Index

_

__init__() (bapred.data.data.BAPredDataset method) (bapred.model.GatedGCNLSPE.GatedGCNLSPELayer method) (bapred.model.GraphGPS.GraphGPS method) (bapred.model.MHA.MultiHeadAttention method) (bapred.model.model.PredictionPKD method) (bindingrmsd.data.data.PoseSelectionDataset method) (bindingrmsd.data.data_bck.PoseSelectionDataset method) (bindingrmsd.model.GatedGCNLSPE.GatedGCNLSPELayer method) (bindingrmsd.model.model.PredictionRMSD method) (bis_protein_structure.DATAGEN.AllResiduesSelector method) (bis_protein_structure.residue_constants.Bond method) (bis_protein_structure.residue_constants.BondAngle method) (deepfold.common.protein.Protein method) (deepfold.common.residue_constants.Bond method) (deepfold.common.residue_constants.BondAngle method) (deepfold.config.AlphaFoldConfig method) (deepfold.config.AuxiliaryHeadsConfig method) (deepfold.config.CenterOfMassConfig method) (deepfold.config.DistogramHeadConfig method) (deepfold.config.DistogramLossConfig method) (deepfold.config.EvoformerStackConfig method) (deepfold.config.ExperimentallyResolvedHeadConfig method) (deepfold.config.ExperimentallyResolvedLossConfig method) (deepfold.config.ExtraMSAEmbedderConfig method) (deepfold.config.ExtraMSAStackConfig method) (deepfold.config.FAPELossConfig method) (deepfold.config.FeaturePipelineConfig method) (deepfold.config.InputEmbedderConfig method) (deepfold.config.LossConfig method) (deepfold.config.MaskedMSAHeadConfig method) (deepfold.config.MaskedMSALossConfig method) (deepfold.config.PerResidueLDDTCaPredictorConfig method) (deepfold.config.PLDDTLossConfig method) (deepfold.config.RecyclingEmbedderConfig method) (deepfold.config.StructureModuleConfig method) (deepfold.config.SupervisedChiLossConfig method) (deepfold.config.TemplateAngleEmbedderConfig method) (deepfold.config.TemplatePairEmbedderConfig method) (deepfold.config.TemplatePairStackConfig method) (deepfold.config.TemplatePointwiseAttentionConfig method) (deepfold.config.TemplateProjectionConfig method) (deepfold.config.TMLossConfig method) (deepfold.config.TMScoreHeadConfig method) (deepfold.config.TrainingConfig method) (deepfold.config.ViolationLossConfig method) (deepfold.data.monomer.AtomMap method) (deepfold.data.monomer.Ligand method) (deepfold.data.multimer.input_features.ComplexInfo method) (deepfold.data.pdbio.IO method) (deepfold.data.pdbio.PDBIO method) (deepfold.data.pdbx_parsing.AssemblyGenerator method) (deepfold.data.pdbx_parsing.AtomSite method) (deepfold.data.pdbx_parsing.ModResidue method) (deepfold.data.pdbx_parsing.Monomer method) (deepfold.data.pdbx_parsing.Op method) (deepfold.data.pdbx_parsing.ParsingResult method) (deepfold.data.pdbx_parsing.PDBxHeader method) (deepfold.data.pdbx_parsing.PDBxObject method) (deepfold.data.pdbx_parsing.PDBxParser method) (deepfold.data.pdbx_parsing.ResidueAtPosition method) (deepfold.data.pdbx_parsing.ResiduePosition method) (deepfold.data.search.parsers.HitMetadata method) (deepfold.data.search.parsers.TemplateHit method) (deepfold.data.search.templates.TemplateFeaturesResult method) (deepfold.data.search.templates.TemplateHitFeaturizer method) (deepfold.data.tools.hhblits.HHBlits method) (deepfold.data.tools.hhsearch.HHSearch method) (deepfold.data.tools.hmmbuild.Hmmbuild method) (deepfold.data.tools.hmmsearch.Hmmsearch method) (deepfold.data.tools.jackhmmer.Jackhmmer method) (deepfold.data.tools.kalign.Kalign method) (deepfold.distributed.model_parallel.Disable method) (deepfold.distributed.model_parallel.Enable method) (deepfold.distributed.utils.GlobalMemoryBuffer method) (deepfold.eval.cell_lists.CellLists method) (deepfold.eval.cell_lists.Particle method) (deepfold.eval.contact.Atom method) (deepfold.loss.AlphaFoldLoss method) (deepfold.losses.procrustes.Procrustes 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.dropout.DropoutColumnwise method) (deepfold.modules.dropout.DropoutRowwise 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.linear.Linear 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_attention.TriangleAttentionEndingNode method) (deepfold.modules.triangular_attention.TriangleAttentionStartingNode method) (deepfold.modules.triangular_multiplicative_update.TriangleMultiplicationIncoming method) (deepfold.modules.triangular_multiplicative_update.TriangleMultiplicationOutgoing method) (deepfold.modules.triangular_multiplicative_update.TriangleMultiplicativeUpdate method) (deepfold.relax.relax.AmberRelaxation method) (deepfold.runner.parser.Lexer method) (deepfold.runner.parser.Parser method) (deepfold.testing.common.MultiProcessTestCase method) (deepfold.train.gradient_clipping.AsyncGradientClipping method) (deepfold.train.lr_scheduler.AlphaFoldLRScheduler method) (deepfold.train.lr_scheduler.OpenFoldBenchmarkLRScheduler method) (deepfold.utils.geometry.quat_rigid.QuatRigid method) (deepfold.utils.geometry.rigid_matrix_vector.Rigid3Array method) (deepfold.utils.geometry.rotation_matrix.Rot3Array method) (deepfold.utils.geometry.vector.Vec3Array method) (deepfold.utils.import_utils.Param method) (deepfold.utils.import_utils.ParamType method) (deepfold.utils.log_utils.TqdmHandler method) (deepfold.utils.rigid_utils.Rigid method) (deepfold.utils.rigid_utils.Rotation method) (deepfold.utils.swa_utils.AlphaFoldSWA method) (deepfold.utils.swa_utils.swa_avg_fn method) (diffalign.models.common.MultiLayerPerceptron method) (diffalign.models.encoder.cross_attention.CrossAttention method) (diffalign.models.encoder.cross_attention.CrossGraphAligner method) (diffalign.models.encoder.edge.MLPEdgeEncoder method) (diffalign.models.encoder.egnn.E_GCL method) (diffalign.models.encoder.egnn.EGNN method) (diffalign.models.epsnet.diffusion.DDPMTimeEncoder method) (diffalign.models.epsnet.diffusion.DiffAlign method) (diffalign.models.epsnet.diffusion.SinusoidalPosEmb method) (gd_dl.lib_pdb_mol2.Atom method) (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.PDBline method) (gd_dl.lib_pdb_mol2.Residue 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) (miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.EMA method) (miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.ModelVisulizer method) (miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.Attention method) (miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.AttentionWithBias method) (miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.BiasedAxialAttention method) (miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.FeedForwardLayer method) (miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.GraphTriangleAttention method) (miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.MSAColAttention method) (miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.MSAColGlobalAttention method) (miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.MSARowAttentionWithBias method) (miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.SequenceWeight method) (miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.StateAttentionGate method) (miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module.TriangleMultiplication method) (miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.BinderNetwork method) (miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.DistanceNetwork method) (miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.ExpResolvedNetwork method) (miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.LDDTNetwork method) (miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.MaskedTokenNetwork method) (miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor.PAENetwork method) (miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.Extra_emb method) (miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.InteractionEmb method) (miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.MSA_emb method) (miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.PositionalEncoding2D method) (miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.Recycling method) (miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.Species_emb method) (miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.Templ_emb method) (miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.TemplatePairStack method) (miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings.TemplateTorsionStack method) (miniworld.models_MiniWorld_v1_5_use_interaction.MiniWorld.MiniWorldModule method) (miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.IPA method) (miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.IterativeSimulator method) (miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.IterBlock method) (miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.MSA2Pair method) (miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.MSAPairStr2MSA method) (miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.PairStr2Pair method) (miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.SCPred method) (miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.SeqSep method) (miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.Str2Chain_IPA method) (miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.Str2Residue_IPA method) (miniworld.models_MiniWorld_v1_5_use_interaction.Track_module.UpdatePairByValue method) (miniworld.models_MiniWorld_v1_5_use_interaction.value_network.MPNN_block method) (miniworld.models_MiniWorld_v1_5_use_interaction.value_network.PositionWiseFeedForward method) (miniworld.models_MiniWorld_v1_5_use_interaction.value_network.StrSeqValueNet method) (miniworld.utils.DataClass.MiniWorldBatchedDataClass method) (miniworld.utils.DataClass.MiniWorldDataClass method) (miniworld.utils.DataClass.MiniWorldLabelClass method) (miniworld.utils.DataClass.MiniWorldMSAClass method) (miniworld.utils.DataClass.MiniWorldTemplateClass method) (miniworld.utils.DataClass.MiniWorldWrongDataClass method) (miniworld.utils.ffindex.FFindexEntry method) (miniworld.utils.ProteinClass.Protein method) (miniworld.utils.ProteinClass.ProteinMSA method) (miniworld.utils.ProteinClass.ProteinSequence method) (miniworld.utils.ProteinClass.ProteinStructure method) (miniworld.utils.ProteinClass.ProteinTemplate method) (miniworld.utils.ProteinClass.ProteinTemplates method) (miniworld.utils.util_module.ComputeAllAtomCoords method) (miniworld.utils.util_module.Dropout method) (miniworld.utils.util_module.XYZConverter method) (promptbind.data.data.FABindDataSet 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) (promptbind.test_promptbind.PromptBindInference method) (promptbind.utils.fabind_inference_dataset.InferenceDataset method) (promptbind.utils.logging_utils.Logger method)

A

a3m_parse() (in module miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction) a3m_pickling() (in module miniworld.utils.data_refactoring) aatype_to_str_sequence() (in module deepfold.common.residue_constants) accelerator (promptbind.test_promptbind.PromptBindInference attribute) accept_residue() (bis_protein_structure.DATAGEN.AllResiduesSelector method) add() (in module deepfold.utils.tensor_utils) add_assembly_features() (in module deepfold.data.multimer.input_features) add_pdb_headers() (in module deepfold.common.protein) add_weight_decay() (in module miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction) AF_Results_filtering() (in module miniworld.utils.data_refactoring) AF_Results_json_filtering() (in module miniworld.utils.data_refactoring) AF_Results_json_viewer() (in module miniworld.utils.data_refactoring) affinity_metrics() (in module promptbind.utils.metrics) align_two_protein() (in module miniworld.utils.output_visualize) 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) AngleResnet (class in deepfold.modules.angle_resnet) AngleResnetBlock (class in deepfold.modules.angle_resnet) angles_to_sincos() (in module bis_protein_structure.TORSION2) args (promptbind.test_promptbind.PromptBindInference 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) AsyncGradientClipping (class in deepfold.train.gradient_clipping) Atom (class in deepfold.eval.contact) (class in gd_dl.lib_pdb_mol2) atom_feature() (in module bapred.data.atom_feature) (in module bindingrmsd.data.ligand_atom_feature) atom_to_pdb_line() (in module miniworld.utils.output_visualize) AtomMap (class in deepfold.data.monomer) AtomSite (class in deepfold.data.pdbx_parsing) Attention (class in miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module) (class in promptbind.models.model_utils) AttentionWithBias (class in miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module) AuxiliaryHeads (class in deepfold.modules.auxiliary_heads) AuxiliaryHeadsConfig (class in deepfold.config) avgQ() (in module miniworld.utils.kinematics)

B

backbone_loss() (in module deepfold.losses.geometry) BackboneUpdate (class in deepfold.modules.backbone_update) bapred module bapred.cli module bapred.data module bapred.data.atom_feature module bapred.data.data module bapred.data.utils module bapred.inference module bapred.logger module bapred.model module bapred.model.GatedGCNLSPE module bapred.model.GraphGPS module bapred.model.MHA module bapred.model.model module BAPredDataset (class in bapred.data.data) 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) BiasedAxialAttention (class in miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module) bin_edges_np() (in module deepfold.eval.distogram) binarize() (in module promptbind.utils.feature_utils) (in module promptbind.utils.generation_utils) (in module promptbind.utils.inference_mol_utils) BinderNetwork (class in miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor) bindingrmsd module bindingrmsd.data module bindingrmsd.data.data module bindingrmsd.data.data_bck module

bindingrmsd.data.ligand_atom_feature module bindingrmsd.data.protein_atom_feature module bindingrmsd.data.utils module bindingrmsd.inference module bindingrmsd.model module bindingrmsd.model.GatedGCNLSPE module bindingrmsd.model.model module bis_protein_structure module bis_protein_structure.CROSSLINK module bis_protein_structure.DATAGEN module bis_protein_structure.DISULFIDE module bis_protein_structure.MMEVAL module bis_protein_structure.residue_constants module bis_protein_structure.SOLVENTACC module bis_protein_structure.split_pdb module bis_protein_structure.TORSION2 module block_diag() (in module deepfold.data.multimer.msa_pairing) Bond (class in bis_protein_structure.residue_constants) (class in deepfold.common.residue_constants) bond_feature() (in module bapred.data.atom_feature) (in module bindingrmsd.data.ligand_atom_feature) 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_query_to_hit_index_mapping() (in module deepfold.data.search.templates)

C

c6d_to_bins() (in module miniworld.utils.kinematics) c6d_to_bins2() (in module miniworld.utils.kinematics) cal_integrated_frame() (in module miniworld.utils.util) 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_pair_distance() (in module bapred.data.utils) (in module bindingrmsd.data.ligand_atom_feature) calculate_sa_map() (in module bis_protein_structure.CROSSLINK) calculate_tryptic_map() (in module bis_protein_structure.CROSSLINK) cat_neighbors_nodes() (in module miniworld.models_MiniWorld_v1_5_use_interaction.value_network) CellLists (class in deepfold.eval.cell_lists) center_and_realign_missing() (in module miniworld.feature.MiniWorld_featuring_species) (in module miniworld.utils.parser_util) (in module miniworld.utils.util) centering_RT() (in module miniworld.utils.util) CenterOfMassConfig (class in deepfold.config) Cgc_block (class in gd_dl.models) (class in gd_dl.rerank_model) chain_break_cropping() (in module miniworld.feature.MiniWorld_featuring_species) chain_centre_mass_loss() (in module deepfold.losses.auxillary) check_hhr_loaded() (in module miniworld.utils.data_refactoring) chi_angle_atom() (in module bis_protein_structure.residue_constants) (in module deepfold.common.residue_constants) chunk_layer() (in module deepfold.utils.chunk_utils) clean_protein() (in module deepfold.relax.amber_minimize) clean_structure() (in module deepfold.relax.cleanup) cls_metric() (in module promptbind.utils.metrics) cluster_sum() (in module miniworld.feature.MiniWorld_featuring_species) col_to_row() (in module deepfold.distributed.model_parallel) collate() (in module deepfold.utils.tensor_utils) com_coord_criterion (promptbind.test_promptbind.PromptBindInference attribute) ComplexGraph (class in promptbind.models.att_model) ComplexInfo (class in deepfold.data.multimer.input_features) 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) ComputeAllAtomCoords (class in miniworld.utils.util_module) config_path (promptbind.test_promptbind.PromptBindInference attribute) construct_data_from_graph_gvp_mean() (in module promptbind.utils.utils) 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() (in module promptbind.models.egnn) copy_to_model_parallel_reigon() (in module deepfold.distributed.model_parallel) cosine_beta_schedule() (in module diffalign.models.epsnet.diffusion) count_parameters() (in module miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction) 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_custom_forward() (in module miniworld.utils.util_module) 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) criterion (promptbind.test_promptbind.PromptBindInference attribute) 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) cross() (in module deepfold.utils.geometry.vector) cross_product_matrix() (in module miniworld.utils.parser_util) (in module miniworld.utils.util) CrossAttention (class in diffalign.models.encoder.cross_attention) CrossAttentionModule (class in promptbind.models.cross_att) CrossAttentionNoGate (class in deepfold.modules.attention) CrossGraphAligner (class in diffalign.models.encoder.cross_attention) cutoff_chain_num() (in module miniworld.feature.MiniWorld_featuring_species)

D

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

deepfold.modules.structure_module module deepfold.modules.template_angle_embedder module deepfold.modules.template_pair_block module deepfold.modules.template_pair_embedder module deepfold.modules.template_pair_stack module deepfold.modules.template_pointwise_attention module deepfold.modules.template_projection module deepfold.modules.triangular_attention module deepfold.modules.triangular_multiplicative_update module deepfold.modules.tweaks module deepfold.modules.tweaks.evo_attn module deepfold.ops module deepfold.ops.evoformer_attention module deepfold.package_info module deepfold.relax module deepfold.relax.amber_minimize module deepfold.relax.cleanup module deepfold.relax.relax module deepfold.relax.utils module deepfold.runner module deepfold.runner.config_utils module deepfold.runner.parser module deepfold.runner.utils module deepfold.testing module deepfold.testing.common module deepfold.testing.utils module deepfold.train module deepfold.train.gradient_clipping module deepfold.train.lr_scheduler module deepfold.train.validation_metrics module deepfold.utils module deepfold.utils.checkpoint_utils module deepfold.utils.chunk_utils module deepfold.utils.crop_utils module deepfold.utils.datetime_utils module deepfold.utils.dist_utils module deepfold.utils.feats_utils module deepfold.utils.file_utils module deepfold.utils.geometry module deepfold.utils.geometry.quat_rigid module deepfold.utils.geometry.rigid_matrix_vector module deepfold.utils.geometry.rotation_matrix module deepfold.utils.geometry.utils module deepfold.utils.geometry.vector module deepfold.utils.hash_utils module deepfold.utils.import_utils module deepfold.utils.iter_utils module deepfold.utils.log_utils module deepfold.utils.precision module deepfold.utils.random module deepfold.utils.rigid_utils module deepfold.utils.script_utils module deepfold.utils.swa_utils module deepfold.utils.tensor_utils module deepspeed_evo_attn() (in module deepfold.ops.evoformer_attention) device (promptbind.test_promptbind.PromptBindInference attribute) dict_map() (in module deepfold.utils.tensor_utils) dict_multimap() (in module deepfold.utils.tensor_utils) diffalign module DiffAlign (class in diffalign.models.epsnet.diffusion) diffalign.models module diffalign.models.common module diffalign.models.encoder module diffalign.models.encoder.cross_attention module diffalign.models.encoder.edge module diffalign.models.encoder.egnn module diffalign.models.epsnet module diffalign.models.epsnet.diffusion module diffalign.utils module diffalign.utils.chem module dihedral_angle() (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) display_top() (in module miniworld.feature.MiniWorld_featuring_species) dist_to_bins() (in module miniworld.utils.kinematics) dist_to_onehot() (in module miniworld.utils.kinematics) distance_loss_function() (in module promptbind.utils.generation_utils) distance_optimize_compound_coords() (in module promptbind.utils.generation_utils) DistanceNetwork (class in miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor) distogram_loss() (in module deepfold.losses.geometry) DistogramHead (class in deepfold.modules.auxiliary_heads) DistogramHeadConfig (class in deepfold.config) DistogramLossConfig (class in deepfold.config) divide() (in module deepfold.distributed.utils) donorHs() (in module miniworld.utils.parser_util) (in module miniworld.utils.util) dot() (in module deepfold.utils.geometry.vector) draw_attn() (in module miniworld.utils.util) draw_attn_multirow() (in module miniworld.utils.util) draw_mol_svg() (in module diffalign.utils.chem) draw_pae() (in module miniworld.utils.util) drmsd() (in module deepfold.train.validation_metrics) Dropout (class in deepfold.modules.dropout) (class in miniworld.utils.util_module) DropoutColumnwise (class in deepfold.modules.dropout) DropoutRowwise (class in deepfold.modules.dropout) dump_pickle() (in module deepfold.utils.file_utils)

E

E_GCL (class in diffalign.models.encoder.egnn) EfficientMCAttModel (class in promptbind.models.att_model) EGNN (class in diffalign.models.encoder.egnn) EMA (class in miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction) 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) ensure_divisibility() (in module deepfold.distributed.utils) euclidean_distance() (in module deepfold.utils.geometry.vector) eval_interface() (in module bis_protein_structure.MMEVAL) evaluate_mean_pocket_cls_coord_multi_task() (in module promptbind.utils.utils) evaluate_mean_pocket_cls_coord_pocket_pred() (in module promptbind.utils.utils) 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) experimentally_resolved_loss() (in module deepfold.losses.auxillary) ExperimentallyResolvedHead (class in deepfold.modules.auxiliary_heads) ExperimentallyResolvedHeadConfig (class in deepfold.config)

ExperimentallyResolvedLossConfig (class in deepfold.config) ExpResolvedNetwork (class in miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor) extend_graph_order_radius() (in module diffalign.models.common) extend_to_cross_attention() (in module diffalign.models.common) Extra_emb (class in miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings) 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_tip_atom_xyz() (in module miniworld.utils.util) 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) FAPELossConfig (class in deepfold.config) FeaturePipelineConfig (class in deepfold.config) FeedForwardLayer (class in miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module) fetch_ligand() (in module deepfold.data.monomer) fetch_mmcif() (in module deepfold.data.pdbx_parsing) FFindexEntry (class in miniworld.utils.ffindex) final_init_() (in module deepfold.modules.linear) find_chain_combinations() (in module miniworld.feature.MiniWorld_featuring_species) 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) finish_db() (in module miniworld.utils.ffindex) fix_pdb() (in module deepfold.relax.cleanup) 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) from_pdb_string() (in module deepfold.common.protein) from_prediction() (in module deepfold.common.protein) from_relaxation() (in module deepfold.common.protein)

G

GatedGCNLSPELayer (class in bapred.model.GatedGCNLSPE) (class in bindingrmsd.model.GatedGCNLSPE) gather() (in module deepfold.distributed.model_parallel) gather_edges() (in module miniworld.models_MiniWorld_v1_5_use_interaction.value_network) gather_from_model_parallel_region() (in module deepfold.distributed.model_parallel) gather_nodes() (in module miniworld.models_MiniWorld_v1_5_use_interaction.value_network) gating_init_() (in module deepfold.modules.linear) GaussianSmearing (class in promptbind.models.model_utils) gd_dl module gd_dl.data module gd_dl.data.all_ML_rerank module gd_dl.data.ML_inference module gd_dl.data.ML_rerank module gd_dl.data.single_ML_rerank module gd_dl.lib_pdb_mol2 module gd_dl.models module gd_dl.path_setting module gd_dl.rerank_model module gd_dl.utils module 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_combinations() (in module miniworld.feature.MiniWorld_featuring_species) 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_initial_xyz() (in module miniworld.utils.util) generate_random_xyz() (in module miniworld.utils.util) 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) generate_symmetric_operation() (in module miniworld.utils.util) generate_symmetric_xyz() (in module miniworld.utils.util) get_2D_mol() (in module diffalign.utils.chem) get_all_graph() (in module bindingrmsd.data.protein_atom_feature) get_ang() (in module miniworld.utils.kinematics) get_args() (in module miniworld.utils.arguments_MiniWorld) (in module miniworld.utils.template_parser) get_assemblies() (in module deepfold.data.pdbx_parsing) get_asym_mask() (in module deepfold.losses.auxillary) get_atom_feature() (in module bapred.data.atom_feature) (in module bindingrmsd.data.ligand_atom_feature) 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_basename() (in module deepfold.utils.script_utils) get_best_rmsd() (in module diffalign.utils.chem) get_bond_feature() (in module bapred.data.atom_feature) (in module bindingrmsd.data.ligand_atom_feature) get_bondangle() (in module bis_protein_structure.TORSION2) get_canonical_smiles() (in module promptbind.utils.feature_utils) get_Cb() (in module miniworld.utils.parser_util) (in module miniworld.utils.util) get_chain_features() (in module deepfold.data.pdbx_parsing) get_clean_res_list() (in module promptbind.utils.feature_utils) (in module promptbind.utils.inference_pdb_utils) get_clones() (in module miniworld.utils.util_module) get_complex_crop() (in module miniworld.feature.MiniWorld_featuring_species) 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_crop() (in module miniworld.feature.MiniWorld_featuring_species) get_csv() (in module miniworld.utils.data_refactoring) get_data() (in module promptbind.data.data) get_dih() (in module miniworld.utils.kinematics) get_distance() (in module diffalign.models.epsnet.diffusion) get_distance_feature() (in module bapred.data.atom_feature) (in module bindingrmsd.data.ligand_atom_feature) get_edges() (in module promptbind.models.egnn) get_edges_batch() (in module promptbind.models.egnn) get_entry_by_name() (in module miniworld.utils.ffindex) 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_hash_dict() (in module miniworld.utils.data_refactoring) get_ICS() (in module bis_protein_structure.MMEVAL) get_ID_to_source_dict() (in module miniworld.utils.data_refactoring) get_identifiers() (in module deepfold.data.search.msa_identifiers) get_indices() (in module bapred.data.atom_feature) (in module bindingrmsd.data.ligand_atom_feature) get_indices_sparse() (in module bapred.data.atom_feature) (in module bindingrmsd.data.ligand_atom_feature) get_info_pred_distance() (in module promptbind.utils.generation_utils) get_interact_feature() (in module bapred.data.atom_feature) (in module bindingrmsd.data.ligand_atom_feature) 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_model() (in module promptbind.models.model) get_mol_coordinate() (in module bapred.data.atom_feature) (in module bindingrmsd.data.ligand_atom_feature) get_mol_info() (in module promptbind.data.inference_preprocess_mol_confs) get_optimal_transform() (in module deepfold.losses.geometry) get_pad_size() (in module deepfold.utils.dist_utils) get_pair_dist() (in module miniworld.utils.kinematics) 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_query_from_a3m() (in module miniworld.utils.data_refactoring) 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_same_crop_idx() (in module miniworld.feature.MiniWorld_featuring_species) get_seed_from_string() (in module deepfold.utils.random) get_seed_randomly() (in module deepfold.utils.random) get_seqsep() (in module miniworld.utils.util_module) get_smarts_feature() (in module bapred.data.atom_feature) (in module bindingrmsd.data.ligand_atom_feature) get_spatial_crop() (in module miniworld.feature.MiniWorld_featuring_species) get_SS_ver5() (in module bis_protein_structure.DISULFIDE) get_STRING_crop() (in module miniworld.feature.MiniWorld_featuring_species) get_timestamp_string() (in module deepfold.utils.datetime_utils) get_topk() (in module miniworld.utils.util_module) get_torsion() (in module bis_protein_structure.TORSION2) get_torsions() (in module promptbind.utils.utils) get_train_valid_data_dir_dictionary() (in module miniworld.utils.util) get_violation_metrics() (in module deepfold.relax.amber_minimize) getDistogram() (in module bis_protein_structure.TORSION2) getsize() (in module miniworld.feature.MiniWorld_featuring_species) 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) GraphGPS (class in bapred.model.GraphGPS) GraphTriangleAttention (class in miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module) group() (in module deepfold.distributed.model_parallel) group_rank() (in module deepfold.distributed.model_parallel) gumbel_softmax_no_random() (in module promptbind.utils.utils) gzip_files() (in module miniworld.utils.data_refactoring)

H

hash_string_into_number() (in module deepfold.utils.hash_utils) he_normal_init_() (in module deepfold.modules.linear) HHBlits (class in deepfold.data.tools.hhblits) hhpred_parser() (in module miniworld.utils.hhpred_parser) hhr_dir_rerefactoring() (in module miniworld.utils.data_refactoring)

hhr_file_rerefactoring() (in module miniworld.utils.data_refactoring) hhr_refactoring() (in module miniworld.utils.data_refactoring) HHSearch (class in deepfold.data.tools.hhsearch) HitMetadata (class in deepfold.data.search.parsers) Hmmbuild (class in deepfold.data.tools.hmmbuild) Hmmsearch (class in deepfold.data.tools.hmmsearch)

I

IaBNet_mean_and_pocket_prediction_cls_coords_dependent (class in promptbind.models.model) ideal_atom_mask() (in module deepfold.common.protein) 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) inference() (in module bapred.inference) (in module bindingrmsd.inference) InferenceDataset (class in promptbind.utils.fabind_inference_dataset) init_lecun_normal() (in module miniworld.utils.util_module) init_lecun_normal_param() (in module miniworld.utils.util_module) initialize() (in module deepfold.distributed.model_parallel) InputEmbedder (class in deepfold.modules.input_embedder) InputEmbedderConfig (class in deepfold.config) InputEmbedderMultimer (class in deepfold.modules.input_embedder) int_id_to_str_id() (in module deepfold.data.multimer.input_features) InteractionEmb (class in miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings) InteractionModule (class in promptbind.models.model_utils)

InvariantPointAttention (class in deepfold.modules.invariant_point_attention) InvariantPointAttentionMultimer (class in deepfold.modules.invariant_point_attention) invert_quat() (in module deepfold.utils.rigid_utils) invert_rot_mat() (in module deepfold.utils.rigid_utils) IO (class in deepfold.data.pdbio) IPA (class in miniworld.models_MiniWorld_v1_5_use_interaction.Track_module) ipa_point_weights_init_() (in module deepfold.modules.invariant_point_attention) 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_initialized() (in module deepfold.distributed.model_parallel) is_one() (in module bapred.data.utils) (in module bindingrmsd.data.ligand_atom_feature) (in module bindingrmsd.data.utils) IterativeSimulator (class in miniworld.models_MiniWorld_v1_5_use_interaction.Track_module) IterBlock (class in miniworld.models_MiniWorld_v1_5_use_interaction.Track_module)

J

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

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) kalign_mapping() (in module miniworld.utils.kalign_mapping)

L

LayerNorm (class in deepfold.modules.layer_norm) lddt() (in module deepfold.losses.confidence) lddt_ca() (in module deepfold.losses.confidence) LDDTNetwork (class in miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor) lecun_normal_init_() (in module deepfold.modules.linear) Lexer (class in deepfold.runner.parser) Ligand (class in deepfold.data.monomer) Linear (class in deepfold.modules.linear) linear_beta_schedule() (in module diffalign.models.epsnet.diffusion) list_zip() (in module deepfold.utils.iter_utils) load() (in module deepfold.runner.config_utils) load_files() (in module gd_dl.data.ML_inference) load_ligands() (in module bapred.data.data) (in module bindingrmsd.data.data) (in module bindingrmsd.data.data_bck)

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_obj() (in module bapred.data.utils) (in module bindingrmsd.data.ligand_atom_feature) (in module bindingrmsd.data.utils) 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) Logger (class in promptbind.utils.logging_utils) logger (promptbind.test_promptbind.PromptBindInference attribute) loop_to_dict() (in module deepfold.data.pdbx_parsing) loop_to_list() (in module deepfold.data.pdbx_parsing) LossConfig (class in deepfold.config)

M

main() (in module bapred.cli) (in module bindingrmsd.inference) (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) 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_frame() (in module miniworld.utils.parser_util) (in module miniworld.utils.util) make_output_directory() (in module deepfold.utils.script_utils) make_rot_axis() (in module miniworld.utils.util_module) make_rotX() (in module miniworld.utils.util_module) make_rotZ() (in module miniworld.utils.util_module) 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) masked_mean() (in module deepfold.utils.tensor_utils) masked_msa_loss() (in module deepfold.losses.masked_msa) MaskedMSAHead (class in deepfold.modules.auxiliary_heads) MaskedMSAHeadConfig (class in deepfold.config) MaskedMSALossConfig (class in deepfold.config) MaskedTokenNetwork (class in miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor) 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) metrics_runtime_no_prefix() (in module promptbind.utils.metrics_to_tsb) miniworld module miniworld.feature module miniworld.feature.MiniWorld_featuring_species module miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction module miniworld.models_MiniWorld_v1_5_use_interaction module miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module module miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor module miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings module miniworld.models_MiniWorld_v1_5_use_interaction.MiniWorld module miniworld.models_MiniWorld_v1_5_use_interaction.Track_module module miniworld.models_MiniWorld_v1_5_use_interaction.value_network module miniworld.utils module miniworld.utils.arguments_MiniWorld module miniworld.utils.chemical module miniworld.utils.data_refactoring module miniworld.utils.DataClass module miniworld.utils.ffindex module miniworld.utils.hhpred_parser module miniworld.utils.kalign_mapping module miniworld.utils.kinematics module miniworld.utils.My_mistake module miniworld.utils.output_visualize module miniworld.utils.parser_util module miniworld.utils.ProteinClass module miniworld.utils.template_parser module miniworld.utils.util module miniworld.utils.util_module module MiniWorldBatchedDataClass (class in miniworld.utils.DataClass) MiniWorldDataClass (class in miniworld.utils.DataClass) MiniWorldLabelClass (class in miniworld.utils.DataClass) MiniWorldModule (class in miniworld.models_MiniWorld_v1_5_use_interaction.MiniWorld) MiniWorldMSAClass (class in miniworld.utils.DataClass) MiniWorldTemplateClass (class in miniworld.utils.DataClass) MiniWorldWrongDataClass (class in miniworld.utils.DataClass) MLPEdgeEncoder (class in diffalign.models.encoder.edge) mmcif_full_sequence() (in module miniworld.utils.data_refactoring) mmcif_Full_sequence_parsing() (in module miniworld.utils.data_refactoring) mmcif_line_parser() (in module miniworld.utils.data_refactoring) mmcif_loop_parser() (in module miniworld.utils.data_refactoring) mmcif_parsing() (in module miniworld.utils.data_refactoring) mmcif_pickling() (in module miniworld.utils.data_refactoring) mmcif_to_pdbs() (in module bis_protein_structure.DATAGEN) Model (class in gd_dl.lib_pdb_mol2) model (promptbind.test_promptbind.PromptBindInference attribute) ModelVisulizer (class in miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction) ModResidue (class in deepfold.data.pdbx_parsing) module bapred bapred.cli bapred.data bapred.data.atom_feature bapred.data.data bapred.data.utils bapred.inference bapred.logger bapred.model bapred.model.GatedGCNLSPE bapred.model.GraphGPS bapred.model.MHA bapred.model.model bindingrmsd bindingrmsd.data bindingrmsd.data.data bindingrmsd.data.data_bck bindingrmsd.data.ligand_atom_feature bindingrmsd.data.protein_atom_feature bindingrmsd.data.utils bindingrmsd.inference bindingrmsd.model bindingrmsd.model.GatedGCNLSPE bindingrmsd.model.model bis_protein_structure bis_protein_structure.CROSSLINK bis_protein_structure.DATAGEN bis_protein_structure.DISULFIDE bis_protein_structure.MMEVAL bis_protein_structure.residue_constants bis_protein_structure.SOLVENTACC bis_protein_structure.split_pdb bis_protein_structure.TORSION2 deepfold deepfold.common deepfold.common.protein deepfold.common.residue_constants deepfold.config deepfold.data deepfold.data.errors deepfold.data.modules deepfold.data.modules.dataloaders deepfold.data.modules.mmcif_dataset deepfold.data.modules.samplers deepfold.data.modules.single_dataset deepfold.data.monomer deepfold.data.multimer deepfold.data.multimer.input_features deepfold.data.multimer.msa_pairing deepfold.data.pdbio deepfold.data.pdbx_parsing deepfold.data.search deepfold.data.search.crfalign deepfold.data.search.input_features deepfold.data.search.mmcif deepfold.data.search.msa_identifiers deepfold.data.search.parsers deepfold.data.search.templates deepfold.data.tools deepfold.data.tools.hhblits deepfold.data.tools.hhsearch deepfold.data.tools.hmmbuild deepfold.data.tools.hmmsearch deepfold.data.tools.jackhmmer deepfold.data.tools.kalign deepfold.data.tools.utils deepfold.distributed deepfold.distributed.model_parallel deepfold.distributed.utils deepfold.eval deepfold.eval.cell_lists deepfold.eval.contact deepfold.eval.distogram deepfold.eval.msa deepfold.eval.plot deepfold.eval.pseudo_3d deepfold.loss deepfold.losses deepfold.losses.auxillary deepfold.losses.confidence deepfold.losses.geometry deepfold.losses.masked_msa deepfold.losses.procrustes deepfold.losses.utils deepfold.losses.violation deepfold.modules deepfold.modules.alphafold deepfold.modules.angle_resnet deepfold.modules.attention deepfold.modules.auxiliary_heads deepfold.modules.backbone_update deepfold.modules.dropout deepfold.modules.evoformer_block deepfold.modules.evoformer_block_pair_core deepfold.modules.evoformer_stack deepfold.modules.extra_msa_block deepfold.modules.extra_msa_embedder deepfold.modules.extra_msa_stack deepfold.modules.global_attention deepfold.modules.inductor deepfold.modules.input_embedder deepfold.modules.invariant_point_attention deepfold.modules.layer_norm deepfold.modules.linear deepfold.modules.msa_column_attention deepfold.modules.msa_column_global_attention deepfold.modules.msa_row_attention_with_pair_bias deepfold.modules.msa_transition deepfold.modules.outer_product_mean deepfold.modules.pair_transition deepfold.modules.recycling_embedder deepfold.modules.single_transition deepfold.modules.structure_module deepfold.modules.template_angle_embedder deepfold.modules.template_pair_block deepfold.modules.template_pair_embedder deepfold.modules.template_pair_stack deepfold.modules.template_pointwise_attention deepfold.modules.template_projection deepfold.modules.triangular_attention deepfold.modules.triangular_multiplicative_update deepfold.modules.tweaks deepfold.modules.tweaks.evo_attn deepfold.ops deepfold.ops.evoformer_attention deepfold.package_info deepfold.relax deepfold.relax.amber_minimize deepfold.relax.cleanup deepfold.relax.relax deepfold.relax.utils deepfold.runner deepfold.runner.config_utils deepfold.runner.parser deepfold.runner.utils deepfold.testing deepfold.testing.common deepfold.testing.utils deepfold.train deepfold.train.gradient_clipping deepfold.train.lr_scheduler deepfold.train.validation_metrics deepfold.utils deepfold.utils.checkpoint_utils deepfold.utils.chunk_utils deepfold.utils.crop_utils deepfold.utils.datetime_utils deepfold.utils.dist_utils deepfold.utils.feats_utils deepfold.utils.file_utils deepfold.utils.geometry deepfold.utils.geometry.quat_rigid deepfold.utils.geometry.rigid_matrix_vector deepfold.utils.geometry.rotation_matrix deepfold.utils.geometry.utils deepfold.utils.geometry.vector deepfold.utils.hash_utils deepfold.utils.import_utils deepfold.utils.iter_utils deepfold.utils.log_utils deepfold.utils.precision deepfold.utils.random deepfold.utils.rigid_utils deepfold.utils.script_utils deepfold.utils.swa_utils deepfold.utils.tensor_utils diffalign diffalign.models diffalign.models.common diffalign.models.encoder diffalign.models.encoder.cross_attention diffalign.models.encoder.edge diffalign.models.encoder.egnn diffalign.models.epsnet diffalign.models.epsnet.diffusion diffalign.utils diffalign.utils.chem gd_dl gd_dl.data gd_dl.data.all_ML_rerank gd_dl.data.ML_inference gd_dl.data.ML_rerank gd_dl.data.single_ML_rerank gd_dl.lib_pdb_mol2 gd_dl.models gd_dl.path_setting gd_dl.rerank_model gd_dl.utils miniworld miniworld.feature miniworld.feature.MiniWorld_featuring_species miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction miniworld.models_MiniWorld_v1_5_use_interaction miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings miniworld.models_MiniWorld_v1_5_use_interaction.MiniWorld miniworld.models_MiniWorld_v1_5_use_interaction.Track_module miniworld.models_MiniWorld_v1_5_use_interaction.value_network miniworld.utils miniworld.utils.arguments_MiniWorld miniworld.utils.chemical miniworld.utils.data_refactoring miniworld.utils.DataClass miniworld.utils.ffindex miniworld.utils.hhpred_parser miniworld.utils.kalign_mapping miniworld.utils.kinematics miniworld.utils.My_mistake miniworld.utils.output_visualize miniworld.utils.parser_util miniworld.utils.ProteinClass miniworld.utils.template_parser miniworld.utils.util miniworld.utils.util_module promptbind promptbind.data promptbind.data.data promptbind.data.inference_preprocess_mol_confs promptbind.data.inference_preprocess_protein promptbind.models promptbind.models.att_model promptbind.models.cross_att promptbind.models.egnn promptbind.models.model promptbind.models.model_utils promptbind.test_promptbind promptbind.train_promptbind promptbind.utils promptbind.utils.fabind_inference_dataset promptbind.utils.feature_utils promptbind.utils.generation_utils promptbind.utils.inference_mol_utils promptbind.utils.inference_pdb_utils promptbind.utils.logging_utils promptbind.utils.metrics promptbind.utils.metrics_to_tsb promptbind.utils.post_optim_utils promptbind.utils.utils promptbind.visualize_prompt_components

MOL2 (class in gd_dl.lib_pdb_mol2) MOL2_UNIT (class in gd_dl.lib_pdb_mol2) mol_to_graph() (in module bindingrmsd.data.ligand_atom_feature) 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) Monomer (class in deepfold.data.pdbx_parsing) MPNN_block (class in miniworld.models_MiniWorld_v1_5_use_interaction.value_network) MSA2Pair (class in miniworld.models_MiniWorld_v1_5_use_interaction.Track_module) MSA_block_deletion() (in module miniworld.feature.MiniWorld_featuring_species) MSA_change_idx() (in module miniworld.utils.My_mistake) MSA_change_idx_v2() (in module miniworld.utils.My_mistake) MSA_emb (class in miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings) MSA_featurize_wo_statistics() (in module miniworld.feature.MiniWorld_featuring_species) MSA_featurize_wo_statistics_by_chain() (in module miniworld.feature.MiniWorld_featuring_species) MSAColAttention (class in miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module) MSAColGlobalAttention (class in miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module) MSAColumnAttention (class in deepfold.modules.msa_column_attention) MSAColumnGlobalAttention (class in deepfold.modules.msa_column_global_attention) MSAPairStr2MSA (class in miniworld.models_MiniWorld_v1_5_use_interaction.Track_module) MSARowAttentionWithBias (class in miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module) MSARowAttentionWithPairBias (class in deepfold.modules.msa_row_attention_with_pair_bias) MSATransition (class in deepfold.modules.msa_transition) MultiHeadAttention (class in bapred.model.MHA) MultiLayerPerceptron (class in diffalign.models.common) MultiProcessTestCase (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) new_dihedral() (in module bis_protein_structure.TORSION2)

norm() (in module deepfold.utils.geometry.vector) normal_init_() (in module deepfold.modules.linear) normalized() (in module deepfold.utils.geometry.vector) normQ() (in module miniworld.utils.kinematics) numpy_seed() (in module deepfold.utils.random)

O

one_hot() (in module bapred.data.utils) (in module bindingrmsd.data.ligand_atom_feature) (in module bindingrmsd.data.utils) (in module deepfold.utils.tensor_utils) Op (class in deepfold.data.pdbx_parsing)

OpenFoldBenchmarkLRScheduler (class in deepfold.train.lr_scheduler) OuterProductMean (class in deepfold.modules.outer_product_mean) output_to_pdb() (in module miniworld.utils.output_visualize) overwrite_b_factors() (in module deepfold.relax.utils) overwrite_pdb_coordinates() (in module deepfold.relax.utils)

P

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) PAENetwork (class in miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor) pair_and_merge() (in module deepfold.data.multimer.input_features) pair_sequences() (in module deepfold.data.multimer.msa_pairing) PairStr2Pair (class in miniworld.models_MiniWorld_v1_5_use_interaction.Track_module) PairTransition (class in deepfold.modules.pair_transition) parallel_processing() (in module bis_protein_structure.DATAGEN) Param (class in deepfold.utils.import_utils) ParamType (class in deepfold.utils.import_utils) parse_a3m() (in module deepfold.data.search.parsers) (in module miniworld.utils.template_parser) 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_pdb() (in module miniworld.utils.template_parser) parse_pdb_lines() (in module miniworld.utils.template_parser) parse_pdb_lines_w_seq() (in module miniworld.utils.template_parser) parse_pdb_w_seq() (in module miniworld.utils.template_parser) parse_pir() (in module deepfold.data.search.crfalign) parse_segment() (in module miniworld.utils.hhpred_parser) parse_stockholm() (in module deepfold.data.search.parsers) parse_templates_raw() (in module miniworld.utils.template_parser) 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_parsing() (in module miniworld.utils.ProteinClass) PDB_parsing_from_pt() (in module miniworld.utils.data_refactoring) pdb_pickling() (in module miniworld.utils.data_refactoring) pdb_Sampling() (in module miniworld.utils.data_refactoring) PDBIO (class in deepfold.data.pdbio) PDBline (class in gd_dl.lib_pdb_mol2) PDBxHeader (class in deepfold.data.pdbx_parsing) PDBxObject (class in deepfold.data.pdbx_parsing) PDBxParser (class in deepfold.data.pdbx_parsing) permute_final_dims() (in module deepfold.utils.tensor_utils) (in module promptbind.models.model_utils) permute_label() (in module miniworld.feature.MiniWorld_featuring_species) PerResidueLDDTCaPredictor (class in deepfold.modules.auxiliary_heads) PerResidueLDDTCaPredictorConfig (class in deepfold.config) pl_to_c_graph() (in module bindingrmsd.data.protein_atom_feature) plddt_loss() (in module deepfold.losses.confidence) 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_cls_criterion (promptbind.test_promptbind.PromptBindInference attribute) pocket_coord_criterion (promptbind.test_promptbind.PromptBindInference attribute) pocket_direct_metrics() (in module promptbind.utils.metrics) pocket_metrics() (in module promptbind.utils.metrics) PointProjection (class in deepfold.modules.invariant_point_attention) PoseSelectionDataset (class in bindingrmsd.data.data) (class in bindingrmsd.data.data_bck) PositionalEncoding2D (class in miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings) PositionWiseFeedForward (class in miniworld.models_MiniWorld_v1_5_use_interaction.value_network) 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) PredictionPKD (class in bapred.model.model) PredictionRMSD (class in bindingrmsd.model.model) print_amap() (in module deepfold.data.pdbx_parsing)

print_chain_features() (in module deepfold.data.pdbx_parsing) print_hhr_pt() (in module miniworld.utils.data_refactoring) print_metrics() (in module promptbind.utils.metrics) process_dlg() (in module bindingrmsd.data.data_bck) process_final() (in module deepfold.data.multimer.input_features) process_ligand_file() (in module bapred.data.data) (in module bindingrmsd.data.data) (in module bindingrmsd.data.data_bck) 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) Procrustes (class in deepfold.losses.procrustes) procrustes() (in module deepfold.losses.procrustes) promptbind module promptbind.data module promptbind.data.data module promptbind.data.inference_preprocess_mol_confs module promptbind.data.inference_preprocess_protein module promptbind.models module promptbind.models.att_model module promptbind.models.cross_att module promptbind.models.egnn module promptbind.models.model module promptbind.models.model_utils module promptbind.test_promptbind module promptbind.train_promptbind module promptbind.utils module promptbind.utils.fabind_inference_dataset module promptbind.utils.feature_utils module promptbind.utils.generation_utils module promptbind.utils.inference_mol_utils module promptbind.utils.inference_pdb_utils module promptbind.utils.logging_utils module promptbind.utils.metrics module promptbind.utils.metrics_to_tsb module promptbind.utils.post_optim_utils module promptbind.utils.utils module promptbind.visualize_prompt_components module PromptBindInference (class in promptbind.test_promptbind) prot_to_graph() (in module bindingrmsd.data.protein_atom_feature) Protein (class in deepfold.common.protein) (class in miniworld.utils.ProteinClass) protein_to_pdb() (in module miniworld.utils.output_visualize) protein_to_template() (in module miniworld.utils.data_refactoring) ProteinMSA (class in miniworld.utils.ProteinClass) ProteinSequence (class in miniworld.utils.ProteinClass) ProteinStructure (class in miniworld.utils.ProteinClass) ProteinTemplate (class in miniworld.utils.ProteinClass) ProteinTemplates (class in miniworld.utils.ProteinClass) pts_to_distogram() (in module deepfold.utils.tensor_utils)

Q

Qs2Rs() (in module miniworld.utils.kinematics) 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)

R

random_rot_trans() (in module miniworld.utils.parser_util) (in module miniworld.utils.util) random_split() (in module miniworld.feature.MiniWorld_featuring_species) rank() (in module deepfold.distributed.model_parallel) rbf() (in module miniworld.utils.util_module) RBFDistanceModule (class in promptbind.models.model_utils) read_data() (in module miniworld.utils.ffindex) read_entry_data() (in module miniworld.utils.ffindex) read_entry_lines() (in module miniworld.utils.ffindex) read_fasta() (in module bis_protein_structure.DATAGEN) read_index() (in module miniworld.utils.ffindex) read_ligand() (in module deepfold.data.monomer) 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_template_pdb() (in module miniworld.utils.template_parser) read_templates() (in module miniworld.utils.template_parser) 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) Recycling (class in miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings) 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)

refactoring_hhr_file() (in module miniworld.utils.data_refactoring) 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) reorder_paired_rows() (in module deepfold.data.multimer.msa_pairing) repr_norm_loss() (in module deepfold.losses.auxillary) Rerank_model (class in gd_dl.models) (class in gd_dl.rerank_model) reshape_weight() (in module deepfold.utils.import_utils) Residue (class in gd_dl.lib_pdb_mol2) ResidueAtPosition (class in deepfold.data.pdbx_parsing) ResiduePosition (class in deepfold.data.pdbx_parsing) 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) Rigid (class in deepfold.utils.rigid_utils) Rigid3Array (class in deepfold.utils.geometry.rigid_matrix_vector) rigid_from_3_points() (in module miniworld.utils.parser_util) (in module miniworld.utils.util) rigid_from_3_points_v2() (in module miniworld.utils.util) rigid_points_registration() (in module deepfold.losses.procrustes) rigid_vectors_registration() (in module deepfold.losses.procrustes) Rot3Array (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.rigid_utils) row_to_col() (in module deepfold.distributed.model_parallel) RowAttentionBlock (class in promptbind.models.cross_att) RowTriangleAttentionBlock (class in promptbind.models.cross_att) Rs2Qs() (in module miniworld.utils.kinematics) run_pipeline() (in module deepfold.relax.amber_minimize)

S

safe_filename() (in module deepfold.runner.utils) safely_set_viewless_tensor_data() (in module deepfold.distributed.utils) 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_obj() (in module bapred.data.utils) (in module bindingrmsd.data.ligand_atom_feature) (in module bindingrmsd.data.utils) save_val_checkpoint() (in module deepfold.utils.checkpoint_utils) scaler() (in module bindingrmsd.data.protein_atom_feature) scatter() (in module deepfold.distributed.model_parallel) scatter_to_model_parallel_region() (in module deepfold.distributed.model_parallel) SCPred (class in miniworld.models_MiniWorld_v1_5_use_interaction.Track_module) Seed_everything() (in module promptbind.train_promptbind) (in module promptbind.utils.feature_utils) select_chain_within_cutoff_to_ligand_v2() (in module promptbind.utils.feature_utils) SelfAttentionWithGate (class in deepfold.modules.attention) SeqSep (class in miniworld.models_MiniWorld_v1_5_use_interaction.Track_module) sequence_to_onehot() (in module bis_protein_structure.residue_constants) (in module deepfold.common.residue_constants) SequenceWeight (class in miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module) sequential_and() (in module promptbind.models.att_model) sequential_or() (in module promptbind.models.att_model) 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) SetDihedral() (in module promptbind.utils.utils) setup_logger() (in module bapred.logger)

setup_logging() (in module deepfold.utils.log_utils) sidechain_loss() (in module deepfold.losses.geometry) sidechain_sym_angle() (in module bis_protein_structure.TORSION2) sigmoid_cross_entropy() (in module deepfold.losses.utils) SingleTransition (class in deepfold.modules.single_transition) SinusoidalPosEmb (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) Species_emb (class in miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings) 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.vector) stacked() (in module deepfold.utils.import_utils) StateAttentionGate (class in miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module) str2bool() (in module gd_dl.utils) Str2Chain_IPA (class in miniworld.models_MiniWorld_v1_5_use_interaction.Track_module) Str2Residue_IPA (class in miniworld.models_MiniWorld_v1_5_use_interaction.Track_module) str_hash() (in module deepfold.utils.random) STRING_refactoring() (in module miniworld.utils.data_refactoring) StrSeqValueNet (class in miniworld.models_MiniWorld_v1_5_use_interaction.value_network) StructureModule (class in deepfold.modules.structure_module) StructureModuleConfig (class in deepfold.config) superimpose() (in module deepfold.losses.geometry) supervised_chi_loss() (in module deepfold.losses.geometry) SupervisedChiLossConfig (class in deepfold.config) svd() (in module deepfold.losses.procrustes) swa_avg_fn (class in deepfold.utils.swa_utils)

T

Templ_emb (class in miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings) template_featurize() (in module miniworld.feature.MiniWorld_featuring_species) TemplateAngleEmbedder (class in deepfold.modules.template_angle_embedder) TemplateAngleEmbedderConfig (class in deepfold.config) 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) (class in miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings) 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) TemplateTorsionStack (class in miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings) tensor_to_pdb() (in module miniworld.utils.output_visualize) test_a3m() (in module miniworld.utils.data_refactoring) test_a3m_file() (in module miniworld.utils.data_refactoring) test_loader (promptbind.test_promptbind.PromptBindInference attribute) test_unseen_loader (promptbind.test_promptbind.PromptBindInference attribute) th_ang_v() (in module miniworld.utils.parser_util) (in module miniworld.utils.util) th_dih() (in module miniworld.utils.parser_util) (in module miniworld.utils.util)

th_dih_v() (in module miniworld.utils.parser_util) (in module miniworld.utils.util) timing() (in module deepfold.data.tools.utils) tm_loss() (in module deepfold.losses.confidence) TMalign() (in module miniworld.utils.output_visualize) 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_date() (in module deepfold.data.tools.utils) to_modelcif() (in module deepfold.common.protein) to_pdb() (in module deepfold.common.protein) torsion_angle_loss() (in module bis_protein_structure.TORSION2) TqdmHandler (class in deepfold.utils.log_utils) TrainingConfig (class in deepfold.config) Transition (class in promptbind.models.model_utils) Transition_diff_out_dim (class in promptbind.models.model) transpose_on_model_parallel_region() (in module deepfold.distributed.model_parallel) tree_map() (in module deepfold.utils.tensor_utils) TriangleAttention (class in deepfold.modules.triangular_attention) TriangleAttentionEndingNode (class in deepfold.modules.triangular_attention) TriangleAttentionStartingNode (class in deepfold.modules.triangular_attention) TriangleMultiplication (class in miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module) TriangleMultiplicationIncoming (class in deepfold.modules.triangular_multiplicative_update) TriangleMultiplicationOutgoing (class in deepfold.modules.triangular_multiplicative_update) TriangleMultiplicativeUpdate (class in deepfold.modules.triangular_multiplicative_update) 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)

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) update_symm_Rs() (in module miniworld.models_MiniWorld_v1_5_use_interaction.Track_module) update_symm_subs() (in module miniworld.models_MiniWorld_v1_5_use_interaction.Track_module) UpdatePairByValue (class in miniworld.models_MiniWorld_v1_5_use_interaction.Track_module)

V

Vec3Array (class in deepfold.utils.geometry.vector) violation_loss() (in module deepfold.losses.violation) ViolationLossConfig (class in deepfold.config) visualize_2D_heatmap() (in module miniworld.utils.output_visualize)

visualize_2D_heatmaps() (in module miniworld.utils.output_visualize) visualize_2D_tensor() (in module miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction) (in module miniworld.utils.output_visualize) visualize_t_map() (in module miniworld.utils.output_visualize)

W

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) write_entries_to_db() (in module miniworld.utils.ffindex) write_entry() (in module miniworld.utils.ffindex)

write_entry_with_file() (in module miniworld.utils.ffindex) 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) writepdb() (in module miniworld.utils.parser_util) (in module miniworld.utils.util)

X

xyz_to_bbtor() (in module miniworld.utils.kinematics) xyz_to_c6d() (in module miniworld.utils.kinematics)

xyz_to_chi1() (in module miniworld.utils.kinematics) xyz_to_t2d() (in module miniworld.utils.kinematics) XYZConverter (class in miniworld.utils.util_module)

Z

zero_center_atom_positions() (in module deepfold.data.search.mmcif)