb_mol2.Atom method) (gd_dl.lib_pdb_mol2.Residue method) Atom (class in deepfold.eval.contact) (class in gd_dl.lib_pdb_mol2) atom1_name (bis_protein_structure.residue_constants.Bond attribute) (bis_protein_structure.residue_constants.BondAngle attribute) (deepfold.common.residue_constants.Bond attribute) (deepfold.common.residue_constants.BondAngle attribute) atom2_name (bis_protein_structure.residue_constants.Bond attribute) (bis_protein_structure.residue_constants.BondAngle attribute) (deepfold.common.residue_constants.Bond attribute) (deepfold.common.residue_constants.BondAngle attribute) atom3name (bis_protein_structure.residue_constants.BondAngle attribute) (deepfold.common.residue_constants.BondAngle attribute) atom_mask (deepfold.common.protein.Protein attribute) atom_positions (deepfold.common.protein.Protein attribute) atom_type (deepfold.eval.contact.Atom attribute) AtomMap (class in deepfold.data.monomer) AtomSite (class in deepfold.data.pdbx_parsing) att_model() (promptbind.models.egnn.MC_Att_L method) Attention (class in promptbind.models.model_utils) auth_asym_id (deepfold.data.pdbx_parsing.ResiduePosition attribute) auth_seq_id (deepfold.data.pdbx_parsing.ResiduePosition attribute) auth_to_label (deepfold.data.pdbx_parsing.PDBxObject attribute) author_chain_id (deepfold.data.pdbx_parsing.AtomSite attribute) author_seq_num (deepfold.data.pdbx_parsing.AtomSite attribute) auxiliary_heads_config (deepfold.config.AlphaFoldConfig attribute) AuxiliaryHeads (class in deepfold.modules.auxiliary_heads) AuxiliaryHeadsConfig (class in deepfold.config) average_clashes (deepfold.config.ViolationLossConfig attribute)

B

b_factors (deepfold.common.protein.Protein attribute) backbone_clamp_distance (deepfold.config.FAPELossConfig attribute) backbone_loss() (in module deepfold.losses.geometry) backbone_loss_unit_distance (deepfold.config.FAPELossConfig attribute) backbone_weight (deepfold.config.FAPELossConfig attribute) BackboneUpdate (class in deepfold.modules.backbone_update) backward() (deepfold.distributed.model_parallel.Disable static method) (deepfold.distributed.model_parallel.Enable static method) (deepfold.losses.procrustes.Procrustes static method) batched_gather() (in module deepfold.utils.tensor_utils) between_residue_bond_loss() (in module deepfold.losses.violation) between_residue_clash_loss() (in module deepfold.losses.violation) bin_edges_np() (in module deepfold.eval.distogram) binarize() (diffalign.utils.transforms.AddHigherOrderEdges method) (in module promptbind.utils.feature_utils) (in module promptbind.utils.generation_utils) (in module promptbind.utils.inference_mol_utils) bis_protein_structure module, [1] bis_protein_structure.CROSSLINK module, [1] bis_protein_structure.DATAGEN module, [1] bis_protein_structure.DISULFIDE module, [1] bis_protein_structure.MMEVAL module, [1]

bis_protein_structure.residue_constants module, [1] bis_protein_structure.SOLVENTACC module, [1] bis_protein_structure.split_pdb module, [1] bis_protein_structure.TORSION2 module, [1] BlackHole (class in diffalign.utils.misc) block_delete_msa_enabled (deepfold.config.FeaturePipelineConfig attribute) block_diag() (in module deepfold.data.multimer.msa_pairing) block_size_tri_mul (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) (deepfold.config.TemplatePairStackConfig attribute) Bond (class in bis_protein_structure.residue_constants) (class in deepfold.common.residue_constants) bond_type_to_int() (in module diffalign.utils.chem) BondAngle (class in bis_protein_structure.residue_constants) (class in deepfold.common.residue_constants) broadcast() (in module deepfold.distributed.model_parallel) broadcast_on_model_parallel_region() (in module deepfold.distributed.model_parallel) build_atom_map() (in module deepfold.data.monomer) build_profile_from_a3m() (deepfold.data.tools.hmmbuild.Hmmbuild method) build_profile_from_sto() (deepfold.data.tools.hmmbuild.Hmmbuild method) build_query_to_hit_index_mapping() (in module deepfold.data.search.templates) build_template_pair_feat() (deepfold.modules.template_pair_embedder.TemplatePairEmbedder method) (deepfold.modules.template_pair_embedder.TemplatePairEmbedderMultimer method)

C

c_aatype (deepfold.config.TemplatePairEmbedderConfig attribute) c_dgram (deepfold.config.TemplatePairEmbedderConfig attribute) c_e (deepfold.config.ExtraMSAEmbedderConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) c_hidden (deepfold.config.PerResidueLDDTCaPredictorConfig attribute) (deepfold.config.TemplatePointwiseAttentionConfig attribute) c_hidden_ang_res (deepfold.config.StructureModuleConfig attribute) c_hidden_ipa (deepfold.config.StructureModuleConfig attribute) c_hidden_msa_att (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) c_hidden_opm (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) c_hidden_tri_att (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) (deepfold.config.TemplatePairStackConfig attribute) c_hidden_tri_mul (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) (deepfold.config.TemplatePairStackConfig attribute) c_m (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.InputEmbedderConfig attribute) (deepfold.config.MaskedMSAHeadConfig attribute) (deepfold.config.RecyclingEmbedderConfig attribute) (deepfold.config.TemplateAngleEmbedderConfig attribute) c_out (deepfold.config.ExperimentallyResolvedHeadConfig attribute) (deepfold.config.MaskedMSAHeadConfig attribute) c_s (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExperimentallyResolvedHeadConfig attribute) (deepfold.config.PerResidueLDDTCaPredictorConfig attribute) (deepfold.config.StructureModuleConfig attribute) c_t (deepfold.config.TemplatePairEmbedderConfig attribute) (deepfold.config.TemplatePairStackConfig attribute) (deepfold.config.TemplatePointwiseAttentionConfig attribute) (deepfold.config.TemplateProjectionConfig attribute) c_z (deepfold.config.DistogramHeadConfig attribute) (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) (deepfold.config.InputEmbedderConfig attribute) (deepfold.config.RecyclingEmbedderConfig attribute) (deepfold.config.StructureModuleConfig attribute) (deepfold.config.TemplatePairEmbedderConfig attribute) (deepfold.config.TemplatePointwiseAttentionConfig attribute) (deepfold.config.TemplateProjectionConfig attribute) (deepfold.config.TMScoreHeadConfig attribute) CaDistanceError calc_e() (in module gd_dl.data.all_ML_rerank) (in module gd_dl.data.ML_inference) (in module gd_dl.data.ML_rerank) (in module gd_dl.data.single_ML_rerank) calculate_bin_centers() (in module deepfold.losses.utils) calculate_bin_centers_np() (in module deepfold.eval.distogram) calculate_calpha_distogram() (in module bis_protein_structure.CROSSLINK) calculate_energy() (in module gd_dl.data.ML_inference) calculate_lys_leu_map() (in module bis_protein_structure.CROSSLINK) calculate_neighbor_offsets() (deepfold.eval.cell_lists.CellLists method) calculate_sa_map() (in module bis_protein_structure.CROSSLINK) calculate_tryptic_map() (in module bis_protein_structure.CROSSLINK) cat() (deepfold.utils.geometry.Rigid static method) (deepfold.utils.geometry.Rigid3Array class method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array class method) (deepfold.utils.geometry.Rot3Array class method) (deepfold.utils.geometry.Rotation static method) (deepfold.utils.geometry.rotation_matrix.Rot3Array class method) (deepfold.utils.geometry.Vec3Array class method) (deepfold.utils.geometry.vector.Vec3Array class method) (deepfold.utils.rigid_utils.Rigid static method) (deepfold.utils.rigid_utils.Rotation static method) CategoryNotFoundError CellLists (class in deepfold.eval.cell_lists) CenterOfMassConfig (class in deepfold.config) Cgc_block (class in gd_dl.models) (class in gd_dl.rerank_model) chain (deepfold.data.search.parsers.HitMetadata attribute) chain_center_of_mass_config (deepfold.config.LossConfig attribute) chain_centre_mass_loss() (in module deepfold.losses.auxillary) chain_ids (deepfold.data.pdbx_parsing.PDBxObject attribute) chain_index (deepfold.common.protein.Protein attribute) (deepfold.eval.contact.Atom attribute) chain_to_entity (deepfold.data.pdbx_parsing.PDBxObject attribute) chain_to_structure (deepfold.data.pdbx_parsing.PDBxObject attribute) chainID() (gd_dl.lib_pdb_mol2.Residue method) check_bb() (gd_dl.lib_pdb_mol2.Residue method) chi_angle_atom() (in module bis_protein_structure.residue_constants) (in module deepfold.common.residue_constants) chi_weight (deepfold.config.SupervisedChiLossConfig attribute) chunk_layer() (in module deepfold.utils.chunk_utils) chunk_size (deepfold.config.TemplatePointwiseAttentionConfig attribute) chunk_size_msa_att (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) chunk_size_opm (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) chunk_size_tri_att (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) (deepfold.config.TemplatePairStackConfig attribute) clamp_distance (deepfold.config.CenterOfMassConfig attribute) clamped_fape_enabled (deepfold.config.FeaturePipelineConfig attribute) clamped_fape_probability (deepfold.config.FeaturePipelineConfig attribute)

clash_overlap_tolerance (deepfold.config.ViolationLossConfig attribute) clean_protein() (in module deepfold.relax.amber_minimize) clean_structure() (in module deepfold.relax.cleanup) clear() (deepfold.eval.cell_lists.CellLists method) clip_grad_max_nrom (deepfold.config.TrainingConfig attribute) clone() (deepfold.utils.geometry.Vec3Array method) (deepfold.utils.geometry.vector.Vec3Array method) cls_metric() (in module promptbind.utils.metrics) col_to_row() (in module deepfold.distributed.model_parallel) collate() (in module deepfold.utils.tensor_utils) collate_fn() (diffalign.utils.datasets.SidechainConformationDataset static method) Collater (class in diffalign.utils.dataloader) ComplexGraph (class in promptbind.models.att_model) ComplexInfo (class in deepfold.data.multimer.input_features) compose() (deepfold.utils.geometry.Rigid method) (deepfold.utils.geometry.Rigid3Array method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array method) (deepfold.utils.rigid_utils.Rigid method) compose_q() (deepfold.utils.geometry.Rotation method) (deepfold.utils.rigid_utils.Rotation method) compose_q_update_vec() (deepfold.utils.geometry.Rigid method) (deepfold.utils.geometry.Rotation method) (deepfold.utils.rigid_utils.Rigid method) (deepfold.utils.rigid_utils.Rotation method) compose_r() (deepfold.utils.geometry.Rotation method) (deepfold.utils.rigid_utils.Rotation method) compose_rotation() (deepfold.utils.geometry.Rigid3Array method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array method) compute_dis_between_two_vector() (in module promptbind.utils.utils) compute_dis_between_two_vector_tensor() (in module promptbind.utils.utils) compute_distogram() (in module deepfold.eval.distogram) (in module deepfold.losses.geometry) compute_fape() (in module deepfold.losses.geometry) compute_individual_metrics() (in module promptbind.utils.metrics) compute_neff_v1() (in module deepfold.eval.msa) compute_neff_v2() (in module deepfold.eval.msa) compute_plddt() (in module deepfold.losses.confidence) compute_predicted_aligned_error() (in module deepfold.losses.confidence) compute_predicted_distogram() (in module deepfold.eval.distogram) compute_renamed_ground_truth() (in module deepfold.losses.geometry) compute_RMSD() (in module promptbind.utils.generation_utils) (in module promptbind.utils.post_optim_utils) compute_tm() (in module deepfold.losses.confidence) compute_validation_metrics() (in module deepfold.train.validation_metrics) compute_violation_metrics() (in module deepfold.losses.violation) compute_violation_metrics_np() (in module deepfold.losses.violation) ConformationDataset (class in diffalign.utils.datasets) construct_data_from_graph_gvp_mean() (in module promptbind.utils.utils) construct_edges() (promptbind.models.att_model.ComplexGraph method) contact_map() (in module deepfold.eval.contact) contains_non_numeric() (in module bis_protein_structure.SOLVENTACC) convert_mmcif_to_dssp() (in module bis_protein_structure.SOLVENTACC) convert_mmcif_to_dssp_parallel() (in module bis_protein_structure.SOLVENTACC) convert_monomer_features() (in module deepfold.data.multimer.input_features) convert_pdb_to_dssp() (in module bis_protein_structure.SOLVENTACC) convert_stockholm_to_a3m() (in module deepfold.data.search.parsers) convert_string() (in module bis_protein_structure.MMEVAL) coord2radial() (diffalign.models.encoder.egnn.E_GCL method) (in module promptbind.models.egnn) coord_model() (diffalign.models.encoder.egnn.E_GCL method) (promptbind.models.egnn.MC_Att_L method) (promptbind.models.egnn.MC_E_GCL method) (promptbind.models.egnn.MC_E_GCL_Prompt method) copy_to_model_parallel_reigon() (in module deepfold.distributed.model_parallel) CountNodesPerGraph (class in diffalign.utils.transforms) CovMatEvaluator (class in diffalign.utils.evaluation.covmat) create_all_seq_msa_features() (in module deepfold.data.multimer.input_features) create_all_seq_msa_features_from_a3m() (in module deepfold.data.multimer.input_features) create_empty_template_feats() (in module deepfold.data.search.templates) create_mmcif_features() (in module deepfold.data.search.input_features) create_msa_features() (in module deepfold.data.search.input_features) create_multimer_features() (in module deepfold.data.multimer.input_features) create_paired_features() (in module deepfold.data.multimer.msa_pairing) create_pdb_features() (in module deepfold.data.search.input_features) create_protein_features() (in module deepfold.data.search.input_features) create_sequence_features() (in module deepfold.data.search.input_features) create_structure_from_feature() (in module bis_protein_structure.DATAGEN) (in module bis_protein_structure.SOLVENTACC) create_template_features() (in module deepfold.data.search.input_features) create_template_features_from_hhr_string() (in module deepfold.data.search.input_features) create_template_features_from_hmmsearch_sto_string() (in module deepfold.data.search.input_features) crop_a3m_string() (in module deepfold.utils.feats_utils) crop_chains() (in module deepfold.data.multimer.input_features) crop_features() (in module deepfold.utils.feats_utils) crop_size (deepfold.config.FeaturePipelineConfig attribute) cross() (deepfold.utils.geometry.Vec3Array method) (deepfold.utils.geometry.vector.Vec3Array method) (in module deepfold.utils.geometry.vector) CrossAttentionModule (class in promptbind.models.cross_att) CrossAttentionNoGate (class in deepfold.modules.attention) cuda() (deepfold.utils.geometry.Rigid method) (deepfold.utils.geometry.Rigid3Array method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array method) (deepfold.utils.geometry.Rotation method) (deepfold.utils.rigid_utils.Rigid method) (deepfold.utils.rigid_utils.Rotation method) cutoff (deepfold.config.PLDDTLossConfig attribute)

D

DataLoader (class in diffalign.utils.dataloader) DateError datetime_from_string() (in module deepfold.utils.datetime_utils) datetime_to_string() (in module deepfold.utils.datetime_utils) DDIM_CFG_Sampling() (diffalign.models.epsnet.diffusion.DiffAlign method) DDPM_CFG_Sampling() (diffalign.models.epsnet.diffusion.DiffAlign method) DDPM_Sampling() (diffalign.models.epsnet.diffusion.DiffAlign method) deduplicate_stockholm_msa() (in module deepfold.data.search.parsers) deduplicate_unpaired_sequences() (in module deepfold.data.multimer.msa_pairing) deepfold module, [1] deepfold.common module, [1] deepfold.common.protein module, [1] deepfold.common.residue_constants module, [1] deepfold.config module, [1] deepfold.data module, [1] deepfold.data.errors module, [1] deepfold.data.modules module, [1] deepfold.data.modules.dataloaders module, [1] deepfold.data.modules.mmcif_dataset module, [1] deepfold.data.modules.samplers module, [1] deepfold.data.modules.single_dataset module, [1] deepfold.data.monomer module, [1] deepfold.data.multimer module, [1] deepfold.data.multimer.input_features module, [1] deepfold.data.multimer.msa_pairing module, [1] deepfold.data.pdbio module, [1] deepfold.data.pdbx_parsing module, [1] deepfold.data.search module, [1] deepfold.data.search.crfalign module, [1] deepfold.data.search.input_features module, [1] deepfold.data.search.mmcif module, [1] deepfold.data.search.msa_identifiers module, [1] deepfold.data.search.parsers module, [1] deepfold.data.search.templates module, [1] deepfold.data.tools module, [1] deepfold.data.tools.hhblits module, [1] deepfold.data.tools.hhsearch module, [1] deepfold.data.tools.hmmbuild module, [1] deepfold.data.tools.hmmsearch module, [1] deepfold.data.tools.jackhmmer module, [1] deepfold.data.tools.kalign module, [1] deepfold.data.tools.utils module, [1] deepfold.distributed module, [1] deepfold.distributed.model_parallel module, [1] deepfold.distributed.utils module, [1] deepfold.eval module, [1] deepfold.eval.cell_lists module, [1] deepfold.eval.contact module, [1] deepfold.eval.distogram module, [1] deepfold.eval.msa module, [1] deepfold.eval.plot module, [1] deepfold.eval.pseudo_3d module, [1] deepfold.loss module, [1] deepfold.losses module, [1] deepfold.losses.auxillary module, [1] deepfold.losses.confidence module, [1] deepfold.losses.geometry module, [1] deepfold.losses.masked_msa module, [1] deepfold.losses.procrustes module, [1] deepfold.losses.utils module, [1] deepfold.losses.violation module, [1] deepfold.modules module, [1] deepfold.modules.alphafold module, [1] deepfold.modules.angle_resnet module, [1] deepfold.modules.attention module, [1] deepfold.modules.auxiliary_heads module, [1] deepfold.modules.backbone_update module, [1] deepfold.modules.dropout module, [1] deepfold.modules.evoformer_block module, [1] deepfold.modules.evoformer_block_pair_core module, [1] deepfold.modules.evoformer_stack module, [1] deepfold.modules.extra_msa_block module, [1] deepfold.modules.extra_msa_embedder module, [1] deepfold.modules.extra_msa_stack module, [1] deepfold.modules.global_attention module, [1] deepfold.modules.inductor module, [1] deepfold.modules.input_embedder module, [1] deepfold.modules.invariant_point_attention module, [1] deepfold.modules.layer_norm module, [1] deepfold.modules.linear module, [1] deepfold.modules.msa_column_attention module, [1] deepfold.modules.msa_column_global_attention module, [1] deepfold.modules.msa_row_attention_with_pair_bias module, [1] deepfold.modules.msa_transition module, [1] deepfold.modules.outer_product_mean module, [1] deepfold.modules.pair_transition module, [1] deepfold.modules.recycling_embedder module, [1] deepfold.modules.single_transition module, [1] deepfold.modules.structure_module module, [1] deepfold.modules.template_angle_embedder module, [1] deepfold.modules.template_pair_block module, [1] deepfold.modules.template_pair_embedder module, [1] deepfold.modules.template_pair_stack module, [1] deepfold.modules.template_pointwise_attention module, [1]

deepfold.modules.template_projection module, [1] deepfold.modules.triangular_attention module, [1] deepfold.modules.triangular_multiplicative_update module, [1] deepfold.modules.tweaks module, [1] deepfold.modules.tweaks.evo_attn module, [1] deepfold.ops module, [1] deepfold.ops.evoformer_attention module, [1] deepfold.package_info module, [1] deepfold.relax module, [1] deepfold.relax.amber_minimize module, [1] deepfold.relax.cleanup module, [1] deepfold.relax.relax module, [1] deepfold.relax.utils module, [1] deepfold.runner module, [1] deepfold.runner.config_utils module, [1] deepfold.runner.parser module, [1] deepfold.runner.utils module, [1] deepfold.testing module, [1] deepfold.testing.common module, [1] deepfold.testing.utils module, [1] deepfold.train module, [1] deepfold.train.gradient_clipping module, [1] deepfold.train.lr_scheduler module, [1] deepfold.train.validation_metrics module, [1] deepfold.utils module, [1] deepfold.utils.checkpoint_utils module, [1] deepfold.utils.chunk_utils module, [1] deepfold.utils.crop_utils module, [1] deepfold.utils.datetime_utils module, [1] deepfold.utils.dist_utils module, [1] deepfold.utils.feats_utils module, [1] deepfold.utils.file_utils module, [1] deepfold.utils.geometry module, [1] deepfold.utils.geometry.quat_rigid module, [1] deepfold.utils.geometry.rigid_matrix_vector module, [1] deepfold.utils.geometry.rotation_matrix module, [1] deepfold.utils.geometry.utils module, [1] deepfold.utils.geometry.vector module, [1] deepfold.utils.hash_utils module, [1] deepfold.utils.import_utils module, [1] deepfold.utils.iter_utils module, [1] deepfold.utils.log_utils module, [1] deepfold.utils.precision module, [1] deepfold.utils.random module, [1] deepfold.utils.rigid_utils module, [1] deepfold.utils.script_utils module, [1] deepfold.utils.swa_utils module, [1] deepfold.utils.tensor_utils module, [1] deepspeed_evo_attn() (in module deepfold.ops.evoformer_attention) deposition_date (deepfold.data.pdbx_parsing.PDBxHeader attribute) descriptions (deepfold.data.multimer.input_features.ComplexInfo attribute) detach() (deepfold.utils.geometry.Rotation method) (deepfold.utils.rigid_utils.Rotation method) device (deepfold.utils.geometry.Rigid property) (deepfold.utils.geometry.Rigid3Array property) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array property) (deepfold.utils.geometry.Rotation property) (deepfold.utils.rigid_utils.Rigid property) (deepfold.utils.rigid_utils.Rotation property) dict_map() (in module deepfold.utils.tensor_utils) dict_multimap() (in module deepfold.utils.tensor_utils) diffalign module, [1] DiffAlign (class in diffalign.models.epsnet.diffusion) diffalign.models module, [1] diffalign.models.common module, [1] diffalign.models.encoder module, [1] diffalign.models.encoder.edge module, [1] diffalign.models.encoder.egnn module, [1] diffalign.models.epsnet module, [1] diffalign.models.epsnet.diffusion module, [1] diffalign.utils module, [1] diffalign.utils.chem module, [1] diffalign.utils.common module, [1] diffalign.utils.dataloader module, [1] diffalign.utils.datasets module, [1] diffalign.utils.evaluation module, [1] diffalign.utils.evaluation.covmat module, [1] diffalign.utils.misc module, [1] diffalign.utils.transforms module, [1] diffalign.utils.visualize module, [1] dihedral_angle() (in module deepfold.utils.geometry) (in module deepfold.utils.geometry.vector) Disable (class in deepfold.distributed.model_parallel) disable() (in module deepfold.distributed.model_parallel) (in module deepfold.modules.inductor) (in module deepfold.modules.tweaks.evo_attn) distance_loss_function() (in module promptbind.utils.generation_utils) distance_optimize_compound_coords() (in module promptbind.utils.generation_utils) distogram_head_config (deepfold.config.AuxiliaryHeadsConfig attribute) distogram_loss() (in module deepfold.losses.geometry) distogram_loss_config (deepfold.config.LossConfig attribute) DistogramHead (class in deepfold.modules.auxiliary_heads) DistogramHeadConfig (class in deepfold.config) DistogramLossConfig (class in deepfold.config) divide() (in module deepfold.distributed.utils) dot() (deepfold.utils.geometry.Vec3Array method) (deepfold.utils.geometry.vector.Vec3Array method) (in module deepfold.utils.geometry.vector) draw_mol_svg() (in module diffalign.utils.chem) drmsd() (in module deepfold.train.validation_metrics) Dropout (class in deepfold.modules.dropout) dropout_rate (deepfold.config.StructureModuleConfig attribute) (deepfold.config.TemplatePairStackConfig attribute) DropoutColumnwise (class in deepfold.modules.dropout) DropoutRowwise (class in deepfold.modules.dropout) dtype (deepfold.utils.geometry.Rigid property) (deepfold.utils.geometry.Rigid3Array property) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array property) (deepfold.utils.geometry.Rotation property) (deepfold.utils.rigid_utils.Rigid property) (deepfold.utils.rigid_utils.Rotation property) dump_pickle() (in module deepfold.utils.file_utils) DuplicateError

E

E_GCL (class in diffalign.models.encoder.egnn) edge_model() (diffalign.models.encoder.egnn.E_GCL method) (promptbind.models.egnn.MC_E_GCL method) (promptbind.models.egnn.MC_E_GCL_Prompt method) EfficientMCAttModel (class in promptbind.models.att_model) EGNN (class in diffalign.models.encoder.egnn) EGNN_old (class in diffalign.models.encoder.egnn) embed_template_torsion_angles (deepfold.config.AlphaFoldConfig attribute) (deepfold.config.FeaturePipelineConfig attribute) emit() (deepfold.utils.log_utils.TqdmHandler method) emsa_dim (deepfold.config.ExtraMSAEmbedderConfig attribute) Enable (class in deepfold.distributed.model_parallel) enable() (in module deepfold.distributed.model_parallel) (in module deepfold.modules.inductor) (in module deepfold.modules.tweaks.evo_attn) enabled (deepfold.config.CenterOfMassConfig attribute) (deepfold.config.TMLossConfig attribute) end (deepfold.data.search.parsers.HitMetadata attribute) ensure_divisibility() (in module deepfold.distributed.utils) entity_id (deepfold.data.pdbx_parsing.Monomer attribute) entry_id (deepfold.data.pdbx_parsing.PDBxHeader attribute) eps (deepfold.config.CenterOfMassConfig attribute) (deepfold.config.DistogramLossConfig attribute) (deepfold.config.ExperimentallyResolvedLossConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) (deepfold.config.FAPELossConfig attribute) (deepfold.config.MaskedMSALossConfig attribute) (deepfold.config.PLDDTLossConfig attribute) (deepfold.config.StructureModuleConfig attribute) (deepfold.config.SupervisedChiLossConfig attribute) (deepfold.config.TMLossConfig attribute) (deepfold.config.ViolationLossConfig attribute) eps_opm (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) Error error (deepfold.data.search.templates.TemplateFeaturesResult attribute) errors (deepfold.data.pdbx_parsing.ParsingResult attribute)

euclidean_distance() (in module deepfold.utils.geometry) (in module deepfold.utils.geometry.vector) eval_interface() (in module bis_protein_structure.MMEVAL) evaluate_conf() (in module diffalign.utils.evaluation.covmat) evaluate_mean_pocket_cls_coord_multi_task() (in module promptbind.utils.utils) evaluate_mean_pocket_cls_coord_pocket_pred() (in module promptbind.utils.utils) evoformer_stack_config (deepfold.config.AlphaFoldConfig attribute) EvoformerBlock (class in deepfold.modules.evoformer_block) EvoformerBlockPairCore (class in deepfold.modules.evoformer_block_pair_core) EvoformerStack (class in deepfold.modules.evoformer_stack) EvoformerStackConfig (class in deepfold.config) exists() (gd_dl.lib_pdb_mol2.Residue method) experimentally_resolved_head_config (deepfold.config.AuxiliaryHeadsConfig attribute) experimentally_resolved_loss() (in module deepfold.losses.auxillary) experimentally_resolved_loss_config (deepfold.config.LossConfig attribute) ExperimentallyResolvedHead (class in deepfold.modules.auxiliary_heads) ExperimentallyResolvedHeadConfig (class in deepfold.config) ExperimentallyResolvedLossConfig (class in deepfold.config) ExponentialLR_with_minLr (class in diffalign.utils.common) extend_graph_order_radius() (in module diffalign.models.common) extend_to_cross_attention() (in module diffalign.models.common) extra_msa_embedder_config (deepfold.config.AlphaFoldConfig attribute) extra_msa_stack_config (deepfold.config.AlphaFoldConfig attribute) extract() (in module bis_protein_structure.split_pdb) extract_coords_from_pdb() (in module bis_protein_structure.SOLVENTACC) extract_esm_feature() (in module promptbind.utils.inference_pdb_utils) extract_protein_structure() (in module promptbind.utils.inference_pdb_utils) extract_template_features() (in module deepfold.data.search.templates) extract_torchdrug_feature_from_mol() (in module promptbind.utils.feature_utils) (in module promptbind.utils.inference_mol_utils) extract_torchdrug_feature_from_mol_E3Bind() (in module promptbind.utils.feature_utils) ExtraMSABlock (class in deepfold.modules.extra_msa_block) ExtraMSAEmbedder (class in deepfold.modules.extra_msa_embedder) ExtraMSAEmbedderConfig (class in deepfold.config) ExtraMSAStack (class in deepfold.modules.extra_msa_stack) ExtraMSAStackConfig (class in deepfold.config) extreme_ca_ca_distance_violations() (in module deepfold.losses.violation)

F

FABindDataSet (class in promptbind.data.data) fape_loss() (in module deepfold.losses.geometry) fape_loss_config (deepfold.config.LossConfig attribute) FAPELossConfig (class in deepfold.config) feature_names() (deepfold.config.FeaturePipelineConfig method) FeaturePipelineConfig (class in deepfold.config) features (deepfold.data.search.templates.TemplateFeaturesResult attribute) fetch_ligand() (in module deepfold.data.monomer) fetch_mmcif() (in module deepfold.data.pdbx_parsing) final_init_() (in module deepfold.modules.linear) find_cluster_boundaries() (in module deepfold.eval.plot) find_free_port() (in module deepfold.testing.utils) find_paths() (in module deepfold.utils.file_utils) find_structural_violations() (in module deepfold.losses.violation) find_structural_violations_np() (in module deepfold.losses.violation) find_violations() (in module deepfold.relax.amber_minimize) fix_pdb() (in module deepfold.relax.cleanup) fixed_size (deepfold.config.FeaturePipelineConfig attribute) flatten_batch_dims() (in module deepfold.losses.procrustes) flatten_dict() (in module deepfold.utils.iter_utils) flatten_final_dims() (in module deepfold.utils.tensor_utils) (in module promptbind.models.model_utils) forward() (deepfold.distributed.model_parallel.Disable static method) (deepfold.distributed.model_parallel.Enable static method) (deepfold.loss.AlphaFoldLoss method) (deepfold.losses.procrustes.Procrustes static method) (deepfold.modules.alphafold.AlphaFold method) (deepfold.modules.angle_resnet.AngleResnet method) (deepfold.modules.angle_resnet.AngleResnetBlock method) (deepfold.modules.attention.CrossAttentionNoGate method) (deepfold.modules.attention.SelfAttentionWithGate method) (deepfold.modules.auxiliary_heads.AuxiliaryHeads method) (deepfold.modules.auxiliary_heads.DistogramHead method) (deepfold.modules.auxiliary_heads.ExperimentallyResolvedHead method) (deepfold.modules.auxiliary_heads.MaskedMSAHead method) (deepfold.modules.auxiliary_heads.PerResidueLDDTCaPredictor method) (deepfold.modules.auxiliary_heads.TMScoreHead method) (deepfold.modules.backbone_update.BackboneUpdate method) (deepfold.modules.dropout.Dropout method) (deepfold.modules.evoformer_block.EvoformerBlock method) (deepfold.modules.evoformer_block_pair_core.EvoformerBlockPairCore method) (deepfold.modules.evoformer_stack.EvoformerStack method) (deepfold.modules.extra_msa_block.ExtraMSABlock method) (deepfold.modules.extra_msa_embedder.ExtraMSAEmbedder method) (deepfold.modules.extra_msa_stack.ExtraMSAStack method) (deepfold.modules.global_attention.GlobalAttention method) (deepfold.modules.input_embedder.InputEmbedder method) (deepfold.modules.input_embedder.InputEmbedderMultimer method) (deepfold.modules.invariant_point_attention.InvariantPointAttention method) (deepfold.modules.invariant_point_attention.InvariantPointAttentionMultimer method) (deepfold.modules.invariant_point_attention.PointProjection method) (deepfold.modules.layer_norm.LayerNorm method) (deepfold.modules.msa_column_attention.MSAColumnAttention method) (deepfold.modules.msa_column_global_attention.MSAColumnGlobalAttention method) (deepfold.modules.msa_row_attention_with_pair_bias.MSARowAttentionWithPairBias method) (deepfold.modules.msa_transition.MSATransition method) (deepfold.modules.outer_product_mean.OuterProductMean method) (deepfold.modules.pair_transition.PairTransition method) (deepfold.modules.recycling_embedder.RecyclingEmbedder method) (deepfold.modules.single_transition.SingleTransition method) (deepfold.modules.structure_module.StructureModule method) (deepfold.modules.template_angle_embedder.TemplateAngleEmbedder method) (deepfold.modules.template_pair_block.TemplatePairBlock method) (deepfold.modules.template_pair_embedder.TemplatePairEmbedder method) (deepfold.modules.template_pair_embedder.TemplatePairEmbedderMultimer method) (deepfold.modules.template_pair_stack.TemplatePairStack method) (deepfold.modules.template_pointwise_attention.TemplatePointwiseAttention method) (deepfold.modules.template_projection.TemplateProjection method) (deepfold.modules.triangular_attention.TriangleAttention method) (deepfold.modules.triangular_multiplicative_update.TriangleMultiplicativeUpdate method) (deepfold.utils.geometry.quat_rigid.QuatRigid method) (deepfold.utils.swa_utils.AlphaFoldSWA method) (diffalign.models.common.MultiLayerPerceptron method) (diffalign.models.encoder.edge.MLPEdgeEncoder method) (diffalign.models.encoder.egnn.E_GCL method) (diffalign.models.encoder.egnn.EGNN method) (diffalign.models.encoder.egnn.EGNN_old method) (diffalign.models.encoder.egnn.GNN method) (diffalign.models.encoder.egnn.MLP method) (diffalign.models.encoder.egnn.TransformerNN method) (diffalign.models.encoder.egnn.TransformerNN.SetDecoder method) (diffalign.models.epsnet.diffusion.DiffAlign method) (diffalign.models.epsnet.diffusion.SinusoidalTimeEmbeddings method) (gd_dl.models.Cgc_block method) (gd_dl.models.Rerank_model method) (gd_dl.models.Weight_CGConv method) (gd_dl.rerank_model.Cgc_block method) (gd_dl.rerank_model.Rerank_model method) (gd_dl.rerank_model.Weight_CGConv method) (promptbind.models.att_model.ComplexGraph method) (promptbind.models.att_model.EfficientMCAttModel method) (promptbind.models.cross_att.CrossAttentionModule method) (promptbind.models.cross_att.RowAttentionBlock method) (promptbind.models.cross_att.RowTriangleAttentionBlock method) (promptbind.models.egnn.MC_Att_L method) (promptbind.models.egnn.MC_E_GCL method) (promptbind.models.egnn.MC_E_GCL_Prompt method) (promptbind.models.egnn.MCAttEGNN method) (promptbind.models.model.IaBNet_mean_and_pocket_prediction_cls_coords_dependent method) (promptbind.models.model.Transition_diff_out_dim method) (promptbind.models.model_utils.Attention method) (promptbind.models.model_utils.GaussianSmearing method) (promptbind.models.model_utils.InteractionModule method) (promptbind.models.model_utils.RBFDistanceModule method) (promptbind.models.model_utils.Transition method)

from_3_points() (deepfold.utils.geometry.Rigid static method) (deepfold.utils.rigid_utils.Rigid static method) from_array() (deepfold.utils.geometry.Rigid3Array class method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array class method) (deepfold.utils.geometry.Rot3Array class method) (deepfold.utils.geometry.rotation_matrix.Rot3Array class method) (deepfold.utils.geometry.Vec3Array class method) (deepfold.utils.geometry.vector.Vec3Array class method) from_array4x4() (deepfold.utils.geometry.Rigid3Array class method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array class method) from_dict() (deepfold.config.AlphaFoldConfig class method) (deepfold.config.FeaturePipelineConfig class method) (deepfold.config.TrainingConfig class method) from_pdb_string() (in module deepfold.common.protein) from_prediction() (in module deepfold.common.protein) from_preset() (deepfold.config.AlphaFoldConfig class method) (deepfold.config.FeaturePipelineConfig class method) (deepfold.config.TrainingConfig class method) from_quaternion() (deepfold.utils.geometry.Rot3Array class method) (deepfold.utils.geometry.rotation_matrix.Rot3Array class method) from_relaxation() (in module deepfold.common.protein) from_tensor_4x4() (deepfold.utils.geometry.Rigid static method) (deepfold.utils.geometry.Rigid3Array class method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array class method) (deepfold.utils.rigid_utils.Rigid static method) from_tensor_7() (deepfold.utils.geometry.Rigid static method) (deepfold.utils.rigid_utils.Rigid static method) from_two_vectors() (deepfold.utils.geometry.Rot3Array class method) (deepfold.utils.geometry.rotation_matrix.Rot3Array class method)

G

gather() (in module deepfold.distributed.model_parallel) gather_from_model_parallel_region() (in module deepfold.distributed.model_parallel) gating_init_() (in module deepfold.modules.linear) GaussianSmearing (class in promptbind.models.model_utils) gd_dl module, [1] gd_dl.data module, [1] gd_dl.data.all_ML_rerank module, [1] gd_dl.data.ML_inference module, [1] gd_dl.data.ML_rerank module, [1] gd_dl.data.single_ML_rerank module, [1] gd_dl.lib_pdb_mol2 module, [1] gd_dl.models module, [1] gd_dl.path_setting module, [1] gd_dl.rerank_model module, [1] gd_dl.utils module, [1] gdt() (in module deepfold.train.validation_metrics) gdt_ha() (in module deepfold.train.validation_metrics) gdt_ts() (in module deepfold.train.validation_metrics) generate_and_write_sdf_from_smiles_using_rdkit_E3Bind() (in module promptbind.utils.feature_utils) generate_conformation() (in module promptbind.utils.feature_utils) (in module promptbind.utils.inference_mol_utils) generate_feature_dict() (in module bis_protein_structure.DATAGEN) generate_rdkit_conformation_v2() (in module promptbind.utils.feature_utils) generate_sdf_from_smiles_using_rdkit() (in module promptbind.utils.feature_utils) generate_sdf_from_smiles_using_rdkit_E3Bind() (in module promptbind.utils.feature_utils) get() (diffalign.utils.datasets.ConformationDataset method) (promptbind.data.data.FABindDataSet method) (promptbind.utils.fabind_inference_dataset.InferenceDataset method) get_2D_mol() (in module diffalign.utils.chem) get_assemblies() (in module deepfold.data.pdbx_parsing) get_asym_mask() (in module deepfold.losses.auxillary) get_atom_index_list() (gd_dl.lib_pdb_mol2.MOL2_UNIT method) get_atom_mol2_type_list() (gd_dl.lib_pdb_mol2.MOL2_UNIT method) get_atom_positions() (in module deepfold.data.search.templates) get_atom_symbol() (in module diffalign.utils.chem) get_atoms_in_ring() (in module diffalign.utils.chem) get_backbone() (gd_dl.lib_pdb_mol2.Residue method) get_basename() (in module deepfold.utils.script_utils) get_best_rmsd() (in module diffalign.utils.chem) get_bond_dict() (gd_dl.lib_pdb_mol2.MOL2_UNIT method) get_bondangle() (in module bis_protein_structure.TORSION2) get_canonical_smiles() (in module promptbind.utils.feature_utils) get_CB() (gd_dl.lib_pdb_mol2.Residue method) get_chain_features() (in module deepfold.data.pdbx_parsing) get_checkpoint_path() (in module diffalign.utils.misc) get_clean_res_list() (in module promptbind.utils.feature_utils) (in module promptbind.utils.inference_pdb_utils) get_clip_scale() (deepfold.train.gradient_clipping.AsyncGradientClipping method) get_compound_pair_dis_distribution() (in module promptbind.utils.feature_utils) (in module promptbind.utils.inference_mol_utils) get_contact() (in module bis_protein_structure.MMEVAL) get_coordinates() (in module bis_protein_structure.TORSION2) get_coordinates_np_array() (gd_dl.lib_pdb_mol2.MOL2_UNIT method) get_cur_rot() (deepfold.utils.geometry.Rotation method) (deepfold.utils.rigid_utils.Rotation method) get_data() (in module promptbind.data.data) get_distance() (in module diffalign.models.epsnet.diffusion) get_edges() (in module promptbind.models.egnn) get_edges_batch() (in module promptbind.models.egnn) get_fasta() (in module deepfold.data.pdbx_parsing)

get_field_names() (in module deepfold.utils.geometry.utils) get_file_content_and_extension() (in module deepfold.utils.file_utils) get_heavy() (gd_dl.lib_pdb_mol2.Residue method) get_higher_order_adj_matrix() (diffalign.utils.transforms.AddHigherOrderEdges method) get_hydrogen_set() (gd_dl.lib_pdb_mol2.MOL2_UNIT method) get_ICS() (in module bis_protein_structure.MMEVAL) get_identifiers() (in module deepfold.data.search.msa_identifiers) get_index() (deepfold.eval.cell_lists.CellLists method) get_info_pred_distance() (in module promptbind.utils.generation_utils) get_IPS() (in module bis_protein_structure.MMEVAL) get_keepNode() (in module promptbind.utils.utils) get_keepNode_tensor() (in module promptbind.utils.utils) get_LAS_distance_constraint_mask() (in module promptbind.utils.feature_utils) (in module promptbind.utils.generation_utils) (in module promptbind.utils.inference_mol_utils) get_learning_rate() (in module deepfold.train.lr_scheduler) get_ligand() (in module deepfold.data.monomer) get_logger() (in module diffalign.utils.misc) get_loss() (diffalign.models.epsnet.diffusion.DiffAlign method) get_lr() (diffalign.utils.common.ExponentialLR_with_minLr method) get_model() (in module promptbind.models.model) get_neighbors() (deepfold.eval.cell_lists.CellLists method) get_new_log_dir() (in module diffalign.utils.misc) get_optimal_transform() (in module deepfold.losses.geometry) get_optimizer() (in module diffalign.utils.common) get_pad_size() (in module deepfold.utils.dist_utils) get_pdb_headers() (in module deepfold.common.protein) get_protein_edge_features_and_index() (in module promptbind.utils.utils) get_protein_feature() (in module promptbind.utils.feature_utils) get_protein_structure() (in module promptbind.utils.inference_pdb_utils) get_quats() (deepfold.utils.geometry.Rotation method) (deepfold.utils.rigid_utils.Rotation method) get_ref_vec() (in module gd_dl.data.ML_inference) get_refer_atoms() (in module bis_protein_structure.TORSION2) get_res_unique_id() (in module promptbind.utils.feature_utils) get_residue_lines() (gd_dl.lib_pdb_mol2.Model method) get_residues() (gd_dl.lib_pdb_mol2.Model method) get_rmsd_confusion_matrix() (in module diffalign.utils.evaluation.covmat) get_rot_mats() (deepfold.utils.geometry.Rotation method) (deepfold.utils.rigid_utils.Rotation method) get_rots() (deepfold.utils.geometry.Rigid method) (deepfold.utils.rigid_utils.Rigid method) get_sc() (gd_dl.lib_pdb_mol2.Residue method) get_scheduler() (in module diffalign.utils.common) get_seed_from_string() (in module deepfold.utils.random) get_seed_randomly() (in module deepfold.utils.random) get_SS_ver5() (in module bis_protein_structure.DISULFIDE) get_template_features() (deepfold.data.search.templates.TemplateHitFeaturizer method) get_template_hits() (deepfold.data.tools.hhsearch.HHSearch static method) (deepfold.data.tools.hmmsearch.Hmmsearch static method) get_tensor() (deepfold.distributed.utils.GlobalMemoryBuffer method) get_test_set_with_large_num_conf() (in module diffalign.utils.datasets) get_timestamp_string() (in module deepfold.utils.datetime_utils) get_torsion() (in module bis_protein_structure.TORSION2) get_torsions() (in module promptbind.utils.utils) GET_TRACEBACK (deepfold.testing.common.MultiProcessTestCase.Event attribute) get_trans() (deepfold.utils.geometry.Rigid method) (deepfold.utils.rigid_utils.Rigid method) get_violation_metrics() (in module deepfold.relax.amber_minimize) getDistogram() (in module bis_protein_structure.TORSION2) getTMscore() (in module bis_protein_structure.SOLVENTACC) getTorsion_acc() (in module bis_protein_structure.TORSION2) GlobalAttention (class in deepfold.modules.global_attention) GlobalMemoryBuffer (class in deepfold.distributed.utils) glorot_uniform_init_() (in module deepfold.modules.linear) GNN (class in diffalign.models.encoder.egnn) gradient_clipping (deepfold.config.TrainingConfig attribute) graph (deepfold.data.monomer.Ligand attribute) group() (in module deepfold.distributed.model_parallel) group_rank() (in module deepfold.distributed.model_parallel) gumbel_softmax_no_random() (in module promptbind.utils.utils)

H

hash_string_into_number() (in module deepfold.utils.hash_utils) he_normal_init_() (in module deepfold.modules.linear) header (deepfold.data.pdbx_parsing.PDBxObject attribute) hetatm_atom (deepfold.data.pdbx_parsing.AtomSite attribute) hetflag (deepfold.data.pdbx_parsing.ResidueAtPosition attribute)

HHBlits (class in deepfold.data.tools.hhblits) HHSearch (class in deepfold.data.tools.hhsearch) hit_sequence (deepfold.data.search.parsers.TemplateHit attribute) HitMetadata (class in deepfold.data.search.parsers) Hmmbuild (class in deepfold.data.tools.hmmbuild) Hmmsearch (class in deepfold.data.tools.hmmsearch)

I

i_atm() (gd_dl.lib_pdb_mol2.Atom method) (gd_dl.lib_pdb_mol2.Residue method) IaBNet_mean_and_pocket_prediction_cls_coords_dependent (class in promptbind.models.model) id (deepfold.data.monomer.Ligand attribute) ideal_atom_mask() (in module deepfold.common.protein) identity() (deepfold.utils.geometry.Rigid static method) (deepfold.utils.geometry.Rigid3Array class method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array class method) (deepfold.utils.geometry.Rot3Array class method) (deepfold.utils.geometry.Rotation static method) (deepfold.utils.geometry.rotation_matrix.Rot3Array class method) (deepfold.utils.rigid_utils.Rigid static method) (deepfold.utils.rigid_utils.Rotation static method) identity_quats() (in module deepfold.utils.rigid_utils) identity_rot_mats() (in module deepfold.utils.rigid_utils) identity_trans() (in module deepfold.utils.rigid_utils) import_jax_weights_() (in module deepfold.utils.import_utils) index (deepfold.data.search.parsers.TemplateHit attribute) index() (gd_dl.lib_pdb_mol2.Model method) indices_hit (deepfold.data.search.parsers.TemplateHit attribute) indices_query (deepfold.data.search.parsers.TemplateHit attribute) inf (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) (deepfold.config.RecyclingEmbedderConfig attribute) (deepfold.config.StructureModuleConfig attribute) (deepfold.config.TemplatePairStackConfig attribute) (deepfold.config.TemplatePointwiseAttentionConfig attribute) (promptbind.models.cross_att.RowAttentionBlock attribute) (promptbind.models.cross_att.RowTriangleAttentionBlock attribute) inf_iterator() (in module diffalign.utils.misc) inference() (promptbind.models.model.IaBNet_mean_and_pocket_prediction_cls_coords_dependent method) InferenceDataset (class in promptbind.utils.fabind_inference_dataset) initialize() (in module deepfold.distributed.model_parallel) inject() (deepfold.data.pdbx_parsing.PDBxParser method) input_embedder_config (deepfold.config.AlphaFoldConfig attribute) input_format (deepfold.data.tools.hhsearch.HHSearch property) (deepfold.data.tools.hmmsearch.Hmmsearch property) InputEmbedder (class in deepfold.modules.input_embedder) InputEmbedderConfig (class in deepfold.config) InputEmbedderMultimer (class in deepfold.modules.input_embedder) insertion_code (deepfold.data.pdbx_parsing.AtomSite attribute) (deepfold.data.pdbx_parsing.ModResidue attribute) (deepfold.data.pdbx_parsing.ResiduePosition attribute) int_id_to_str_id() (in module deepfold.data.multimer.input_features) int_tuple() (in module diffalign.utils.misc)

InteractionModule (class in promptbind.models.model_utils) interface_clamp_distance (deepfold.config.FAPELossConfig attribute) interface_loss_unit_distance (deepfold.config.FAPELossConfig attribute) interface_threshold (deepfold.config.FeaturePipelineConfig attribute) interface_weight (deepfold.config.FAPELossConfig attribute) InvariantPointAttention (class in deepfold.modules.invariant_point_attention) InvariantPointAttentionMultimer (class in deepfold.modules.invariant_point_attention) inverse() (deepfold.utils.geometry.Rigid3Array method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array method) (deepfold.utils.geometry.Rot3Array method) (deepfold.utils.geometry.rotation_matrix.Rot3Array method) invert() (deepfold.utils.geometry.Rigid method) (deepfold.utils.geometry.Rotation method) (deepfold.utils.rigid_utils.Rigid method) (deepfold.utils.rigid_utils.Rotation method) invert_apply() (deepfold.utils.geometry.Rigid method) (deepfold.utils.geometry.Rigid3Array method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array method) (deepfold.utils.geometry.Rotation method) (deepfold.utils.rigid_utils.Rigid method) (deepfold.utils.rigid_utils.Rotation method) invert_quat() (in module deepfold.utils.rigid_utils) invert_rot_mat() (in module deepfold.utils.rigid_utils) IO (class in deepfold.data.pdbio) ipa_point_weights_init_() (in module deepfold.modules.invariant_point_attention) iptm_weight (deepfold.config.AuxiliaryHeadsConfig attribute) is_enabled() (in module deepfold.distributed.model_parallel) (in module deepfold.modules.inductor) (in module deepfold.modules.tweaks.evo_attn) is_enabled_and_autograd_off() (in module deepfold.modules.inductor) is_fp16_enabled() (in module deepfold.utils.precision) is_identity (deepfold.data.pdbx_parsing.Op attribute) is_initialized() (in module deepfold.distributed.model_parallel) is_master (deepfold.testing.common.MultiProcessTestCase property) is_missing (deepfold.data.pdbx_parsing.ResidueAtPosition attribute) is_multimer (deepfold.config.AlphaFoldConfig attribute) (deepfold.config.FeaturePipelineConfig attribute) (deepfold.config.StructureModuleConfig attribute) isAtom() (gd_dl.lib_pdb_mol2.PDBline method) (gd_dl.lib_pdb_mol2.Residue method) isHetatm() (gd_dl.lib_pdb_mol2.PDBline method) (gd_dl.lib_pdb_mol2.Residue method) isResidue() (gd_dl.lib_pdb_mol2.PDBline method) (gd_dl.lib_pdb_mol2.Residue method) iter_angle_triplet() (diffalign.utils.transforms.AddAngleDihedral static method) iter_dihedral_quartet() (diffalign.utils.transforms.AddAngleDihedral static method)

J

Jackhmmer (class in deepfold.data.tools.jackhmmer)

join_or_run() (deepfold.testing.common.MultiProcessTestCase method)

K

kabsch() (in module deepfold.eval.pseudo_3d) (in module deepfold.losses.procrustes)

kabsch_rmsd() (in module deepfold.losses.geometry) Kalign (class in deepfold.data.tools.kalign)

L

label_asym_id (deepfold.data.pdbx_parsing.ModResidue attribute) (deepfold.data.pdbx_parsing.ResiduePosition attribute) label_chain_id (deepfold.data.pdbx_parsing.AtomSite attribute) label_comp_id (deepfold.data.pdbx_parsing.ModResidue attribute) label_seq_id (deepfold.data.pdbx_parsing.ModResidue attribute) (deepfold.data.pdbx_parsing.ResiduePosition attribute) label_seq_num (deepfold.data.pdbx_parsing.AtomSite attribute) label_to_auth (deepfold.data.pdbx_parsing.PDBxObject attribute) LayerNorm (class in deepfold.modules.layer_norm) lddt() (in module deepfold.losses.confidence) lddt_ca() (in module deepfold.losses.confidence) lecun_normal_init_() (in module deepfold.modules.linear) len() (diffalign.utils.datasets.ConformationDataset method) (promptbind.data.data.FABindDataSet method) (promptbind.utils.fabind_inference_dataset.InferenceDataset method) length (bis_protein_structure.residue_constants.Bond attribute) (deepfold.common.residue_constants.Bond attribute) (deepfold.data.search.parsers.HitMetadata attribute) LengthError Lexer (class in deepfold.runner.parser) Ligand (class in deepfold.data.monomer) Linear (class in deepfold.modules.linear) LinearBiasMHA (deepfold.utils.import_utils.ParamType attribute) LinearMHAOutputWeight (deepfold.utils.import_utils.ParamType attribute)

LinearWeight (deepfold.utils.import_utils.ParamType attribute) LinearWeightMHA (deepfold.utils.import_utils.ParamType attribute) LinearWeightOPM (deepfold.utils.import_utils.ParamType attribute) list_zip() (in module deepfold.utils.iter_utils) load() (in module deepfold.runner.config_utils) load_args() (promptbind.test_promptbind.PromptBindInference method) load_files() (in module gd_dl.data.ML_inference) load_list_from_file() (in module bis_protein_structure.CROSSLINK) load_mmcif_dict() (in module deepfold.data.search.templates) load_mmcif_file() (in module deepfold.data.search.mmcif) load_model() (promptbind.test_promptbind.PromptBindInference method) load_pdb_obsolete_mapping() (in module deepfold.data.search.templates) load_pickle() (in module deepfold.utils.file_utils) load_pickle_file() (in module bis_protein_structure.SOLVENTACC) load_stereo_chemical_props() (in module bis_protein_structure.residue_constants) (in module deepfold.common.residue_constants) log_hyperparams() (in module diffalign.utils.misc) log_message() (promptbind.utils.logging_utils.Logger method) log_stats() (promptbind.utils.logging_utils.Logger method) Logger (class in promptbind.utils.logging_utils) loop_to_dict() (in module deepfold.data.pdbx_parsing) loop_to_list() (in module deepfold.data.pdbx_parsing) loss_config (deepfold.config.AlphaFoldConfig attribute) LossConfig (class in deepfold.config)

M

main() (in module gd_dl.data.all_ML_rerank) (in module gd_dl.data.ML_inference) (in module gd_dl.data.ML_rerank) (in module gd_dl.data.single_ML_rerank) (in module promptbind.visualize_prompt_components) MAIN_PROCESS_RANK (deepfold.testing.common.MultiProcessTestCase attribute) make_atom14_dists_bounds() (in module bis_protein_structure.residue_constants) (in module deepfold.common.residue_constants) make_atom14_positions() (in module deepfold.relax.amber_minimize) make_output_directory() (in module deepfold.utils.script_utils) make_transform_from_reference() (deepfold.utils.geometry.Rigid static method) (deepfold.utils.rigid_utils.Rigid static method) map_dict_values() (in module deepfold.utils.iter_utils) map_init_state_dicts() (in module deepfold.utils.checkpoint_utils) map_structure_with_atom_order() (in module deepfold.common.residue_constants) map_tensor_fn() (deepfold.utils.geometry.Rigid method) (deepfold.utils.geometry.Rigid3Array method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array method) (deepfold.utils.geometry.Rot3Array method) (deepfold.utils.geometry.Rotation method) (deepfold.utils.geometry.rotation_matrix.Rot3Array method) (deepfold.utils.geometry.Vec3Array method) (deepfold.utils.geometry.vector.Vec3Array method) (deepfold.utils.rigid_utils.Rigid method) (deepfold.utils.rigid_utils.Rotation method) mapping (deepfold.data.monomer.AtomMap attribute) masked_mean() (in module deepfold.utils.tensor_utils) masked_msa_enabled (deepfold.config.FeaturePipelineConfig attribute) masked_msa_head_config (deepfold.config.AuxiliaryHeadsConfig attribute) masked_msa_loss() (in module deepfold.losses.masked_msa) masked_msa_loss_config (deepfold.config.LossConfig attribute) masked_msa_profile_prob (deepfold.config.FeaturePipelineConfig attribute) masked_msa_replace_fraction (deepfold.config.FeaturePipelineConfig attribute) masked_msa_same_prob (deepfold.config.FeaturePipelineConfig attribute) masked_msa_uniform_prob (deepfold.config.FeaturePipelineConfig attribute) MaskedMSAHead (class in deepfold.modules.auxiliary_heads) MaskedMSAHeadConfig (class in deepfold.config) MaskedMSALossConfig (class in deepfold.config) max_bin (deepfold.config.DistogramLossConfig attribute) (deepfold.config.RecyclingEmbedderConfig attribute) (deepfold.config.TMLossConfig attribute) (deepfold.config.TMScoreHeadConfig attribute) max_distillation_msa_clusters (deepfold.config.FeaturePipelineConfig attribute) max_extra_msa (deepfold.config.FeaturePipelineConfig attribute) max_msa_clusters (deepfold.config.FeaturePipelineConfig attribute) max_recycling_iters (deepfold.config.FeaturePipelineConfig attribute) max_relative_chain (deepfold.config.InputEmbedderConfig attribute) max_relative_index (deepfold.config.InputEmbedderConfig attribute) max_resolution (deepfold.config.ExperimentallyResolvedLossConfig attribute) (deepfold.config.PLDDTLossConfig attribute) (deepfold.config.TMLossConfig attribute) max_templates (deepfold.config.FeaturePipelineConfig attribute) MC_Att_L (class in promptbind.models.egnn) MC_E_GCL (class in promptbind.models.egnn) MC_E_GCL_Prompt (class in promptbind.models.egnn) MCAttEGNN (class in promptbind.models.egnn) merge_chain_features() (in module deepfold.data.multimer.msa_pairing) merge_graphs_in_batch() (in module diffalign.models.epsnet.diffusion) message() (gd_dl.models.Weight_CGConv method) (gd_dl.rerank_model.Weight_CGConv method) method (deepfold.data.pdbx_parsing.PDBxHeader attribute) metrics_runtime_no_prefix() (in module promptbind.utils.metrics_to_tsb) min_bin (deepfold.config.DistogramLossConfig attribute) (deepfold.config.RecyclingEmbedderConfig attribute) min_resolution (deepfold.config.ExperimentallyResolvedLossConfig attribute) (deepfold.config.PLDDTLossConfig attribute) (deepfold.config.TMLossConfig attribute) MLP (class in diffalign.models.encoder.egnn) MLPEdgeEncoder (class in diffalign.models.encoder.edge) mmcif_object (deepfold.data.pdbx_parsing.ParsingResult attribute) mmcif_to_pdbs() (in module bis_protein_structure.DATAGEN) Model (class in gd_dl.lib_pdb_mol2) model_num (deepfold.data.pdbx_parsing.AtomSite attribute) modres (deepfold.data.pdbx_parsing.PDBxObject attribute) ModResidue (class in deepfold.data.pdbx_parsing) module bis_protein_structure, [1] bis_protein_structure.CROSSLINK, [1] bis_protein_structure.DATAGEN, [1] bis_protein_structure.DISULFIDE, [1] bis_protein_structure.MMEVAL, [1] bis_protein_structure.residue_constants, [1] bis_protein_structure.SOLVENTACC, [1] bis_protein_structure.split_pdb, [1] bis_protein_structure.TORSION2, [1] deepfold, [1] deepfold.common, [1] deepfold.common.protein, [1] deepfold.common.residue_constants, [1] deepfold.config, [1] deepfold.data, [1] deepfold.data.errors, [1] deepfold.data.modules, [1] deepfold.data.modules.dataloaders, [1] deepfold.data.modules.mmcif_dataset, [1] deepfold.data.modules.samplers, [1] deepfold.data.modules.single_dataset, [1] deepfold.data.monomer, [1] deepfold.data.multimer, [1] deepfold.data.multimer.input_features, [1] deepfold.data.multimer.msa_pairing, [1] deepfold.data.pdbio, [1] deepfold.data.pdbx_parsing, [1] deepfold.data.search, [1] deepfold.data.search.crfalign, [1] deepfold.data.search.input_features, [1] deepfold.data.search.mmcif, [1] deepfold.data.search.msa_identifiers, [1] deepfold.data.search.parsers, [1] deepfold.data.search.templates, [1] deepfold.data.tools, [1] deepfold.data.tools.hhblits, [1] deepfold.data.tools.hhsearch, [1] deepfold.data.tools.hmmbuild, [1] deepfold.data.tools.hmmsearch, [1] deepfold.data.tools.jackhmmer, [1] deepfold.data.tools.kalign, [1] deepfold.data.tools.utils, [1] deepfold.distributed, [1] deepfold.distributed.model_parallel, [1] deepfold.distributed.utils, [1] deepfold.eval, [1] deepfold.eval.cell_lists, [1] deepfold.eval.contact, [1] deepfold.eval.distogram, [1] deepfold.eval.msa, [1] deepfold.eval.plot, [1] deepfold.eval.pseudo_3d, [1] deepfold.loss, [1] deepfold.losses, [1] deepfold.losses.auxillary, [1] deepfold.losses.confidence, [1] deepfold.losses.geometry, [1] deepfold.losses.masked_msa, [1] deepfold.losses.procrustes, [1] deepfold.losses.utils, [1] deepfold.losses.violation, [1] deepfold.modules, [1] deepfold.modules.alphafold, [1] deepfold.modules.angle_resnet, [1] deepfold.modules.attention, [1] deepfold.modules.auxiliary_heads, [1] deepfold.modules.backbone_update, [1] deepfold.modules.dropout, [1] deepfold.modules.evoformer_block, [1] deepfold.modules.evoformer_block_pair_core, [1] deepfold.modules.evoformer_stack, [1] deepfold.modules.extra_msa_block, [1] deepfold.modules.extra_msa_embedder, [1] deepfold.modules.extra_msa_stack, [1] deepfold.modules.global_attention, [1] deepfold.modules.inductor, [1] deepfold.modules.input_embedder, [1] deepfold.modules.invariant_point_attention, [1] deepfold.modules.layer_norm, [1] deepfold.modules.linear, [1] deepfold.modules.msa_column_attention, [1] deepfold.modules.msa_column_global_attention, [1] deepfold.modules.msa_row_attention_with_pair_bias, [1] deepfold.modules.msa_transition, [1] deepfold.modules.outer_product_mean, [1] deepfold.modules.pair_transition, [1] deepfold.modules.recycling_embedder, [1] deepfold.modules.single_transition, [1] deepfold.modules.structure_module, [1] deepfold.modules.template_angle_embedder, [1] deepfold.modules.template_pair_block, [1] deepfold.modules.template_pair_embedder, [1] deepfold.modules.template_pair_stack, [1] deepfold.modules.template_pointwise_attention, [1] deepfold.modules.template_projection, [1] deepfold.modules.triangular_attention, [1] deepfold.modules.triangular_multiplicative_update, [1] deepfold.modules.tweaks, [1] deepfold.modules.tweaks.evo_attn, [1] deepfold.ops, [1] deepfold.ops.evoformer_attention, [1] deepfold.package_info, [1] deepfold.relax, [1] deepfold.relax.amber_minimize, [1] deepfold.relax.cleanup, [1] deepfold.relax.relax, [1] deepfold.relax.utils, [1] deepfold.runner, [1] deepfold.runner.config_utils, [1] deepfold.runner.parser, [1] deepfold.runner.utils, [1] deepfold.testing, [1] deepfold.testing.common, [1] deepfold.testing.utils, [1] deepfold.train, [1] deepfold.train.gradient_clipping, [1] deepfold.train.lr_scheduler, [1] deepfold.train.validation_metrics, [1] deepfold.utils, [1] deepfold.utils.checkpoint_utils, [1] deepfold.utils.chunk_utils, [1] deepfold.utils.crop_utils, [1] deepfold.utils.datetime_utils, [1] deepfold.utils.dist_utils, [1] deepfold.utils.feats_utils, [1] deepfold.utils.file_utils, [1] deepfold.utils.geometry, [1] deepfold.utils.geometry.quat_rigid, [1] deepfold.utils.geometry.rigid_matrix_vector, [1] deepfold.utils.geometry.rotation_matrix, [1] deepfold.utils.geometry.utils, [1] deepfold.utils.geometry.vector, [1] deepfold.utils.hash_utils, [1] deepfold.utils.import_utils, [1] deepfold.utils.iter_utils, [1] deepfold.utils.log_utils, [1] deepfold.utils.precision, [1] deepfold.utils.random, [1] deepfold.utils.rigid_utils, [1] deepfold.utils.script_utils, [1] deepfold.utils.swa_utils, [1] deepfold.utils.tensor_utils, [1] diffalign, [1] diffalign.models, [1] diffalign.models.common, [1] diffalign.models.encoder, [1] diffalign.models.encoder.edge, [1] diffalign.models.encoder.egnn, [1] diffalign.models.epsnet, [1] diffalign.models.epsnet.diffusion, [1] diffalign.utils, [1] diffalign.utils.chem, [1] diffalign.utils.common, [1] diffalign.utils.dataloader, [1] diffalign.utils.datasets, [1] diffalign.utils.evaluation, [1] diffalign.utils.evaluation.covmat, [1] diffalign.utils.misc, [1] diffalign.utils.transforms, [1] diffalign.utils.visualize, [1] gd_dl, [1] gd_dl.data, [1] gd_dl.data.all_ML_rerank, [1] gd_dl.data.ML_inference, [1] gd_dl.data.ML_rerank, [1] gd_dl.data.single_ML_rerank, [1] gd_dl.lib_pdb_mol2, [1] gd_dl.models, [1] gd_dl.path_setting, [1] gd_dl.rerank_model, [1] gd_dl.utils, [1] promptbind, [1] promptbind.data, [1] promptbind.data.data, [1] promptbind.models, [1] promptbind.models.att_model, [1] promptbind.models.cross_att, [1] promptbind.models.egnn, [1] promptbind.models.model, [1] promptbind.models.model_utils, [1] promptbind.test_promptbind, [1] promptbind.utils, [1] promptbind.utils.fabind_inference_dataset, [1] promptbind.utils.feature_utils, [1] promptbind.utils.generation_utils, [1] promptbind.utils.inference_mol_utils, [1] promptbind.utils.inference_pdb_utils, [1] promptbind.utils.logging_utils, [1] promptbind.utils.metrics, [1] promptbind.utils.metrics_to_tsb, [1] promptbind.utils.post_optim_utils, [1] promptbind.utils.utils, [1] promptbind.visualize_prompt_components, [1]

MOL2 (class in gd_dl.lib_pdb_mol2) MOL2_UNIT (class in gd_dl.lib_pdb_mol2) mol_to_graph_data_obj() (in module diffalign.utils.chem) mol_to_smiles() (in module diffalign.utils.chem) mol_to_smiles_without_Hs() (in module diffalign.utils.chem) MolClusterData (class in diffalign.utils.datasets) mon_id (deepfold.data.pdbx_parsing.Monomer attribute) Monomer (class in deepfold.data.pdbx_parsing) msa_cluster_features_enabled (deepfold.config.FeaturePipelineConfig attribute) msa_dim (deepfold.config.InputEmbedderConfig attribute) msa_dropout (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) msa_fraction_per_deletion_block (deepfold.config.FeaturePipelineConfig attribute) MSAColumnAttention (class in deepfold.modules.msa_column_attention) MSAColumnGlobalAttention (class in deepfold.modules.msa_column_global_attention) MSARowAttentionWithPairBias (class in deepfold.modules.msa_row_attention_with_pair_bias) MSATransition (class in deepfold.modules.msa_transition) MultiLayerPerceptron (class in diffalign.models.common) MultiProcessTestCase (class in deepfold.testing.common) MultiProcessTestCase.Event (class in deepfold.testing.common) myMetric() (in module promptbind.utils.metrics)

N

n_hops_adj() (in module promptbind.utils.feature_utils) (in module promptbind.utils.generation_utils) (in module promptbind.utils.inference_mol_utils) name (deepfold.data.monomer.Ligand attribute) (deepfold.data.pdbx_parsing.ResidueAtPosition attribute) (deepfold.data.search.parsers.TemplateHit attribute) new_dihedral() (in module bis_protein_structure.TORSION2) NoAtomDataInTemplateError NoChainsError node_model() (diffalign.models.encoder.egnn.E_GCL method) (promptbind.models.egnn.MC_Att_L method) (promptbind.models.egnn.MC_E_GCL method) (promptbind.models.egnn.MC_E_GCL_Prompt method) norm() (deepfold.utils.geometry.Vec3Array method) (deepfold.utils.geometry.vector.Vec3Array method) (in module deepfold.utils.geometry.vector) norm2() (deepfold.utils.geometry.Vec3Array method) (deepfold.utils.geometry.vector.Vec3Array method) normal_init_() (in module deepfold.modules.linear) normalized() (deepfold.utils.geometry.Vec3Array method) (deepfold.utils.geometry.vector.Vec3Array method) (in module deepfold.utils.geometry.vector) num (deepfold.data.pdbx_parsing.Monomer attribute) num_ang_res_blocks (deepfold.config.StructureModuleConfig attribute) num_angles (deepfold.config.StructureModuleConfig attribute)

num_bins (deepfold.config.DistogramHeadConfig attribute) (deepfold.config.DistogramLossConfig attribute) (deepfold.config.PerResidueLDDTCaPredictorConfig attribute) (deepfold.config.PLDDTLossConfig attribute) (deepfold.config.RecyclingEmbedderConfig attribute) (deepfold.config.TMLossConfig attribute) (deepfold.config.TMScoreHeadConfig attribute) num_blocks (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) (deepfold.config.StructureModuleConfig attribute) (deepfold.config.TemplatePairStackConfig attribute) num_chunks (deepfold.config.FeaturePipelineConfig attribute) num_classes (deepfold.config.MaskedMSALossConfig attribute) num_heads (deepfold.config.TemplatePointwiseAttentionConfig attribute) num_heads_ipa (deepfold.config.StructureModuleConfig attribute) num_heads_msa (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) num_heads_tri (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) (deepfold.config.TemplatePairStackConfig attribute) num_msa_deletion_blocks (deepfold.config.FeaturePipelineConfig attribute) num_qk_points (deepfold.config.StructureModuleConfig attribute) num_units (deepfold.data.multimer.input_features.ComplexInfo attribute) num_v_points (deepfold.config.StructureModuleConfig attribute) numpy_seed() (in module deepfold.utils.random)

O

one_hot() (in module deepfold.utils.tensor_utils) Op (class in deepfold.data.pdbx_parsing) op_id (deepfold.data.pdbx_parsing.Op attribute) OpenFoldBenchmarkLRScheduler (class in deepfold.train.lr_scheduler) oper_sequence (deepfold.data.pdbx_parsing.AssemblyGenerator attribute) operations (deepfold.data.pdbx_parsing.PDBxObject attribute) optimal_cell_size() (deepfold.eval.cell_lists.CellLists static method) optimizer_adam_amsgrad (deepfold.config.TrainingConfig attribute) optimizer_adam_beta_1 (deepfold.config.TrainingConfig attribute) optimizer_adam_beta_2 (deepfold.config.TrainingConfig attribute) optimizer_adam_eps (deepfold.config.TrainingConfig attribute)

optimizer_adam_weight_decay (deepfold.config.TrainingConfig attribute) ordinal (deepfold.data.pdbx_parsing.ResidueAtPosition attribute) Other (deepfold.utils.import_utils.ParamType attribute) out_channels (diffalign.models.encoder.edge.MLPEdgeEncoder property) outer_product_mean_first (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) OuterProductMean (class in deepfold.modules.outer_product_mean) output_format (deepfold.data.tools.hhsearch.HHSearch property) (deepfold.data.tools.hmmsearch.Hmmsearch property) overwrite_b_factors() (in module deepfold.relax.utils) overwrite_pdb_coordinates() (in module deepfold.relax.utils)

P

p_array() (deepfold.runner.parser.Parser method) p_begin_array() (deepfold.runner.parser.Parser method) p_begin_dict() (deepfold.runner.parser.Parser method) p_begin_edge() (deepfold.runner.parser.Parser method) p_char() (deepfold.runner.parser.Parser method) p_char_unicode_hex() (deepfold.runner.parser.Parser method) p_chars() (deepfold.runner.parser.Parser method) p_command() (deepfold.runner.parser.Parser method) p_dict() (deepfold.runner.parser.Parser method) p_edge() (deepfold.runner.parser.Parser method) p_edge_list() (deepfold.runner.parser.Parser method) p_edges() (deepfold.runner.parser.Parser method) p_end_array() (deepfold.runner.parser.Parser method) p_end_dict() (deepfold.runner.parser.Parser method) p_end_edge() (deepfold.runner.parser.Parser method) p_entity() (deepfold.runner.parser.Parser method) p_error() (deepfold.runner.parser.Parser method) p_exp() (deepfold.runner.parser.Parser method) p_exp_negative() (deepfold.runner.parser.Parser method) p_exp_positive() (deepfold.runner.parser.Parser method) p_frac() (deepfold.runner.parser.Parser method) p_graph() (deepfold.runner.parser.Parser method) p_id() (deepfold.runner.parser.Parser method) p_int_non_zero() (deepfold.runner.parser.Parser method) p_int_zero() (deepfold.runner.parser.Parser method) p_integer() (deepfold.runner.parser.Parser method) p_integer_exp() (deepfold.runner.parser.Parser method) p_member() (deepfold.runner.parser.Parser method) p_members() (deepfold.runner.parser.Parser method) p_model_definition() (deepfold.runner.parser.Parser method) p_number_float() (deepfold.runner.parser.Parser method) p_number_float_exp() (deepfold.runner.parser.Parser method) p_number_negative() (deepfold.runner.parser.Parser method) p_number_positive() (deepfold.runner.parser.Parser method) p_object() (deepfold.runner.parser.Parser method) p_pred_opt() (deepfold.runner.parser.Parser method) p_pred_opts() (deepfold.runner.parser.Parser method) p_predict() (deepfold.runner.parser.Parser method) p_script() (deepfold.runner.parser.Parser method) p_statement() (deepfold.runner.parser.Parser method) p_statements() (deepfold.runner.parser.Parser method) p_stoi_entry() (deepfold.runner.parser.Parser method) p_stoi_list() (deepfold.runner.parser.Parser method) p_string() (deepfold.runner.parser.Parser method) p_value() (deepfold.runner.parser.Parser method) p_value_false() (deepfold.runner.parser.Parser method) p_value_null() (deepfold.runner.parser.Parser method) p_value_seperator() (deepfold.runner.parser.Parser method) p_value_true() (deepfold.runner.parser.Parser method) p_values() (deepfold.runner.parser.Parser method) p_variable_let() (deepfold.runner.parser.Parser method) PackedConformationDataset (class in diffalign.utils.datasets) pad_features() (in module deepfold.data.multimer.msa_pairing) pad_msa() (in module deepfold.data.multimer.input_features) pad_tensor() (in module deepfold.utils.dist_utils) pair_and_merge() (in module deepfold.data.multimer.input_features) pair_dropout (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) pair_sequences() (in module deepfold.data.multimer.msa_pairing) pair_transition_n (deepfold.config.TemplatePairStackConfig attribute) PairTransition (class in deepfold.modules.pair_transition) parallel_processing() (in module bis_protein_structure.DATAGEN) Param (class in deepfold.utils.import_utils) param (deepfold.utils.import_utils.Param attribute) param_type (deepfold.utils.import_utils.Param attribute) ParamType (class in deepfold.utils.import_utils) parent_comp_id (deepfold.data.pdbx_parsing.ModResidue attribute) parents (deepfold.common.protein.Protein attribute) parents_chain_index (deepfold.common.protein.Protein attribute) parse() (deepfold.data.pdbx_parsing.PDBxParser method) (deepfold.runner.parser.Parser method) parse_a3m() (in module deepfold.data.search.parsers) parse_crf() (in module deepfold.data.search.crfalign) parse_e_values_from_tblout() (in module deepfold.data.search.parsers) parse_fasta() (in module bis_protein_structure.DATAGEN) (in module deepfold.data.search.parsers) (in module deepfold.utils.script_utils) parse_hhr() (in module deepfold.data.search.parsers) parse_hmmsearch_a3m() (in module deepfold.data.search.parsers) parse_hmmsearch_sto() (in module deepfold.data.search.parsers) parse_mmcif() (in module bis_protein_structure.DATAGEN) parse_mmcif_string() (in module deepfold.data.search.mmcif) parse_pir() (in module deepfold.data.search.crfalign) parse_stockholm() (in module deepfold.data.search.parsers) Parser (class in deepfold.runner.parser) ParsingResult (class in deepfold.data.pdbx_parsing) Particle (class in deepfold.eval.cell_lists) PDB (class in gd_dl.lib_pdb_mol2) pdb_id (deepfold.data.search.parsers.HitMetadata attribute) pdb_to_data() (in module diffalign.utils.datasets) PDBIO (class in deepfold.data.pdbio) PDBline (class in gd_dl.lib_pdb_mol2) PDBxConstructionError PDBxConstructionWarning PDBxError PDBxHeader (class in deepfold.data.pdbx_parsing) PDBxObject (class in deepfold.data.pdbx_parsing)

PDBxParser (class in deepfold.data.pdbx_parsing) PDBxWarning per_residue_lddt_ca_predictor_config (deepfold.config.AuxiliaryHeadsConfig attribute) permute_final_dims() (in module deepfold.utils.tensor_utils) (in module promptbind.models.model_utils) PerResidueLDDTCaPredictor (class in deepfold.modules.auxiliary_heads) PerResidueLDDTCaPredictorConfig (class in deepfold.config) plddt_loss() (in module deepfold.losses.confidence) plddt_loss_config (deepfold.config.LossConfig attribute) PLDDTLossConfig (class in deepfold.config) plot_cross_link() (in module bis_protein_structure.CROSSLINK) plot_distogram() (in module deepfold.eval.plot) plot_msa() (in module deepfold.eval.plot) plot_plddt() (in module deepfold.eval.plot) plot_predicted_alignment_error() (in module deepfold.eval.plot) plot_protein() (in module deepfold.eval.pseudo_3d) plot_protein_bb() (in module deepfold.eval.pseudo_3d) pocket_direct_metrics() (in module promptbind.utils.metrics) pocket_metrics() (in module promptbind.utils.metrics) PointProjection (class in deepfold.modules.invariant_point_attention) pos (deepfold.eval.cell_lists.Particle attribute) position (deepfold.data.pdbx_parsing.ResidueAtPosition attribute) post_optim_mol() (in module promptbind.utils.utils) post_optimize_compound_coords() (in module promptbind.utils.post_optim_utils) post_optimize_compound_coords_lbfgs() (in module promptbind.utils.post_optim_utils) post_optimize_loss_function() (in module promptbind.utils.post_optim_utils) PrefilterError prepare_pdb2() (in module diffalign.utils.datasets) prepare_pdb_valtest() (in module diffalign.utils.datasets) prepare_pdblarge() (in module diffalign.utils.datasets) preprocess_GEOM_dataset() (in module diffalign.utils.datasets) preprocess_GEOM_dataset_with_fixed_num_conf() (in module diffalign.utils.datasets) preprocess_iso17_dataset() (in module diffalign.utils.datasets) preset (deepfold.config.FeaturePipelineConfig attribute) primary_raw_feature_names (deepfold.config.FeaturePipelineConfig attribute) print_amap() (in module deepfold.data.pdbx_parsing) print_chain_features() (in module deepfold.data.pdbx_parsing) print_covmat_results() (in module diffalign.utils.evaluation.covmat) print_metrics() (in module promptbind.utils.metrics) process() (deepfold.relax.relax.AmberRelaxation method) process_final() (in module deepfold.data.multimer.input_features) process_mmcif_to_pdbs() (in module bis_protein_structure.DATAGEN) process_multimer_features() (in module deepfold.data.multimer.input_features) process_single_chain() (in module deepfold.data.multimer.input_features) process_unmerged_features() (in module deepfold.data.multimer.input_features) processed_file_names (promptbind.data.data.FABindDataSet property) Procrustes (class in deepfold.losses.procrustes) procrustes() (in module deepfold.losses.procrustes) prompt_generation_module() (promptbind.models.egnn.MC_E_GCL_Prompt method) prompt_interaction_module() (promptbind.models.egnn.MC_E_GCL_Prompt method) promptbind module, [1] promptbind.data module, [1] promptbind.data.data module, [1] promptbind.models module, [1] promptbind.models.att_model module, [1] promptbind.models.cross_att module, [1] promptbind.models.egnn module, [1] promptbind.models.model module, [1] promptbind.models.model_utils module, [1] promptbind.test_promptbind module, [1] promptbind.utils module, [1] promptbind.utils.fabind_inference_dataset module, [1] promptbind.utils.feature_utils module, [1] promptbind.utils.generation_utils module, [1] promptbind.utils.inference_mol_utils module, [1] promptbind.utils.inference_pdb_utils module, [1] promptbind.utils.logging_utils module, [1] promptbind.utils.metrics module, [1] promptbind.utils.metrics_to_tsb module, [1] promptbind.utils.post_optim_utils module, [1] promptbind.utils.utils module, [1] promptbind.visualize_prompt_components module, [1] PromptBindInference (class in promptbind.test_promptbind) Protein (class in deepfold.common.protein) ptm_weight (deepfold.config.AuxiliaryHeadsConfig attribute) pts_to_distogram() (in module deepfold.utils.tensor_utils)

Q

quat_multiply() (in module deepfold.utils.rigid_utils) quat_multiply_by_vec() (in module deepfold.utils.rigid_utils) quat_to_rot() (in module deepfold.utils.rigid_utils) QuatRigid (class in deepfold.utils.geometry.quat_rigid) query (deepfold.data.search.parsers.TemplateHit attribute) query() (deepfold.data.tools.hhblits.HHBlits method) (deepfold.data.tools.hhsearch.HHSearch method) (deepfold.data.tools.hmmsearch.Hmmsearch method) (deepfold.data.tools.jackhmmer.Jackhmmer method)

query_multiple() (deepfold.data.tools.jackhmmer.Jackhmmer method) query_with_hmm() (deepfold.data.tools.hmmsearch.Hmmsearch method) QueryToTemplateAlignError

R

R() (gd_dl.lib_pdb_mol2.Atom method) (gd_dl.lib_pdb_mol2.Residue method) randomize_num_msa_deletion_blocks (deepfold.config.FeaturePipelineConfig attribute) rank() (in module deepfold.distributed.model_parallel) RBFDistanceModule (class in promptbind.models.model_utils) rdmol_cluster_to_data() (in module diffalign.utils.datasets) rdmol_to_data() (in module diffalign.utils.datasets) read() (gd_dl.lib_pdb_mol2.MOL2 method) (gd_dl.lib_pdb_mol2.PDB method) read_fasta() (in module bis_protein_structure.DATAGEN) read_ligand() (in module deepfold.data.monomer) read_line() (gd_dl.lib_pdb_mol2.MOL2_UNIT method) read_logs() (in module deepfold.utils.log_utils) read_mmcif() (in module deepfold.data.pdbx_parsing) read_mol() (in module promptbind.utils.feature_utils) (in module promptbind.utils.generation_utils) (in module promptbind.utils.utils) read_mol_and_renumber() (in module promptbind.utils.inference_mol_utils) read_molecule() (in module promptbind.utils.post_optim_utils) read_pdbbind_data() (in module promptbind.utils.utils) read_smiles() (in module promptbind.utils.inference_mol_utils) read_text() (in module deepfold.utils.file_utils) readMMCIF() (in module bis_protein_structure.CROSSLINK) readMMCIF_label() (in module bis_protein_structure.DISULFIDE) readPDB() (in module bis_protein_structure.CROSSLINK) (in module bis_protein_structure.MMEVAL) (in module bis_protein_structure.TORSION2) recycle_early_stop_enabled (deepfold.config.AlphaFoldConfig attribute) recycle_early_stop_tolerance (deepfold.config.AlphaFoldConfig attribute) recycling_embedder_config (deepfold.config.AlphaFoldConfig attribute) RecyclingEmbedder (class in deepfold.modules.recycling_embedder) RecyclingEmbedderConfig (class in deepfold.config) reduce() (in module deepfold.distributed.model_parallel) reduce_from_model_parallel_region() (in module deepfold.distributed.model_parallel) register_dap_gradient_scaling_hooks() (deepfold.modules.alphafold.AlphaFold method) relpos() (deepfold.modules.input_embedder.InputEmbedderMultimer method) relpos_k (deepfold.config.InputEmbedderConfig attribute) remark (deepfold.common.protein.Protein attribute) remove_duplicate_mols() (in module diffalign.utils.chem) remove_empty_columns_from_stockholm_msa() (in module deepfold.data.search.parsers) remove_hetero_and_extract_ligand() (in module promptbind.utils.feature_utils) removed (deepfold.data.monomer.AtomMap attribute) reorder_paired_rows() (in module deepfold.data.multimer.msa_pairing) repeat_batch() (in module diffalign.utils.common) (in module diffalign.utils.misc) repeat_data() (in module diffalign.utils.common) (in module diffalign.utils.misc) repr_norm_loss() (in module deepfold.losses.auxillary) requires_grad (deepfold.utils.geometry.Rotation property) (deepfold.utils.rigid_utils.Rotation property) Rerank_model (class in gd_dl.models) (class in gd_dl.rerank_model)

resample_msa_in_recycling (deepfold.config.FeaturePipelineConfig attribute) reset_parameters() (gd_dl.models.Weight_CGConv method) (gd_dl.rerank_model.Weight_CGConv method) reshape() (deepfold.utils.geometry.Rigid3Array method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array method) (deepfold.utils.geometry.Rot3Array method) (deepfold.utils.geometry.rotation_matrix.Rot3Array method) (deepfold.utils.geometry.Vec3Array method) (deepfold.utils.geometry.vector.Vec3Array method) reshape_weight() (in module deepfold.utils.import_utils) Residue (class in gd_dl.lib_pdb_mol2) residue_cropping_enabled (deepfold.config.FeaturePipelineConfig attribute) residue_index (deepfold.common.protein.Protein attribute) (deepfold.data.pdbx_parsing.ResidueAtPosition attribute) (deepfold.eval.contact.Atom attribute) residue_name (deepfold.data.pdbx_parsing.AtomSite attribute) ResidueAtPosition (class in deepfold.data.pdbx_parsing) ResiduePosition (class in deepfold.data.pdbx_parsing) resName() (gd_dl.lib_pdb_mol2.Residue method) resNo() (gd_dl.lib_pdb_mol2.Residue method) resNo_char() (gd_dl.lib_pdb_mol2.Residue method) resolution (deepfold.data.pdbx_parsing.PDBxHeader attribute) restore_wrapper() (in module deepfold.utils.file_utils) restype_refer_atoms() (in module bis_protein_structure.MMEVAL) (in module bis_protein_structure.TORSION2) resume_checkpoint() (in module deepfold.utils.checkpoint_utils) resume_from_latest_checkpoint() (in module deepfold.utils.checkpoint_utils) rid (deepfold.eval.contact.Atom attribute) Rigid (class in deepfold.utils.geometry) (class in deepfold.utils.rigid_utils) Rigid3Array (class in deepfold.utils.geometry) (class in deepfold.utils.geometry.rigid_matrix_vector) rigid_points_registration() (in module deepfold.losses.procrustes) rigid_vectors_registration() (in module deepfold.losses.procrustes) rot (deepfold.data.pdbx_parsing.Op attribute) Rot3Array (class in deepfold.utils.geometry) (class in deepfold.utils.geometry.rotation_matrix) rot_matmul() (in module deepfold.utils.rigid_utils) rot_to_quat() (in module deepfold.utils.rigid_utils) rot_vec_mul() (in module deepfold.utils.rigid_utils) Rotation (class in deepfold.utils.geometry) (class in deepfold.utils.rigid_utils) rotation (deepfold.utils.geometry.Rigid3Array attribute) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array attribute) row_to_col() (in module deepfold.distributed.model_parallel) RowAttentionBlock (class in promptbind.models.cross_att) RowTriangleAttentionBlock (class in promptbind.models.cross_att) run_inference() (promptbind.test_promptbind.PromptBindInference method) run_pipeline() (in module deepfold.relax.amber_minimize) run_test() (deepfold.testing.common.MultiProcessTestCase method)

S

safe_filename() (in module deepfold.runner.utils) safely_set_viewless_tensor_data() (in module deepfold.distributed.utils) sample_msa_distillation_enabled (deepfold.config.FeaturePipelineConfig attribute) save() (deepfold.data.pdbio.PDBIO method) save_checkpoint() (in module deepfold.utils.checkpoint_utils) save_cleaned_protein() (in module promptbind.utils.feature_utils) save_last_checkpoint() (in module deepfold.utils.checkpoint_utils) save_logs() (in module deepfold.utils.log_utils) save_val_checkpoint() (in module deepfold.utils.checkpoint_utils) scale_factor (deepfold.config.StructureModuleConfig attribute) scale_translation() (deepfold.utils.geometry.Rigid method) (deepfold.utils.geometry.Rigid3Array method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array method) (deepfold.utils.rigid_utils.Rigid method) scatter() (in module deepfold.distributed.model_parallel) scatter_to_model_parallel_region() (in module deepfold.distributed.model_parallel) seed (deepfold.config.FeaturePipelineConfig attribute) seed_all() (in module diffalign.utils.misc) Seed_everything() (in module promptbind.utils.feature_utils) select_chain_within_cutoff_to_ligand_v2() (in module promptbind.utils.feature_utils) self_distillation_plddt_threshold (deepfold.config.FeaturePipelineConfig attribute) SelfAttentionWithGate (class in deepfold.modules.attention) sequence_to_onehot() (in module bis_protein_structure.residue_constants) (in module deepfold.common.residue_constants) SequenceNotInTemplateError sequential_and() (in module promptbind.models.att_model) sequential_or() (in module promptbind.models.att_model) set_chains() (deepfold.data.pdbio.IO method) set_conformer_positions() (in module diffalign.utils.chem) set_learning_rate() (in module deepfold.train.lr_scheduler) set_prep() (in module gd_dl.utils) set_rdmol_positions() (in module diffalign.utils.chem) set_rdmol_positions_() (in module diffalign.utils.chem) set_structure() (deepfold.data.pdbio.IO method) SetDihedral() (in module promptbind.utils.utils) setUp() (deepfold.testing.common.MultiProcessTestCase method) setup_accelerator() (promptbind.test_promptbind.PromptBindInference method) setup_criterions() (promptbind.test_promptbind.PromptBindInference method) setup_data_loaders() (promptbind.test_promptbind.PromptBindInference method) setup_logger() (promptbind.test_promptbind.PromptBindInference method) setup_logging() (in module deepfold.utils.log_utils) shape (deepfold.utils.geometry.Rigid property) (deepfold.utils.geometry.Rigid3Array property) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array property) (deepfold.utils.geometry.Rotation property) (deepfold.utils.geometry.Vec3Array property) (deepfold.utils.geometry.vector.Vec3Array property) (deepfold.utils.rigid_utils.Rigid property) (deepfold.utils.rigid_utils.Rotation property) shuffle_top_k_prefiltered (deepfold.config.FeaturePipelineConfig attribute) sidechain_clamp_distance (deepfold.config.FAPELossConfig attribute) sidechain_length_scale (deepfold.config.FAPELossConfig attribute) sidechain_loss() (in module deepfold.losses.geometry) sidechain_sym_angle() (in module bis_protein_structure.TORSION2)

sidechain_weight (deepfold.config.FAPELossConfig attribute) SidechainConformationDataset (class in diffalign.utils.datasets) sig (deepfold.eval.cell_lists.Particle attribute) sigmoid_cross_entropy() (in module deepfold.losses.utils) SingleTransition (class in deepfold.modules.single_transition) SinusoidalTimeEmbeddings (class in diffalign.models.epsnet.diffusion) size() (in module deepfold.distributed.model_parallel) skip_if_lt_x_gpu() (in module deepfold.testing.common) skip_if_no_gpu() (in module deepfold.testing.common) slice_generator() (in module deepfold.utils.iter_utils) softmax_cross_entropy() (in module deepfold.losses.utils) spatial_crop_prob (deepfold.config.FeaturePipelineConfig attribute) speical_procrustes() (in module deepfold.losses.procrustes) split_protein_and_ligand() (in module promptbind.utils.feature_utils) split_the_pdb() (in module bis_protein_structure.split_pdb) square_euclidean_distance() (in module deepfold.utils.geometry) (in module deepfold.utils.geometry.vector) stacked (deepfold.utils.import_utils.Param attribute) stacked() (in module deepfold.utils.import_utils) start (deepfold.data.search.parsers.HitMetadata attribute) startswith() (gd_dl.lib_pdb_mol2.PDBline method) states (deepfold.runner.parser.Lexer attribute) stddev (bis_protein_structure.residue_constants.Bond attribute) (bis_protein_structure.residue_constants.BondAngle attribute) (deepfold.common.residue_constants.Bond attribute) (deepfold.common.residue_constants.BondAngle attribute) step() (deepfold.train.lr_scheduler.AlphaFoldLRScheduler method) stop_gradient() (deepfold.utils.geometry.Rot3Array method) (deepfold.utils.geometry.rotation_matrix.Rot3Array method) stop_rot_gradient() (deepfold.utils.geometry.Rigid method) (deepfold.utils.geometry.Rigid3Array method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array method) (deepfold.utils.rigid_utils.Rigid method) str2bool() (in module gd_dl.utils) str_hash() (in module deepfold.utils.random) str_tuple() (in module diffalign.utils.misc) structure (deepfold.data.pdbx_parsing.PDBxObject attribute) structure_module_config (deepfold.config.AlphaFoldConfig attribute) StructureModule (class in deepfold.modules.structure_module) StructureModuleConfig (class in deepfold.config) subsample_templates (deepfold.config.FeaturePipelineConfig attribute) sum() (deepfold.utils.geometry.Vec3Array method) (deepfold.utils.geometry.vector.Vec3Array method) sum_probs (deepfold.data.search.parsers.TemplateHit attribute) superimpose() (in module deepfold.losses.geometry) supervised_chi_loss() (in module deepfold.losses.geometry) supervised_chi_loss_config (deepfold.config.LossConfig attribute) supervised_features_enabled (deepfold.config.FeaturePipelineConfig attribute) supervised_raw_feature_names (deepfold.config.FeaturePipelineConfig attribute) SupervisedChiLossConfig (class in deepfold.config) svd() (in module deepfold.losses.procrustes) swa_avg_fn (class in deepfold.utils.swa_utils) swa_decay_rate (deepfold.config.TrainingConfig attribute) swa_enabled (deepfold.config.TrainingConfig attribute) swap (deepfold.utils.import_utils.Param attribute)

T

t_ANY_error() (deepfold.runner.parser.Lexer method) t_BEGIN_ARRAY() (deepfold.runner.parser.Lexer method) t_BEGIN_OBJECT() (deepfold.runner.parser.Lexer method) t_DECIMAL_POINT (deepfold.runner.parser.Lexer attribute) t_DIGITS (deepfold.runner.parser.Lexer attribute) t_E (deepfold.runner.parser.Lexer attribute) t_escaped_BACKSPACE_CHAR() (deepfold.runner.parser.Lexer method) t_escaped_CARRIAGE_RETURN_CHAR() (deepfold.runner.parser.Lexer method) t_escaped_FORM_FEED_CHAR() (deepfold.runner.parser.Lexer method) t_escaped_ignore (deepfold.runner.parser.Lexer attribute) t_escaped_LINE_FEED_CHAR() (deepfold.runner.parser.Lexer method) t_escaped_QUOTATION_MARK() (deepfold.runner.parser.Lexer method) t_escaped_REVERSE_SOLIDUS() (deepfold.runner.parser.Lexer method) t_escaped_SOLIDUS() (deepfold.runner.parser.Lexer method) t_escaped_TAB_CHAR() (deepfold.runner.parser.Lexer method) t_escaped_UNICODE_HEX() (deepfold.runner.parser.Lexer method) t_FALSE (deepfold.runner.parser.Lexer attribute) t_graph_BEGIN_EDGE_LIST() (deepfold.runner.parser.Lexer method) t_graph_EDGE_SEP() (deepfold.runner.parser.Lexer method) t_graph_END_EDGE_LIST() (deepfold.runner.parser.Lexer method) t_graph_ID() (deepfold.runner.parser.Lexer method) t_graph_ignore (deepfold.runner.parser.Lexer attribute) t_graph_NEWLINE() (deepfold.runner.parser.Lexer method) t_graph_VALUE_SEPARATOR (deepfold.runner.parser.Lexer attribute) t_ID() (deepfold.runner.parser.Lexer method) t_ignore (deepfold.runner.parser.Lexer attribute) t_ignore_COMMENT() (deepfold.runner.parser.Lexer method) t_iterable_END_ARRAY() (deepfold.runner.parser.Lexer method) t_iterable_END_OBJECT() (deepfold.runner.parser.Lexer method) t_iterable_NEWLINE() (deepfold.runner.parser.Lexer method) t_MINUS (deepfold.runner.parser.Lexer attribute) t_NAME_SEPARATOR (deepfold.runner.parser.Lexer attribute) t_NEWLINE() (deepfold.runner.parser.Lexer method) t_NULL (deepfold.runner.parser.Lexer attribute) t_PLUS (deepfold.runner.parser.Lexer attribute) t_QUOTATION_MARK() (deepfold.runner.parser.Lexer method) t_SEMICOLON (deepfold.runner.parser.Lexer attribute) t_stoi_DIGITS() (deepfold.runner.parser.Lexer method) t_stoi_ID() (deepfold.runner.parser.Lexer method) t_stoi_ignore (deepfold.runner.parser.Lexer attribute) t_stoi_NUM_SYM_SEP() (deepfold.runner.parser.Lexer method) t_stoi_STOI_SEP() (deepfold.runner.parser.Lexer method) t_string_ESCAPE() (deepfold.runner.parser.Lexer method) t_string_ignore (deepfold.runner.parser.Lexer attribute) t_string_QUOTATION_MARK() (deepfold.runner.parser.Lexer method) t_string_UNESCAPED() (deepfold.runner.parser.Lexer method) t_TRUE (deepfold.runner.parser.Lexer attribute) t_VALUE_SEPARATOR (deepfold.runner.parser.Lexer attribute) t_ZERO (deepfold.runner.parser.Lexer attribute) ta_dim (deepfold.config.TemplateAngleEmbedderConfig attribute) tearDown() (deepfold.testing.common.MultiProcessTestCase method) template_angle_embedder_config (deepfold.config.AlphaFoldConfig attribute) template_pair_embedder_config (deepfold.config.AlphaFoldConfig attribute) template_pair_feat_distogram_max_bin (deepfold.config.AlphaFoldConfig attribute) template_pair_feat_distogram_min_bin (deepfold.config.AlphaFoldConfig attribute) template_pair_feat_distogram_num_bins (deepfold.config.AlphaFoldConfig attribute) template_pair_feat_eps (deepfold.config.AlphaFoldConfig attribute) template_pair_feat_inf (deepfold.config.AlphaFoldConfig attribute) template_pair_feat_use_unit_vector (deepfold.config.AlphaFoldConfig attribute) template_pair_stack_config (deepfold.config.AlphaFoldConfig attribute) template_pointwise_attention_config (deepfold.config.AlphaFoldConfig attribute) template_projection_config (deepfold.config.AlphaFoldConfig attribute) template_raw_feature_names (deepfold.config.FeaturePipelineConfig attribute) TemplateAngleEmbedder (class in deepfold.modules.template_angle_embedder) TemplateAngleEmbedderConfig (class in deepfold.config) TemplateAtomMaskAllZerosError TemplateFeaturesResult (class in deepfold.data.search.templates) TemplateHit (class in deepfold.data.search.parsers) TemplateHitFeaturizer (class in deepfold.data.search.templates) TemplatePairBlock (class in deepfold.modules.template_pair_block) TemplatePairEmbedder (class in deepfold.modules.template_pair_embedder)

TemplatePairEmbedderConfig (class in deepfold.config) TemplatePairEmbedderMultimer (class in deepfold.modules.template_pair_embedder) TemplatePairStack (class in deepfold.modules.template_pair_stack) TemplatePairStackConfig (class in deepfold.config) TemplatePointwiseAttention (class in deepfold.modules.template_pointwise_attention) TemplatePointwiseAttentionConfig (class in deepfold.config) TemplateProjection (class in deepfold.modules.template_projection) TemplateProjectionConfig (class in deepfold.config) templates_enabled (deepfold.config.AlphaFoldConfig attribute) (deepfold.config.FeaturePipelineConfig attribute) tensor_tree_map() (in module deepfold.utils.tensor_utils) TEST_ERROR_EXIT_CODE (deepfold.testing.common.MultiProcessTestCase attribute) text (deepfold.data.search.parsers.HitMetadata attribute) tf_dim (deepfold.config.InputEmbedderConfig attribute) timing() (in module deepfold.data.tools.utils) tm_loss() (in module deepfold.losses.confidence) tm_loss_config (deepfold.config.LossConfig attribute) tm_score_head_config (deepfold.config.AuxiliaryHeadsConfig attribute) tm_score_head_enabled (deepfold.config.AuxiliaryHeadsConfig attribute) TMLossConfig (class in deepfold.config) tmpdir_manager() (in module deepfold.data.tools.utils) TMScoreHead (class in deepfold.modules.auxiliary_heads) TMScoreHeadConfig (class in deepfold.config) to() (deepfold.utils.geometry.Rotation method) (deepfold.utils.rigid_utils.Rotation method) to_date() (in module deepfold.data.tools.utils) to_dict() (deepfold.config.AlphaFoldConfig method) (deepfold.config.FeaturePipelineConfig method) (deepfold.config.TrainingConfig method) (deepfold.data.pdbx_parsing.Op method) to_modelcif() (in module deepfold.common.protein) to_pdb() (in module deepfold.common.protein) to_tensor() (deepfold.utils.geometry.Rigid3Array method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array method) (deepfold.utils.geometry.Rot3Array method) (deepfold.utils.geometry.rotation_matrix.Rot3Array method) (deepfold.utils.geometry.Vec3Array method) (deepfold.utils.geometry.vector.Vec3Array method) to_tensor_4x4() (deepfold.utils.geometry.Rigid method) (deepfold.utils.geometry.Rigid3Array method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array method) (deepfold.utils.rigid_utils.Rigid method) to_tensor_7() (deepfold.utils.geometry.Rigid method) (deepfold.utils.rigid_utils.Rigid method) tokenize() (deepfold.runner.parser.Lexer method) tokens (deepfold.runner.parser.Lexer attribute) (deepfold.runner.parser.Parser attribute) torsion_angle_loss() (in module bis_protein_structure.TORSION2) tp_dim (deepfold.config.TemplatePairEmbedderConfig attribute) TqdmHandler (class in deepfold.utils.log_utils) TrainingConfig (class in deepfold.config) trans (deepfold.data.pdbx_parsing.Op attribute) TransformerNN (class in diffalign.models.encoder.egnn) TransformerNN.SetDecoder (class in diffalign.models.encoder.egnn) Transition (class in promptbind.models.model_utils) Transition_diff_out_dim (class in promptbind.models.model) transition_n (deepfold.config.EvoformerStackConfig attribute) (deepfold.config.ExtraMSAStackConfig attribute) translation (deepfold.utils.geometry.Rigid3Array attribute) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array attribute) transpose_on_model_parallel_region() (in module deepfold.distributed.model_parallel) tree_map() (in module deepfold.utils.tensor_utils) tri_att_first (deepfold.config.TemplatePairStackConfig attribute) TriangleAttention (class in deepfold.modules.triangular_attention) TriangleAttentionEndingNode (class in deepfold.modules.triangular_attention) TriangleAttentionStartingNode (class in deepfold.modules.triangular_attention) TriangleMultiplicationIncoming (class in deepfold.modules.triangular_multiplicative_update) TriangleMultiplicationOutgoing (class in deepfold.modules.triangular_multiplicative_update) TriangleMultiplicativeUpdate (class in deepfold.modules.triangular_multiplicative_update) trio_encoder() (promptbind.models.egnn.MC_Att_L method) trunc_normal_init_() (in module deepfold.modules.linear) truncate_stockholm_msa() (in module deepfold.data.search.parsers)

U

undigitize() (in module deepfold.eval.distogram) unflatten_batch_dims() (in module deepfold.losses.procrustes) uniform_random_rotation() (in module promptbind.utils.utils) unpad_to_schema_shape_() (in module deepfold.utils.crop_utils) unsorted_segment_mean() (in module promptbind.models.egnn) unsorted_segment_sum() (in module diffalign.models.encoder.egnn) (in module promptbind.models.egnn) unsqueeze() (deepfold.utils.geometry.Rigid method) (deepfold.utils.geometry.Rigid3Array method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array method) (deepfold.utils.geometry.Rot3Array method) (deepfold.utils.geometry.Rotation method) (deepfold.utils.geometry.rotation_matrix.Rot3Array method) (deepfold.utils.geometry.Vec3Array method) (deepfold.utils.geometry.vector.Vec3Array method) (deepfold.utils.rigid_utils.Rigid method) (deepfold.utils.rigid_utils.Rotation method)

update() (deepfold.utils.swa_utils.AlphaFoldSWA method) update_bond() (gd_dl.lib_pdb_mol2.MOL2_UNIT method) update_data_pos_from_rdmol() (in module diffalign.utils.chem) update_data_rdmol_positions() (in module diffalign.utils.chem) update_norm_from_buckets() (in module deepfold.train.gradient_clipping) use_chain_relative (deepfold.config.InputEmbedderConfig attribute)

V

Vec3Array (class in deepfold.utils.geometry) (class in deepfold.utils.geometry.vector) violation_loss() (in module deepfold.losses.violation)

violation_loss_config (deepfold.config.LossConfig attribute) violation_tolerance_factor (deepfold.config.ViolationLossConfig attribute) ViolationLossConfig (class in deepfold.config) visualize_mol() (in module diffalign.utils.visualize)

W

warning (deepfold.data.search.templates.TemplateFeaturesResult attribute) weight (deepfold.config.CenterOfMassConfig attribute) (deepfold.config.DistogramLossConfig attribute) (deepfold.config.ExperimentallyResolvedLossConfig attribute) (deepfold.config.FAPELossConfig attribute) (deepfold.config.MaskedMSALossConfig attribute) (deepfold.config.PLDDTLossConfig attribute) (deepfold.config.SupervisedChiLossConfig attribute) (deepfold.config.TMLossConfig attribute) (deepfold.config.ViolationLossConfig attribute) Weight_CGConv (class in gd_dl.models) (class in gd_dl.rerank_model) will_restrain() (in module deepfold.relax.amber_minimize)

with_nccl_blocking_wait() (in module deepfold.testing.common) within_residue_violations() (in module deepfold.losses.violation) world_size (deepfold.testing.common.MultiProcessTestCase property) write() (gd_dl.lib_pdb_mol2.Model method) (gd_dl.lib_pdb_mol2.MOL2 method) (gd_dl.lib_pdb_mol2.MOL2_UNIT method) (gd_dl.lib_pdb_mol2.PDB method) (gd_dl.lib_pdb_mol2.Residue method) write_mol() (in module promptbind.utils.inference_mol_utils) (in module promptbind.utils.post_optim_utils) write_renumbered_sdf() (in module promptbind.utils.feature_utils) write_with_new_coords() (in module promptbind.utils.feature_utils) (in module promptbind.utils.generation_utils)

X

x (deepfold.utils.geometry.Vec3Array attribute) (deepfold.utils.geometry.vector.Vec3Array attribute) xx (deepfold.utils.geometry.Rot3Array attribute) (deepfold.utils.geometry.rotation_matrix.Rot3Array attribute)

xy (deepfold.utils.geometry.Rot3Array attribute) (deepfold.utils.geometry.rotation_matrix.Rot3Array attribute) xz (deepfold.utils.geometry.Rot3Array attribute) (deepfold.utils.geometry.rotation_matrix.Rot3Array attribute)

Y

y (deepfold.utils.geometry.Vec3Array attribute) (deepfold.utils.geometry.vector.Vec3Array attribute) yx (deepfold.utils.geometry.Rot3Array attribute) (deepfold.utils.geometry.rotation_matrix.Rot3Array attribute)

yy (deepfold.utils.geometry.Rot3Array attribute) (deepfold.utils.geometry.rotation_matrix.Rot3Array attribute) yz (deepfold.utils.geometry.Rot3Array attribute) (deepfold.utils.geometry.rotation_matrix.Rot3Array attribute)

Z

z (deepfold.utils.geometry.Vec3Array attribute) (deepfold.utils.geometry.vector.Vec3Array attribute) zero_center_atom_positions() (in module deepfold.data.search.mmcif) zeros() (deepfold.utils.geometry.Vec3Array class method) (deepfold.utils.geometry.vector.Vec3Array class method)

zx (deepfold.utils.geometry.Rot3Array attribute) (deepfold.utils.geometry.rotation_matrix.Rot3Array attribute) zy (deepfold.utils.geometry.Rot3Array attribute) (deepfold.utils.geometry.rotation_matrix.Rot3Array attribute) zz (deepfold.utils.geometry.Rot3Array attribute) (deepfold.utils.geometry.rotation_matrix.Rot3Array attribute)