Index A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | Q | R | S | T | U | V | W | Y A add_alignment_cols_to_index() (in module pinder.data.get_alignment_similarity) add_all_apo_pairings_to_index() (in module pinder.data.get_apo) add_apo_pairings_to_index() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) add_clusters_to_index() (in module pinder.data.get_clusters) add_ecod_to_metadata() (in module pinder.data.get_dimers) add_edge() (pinder.data.graph_utils.MaxGraph method) add_edges_from() (pinder.data.graph_utils.MaxGraph method) add_entity_info() (in module pinder.data.annotation.graphql) add_enzyme_classification() (in module pinder.data.get_dimers) add_neff_to_index() (in module pinder.data.get_splits) add_pinder_set() (in module pinder.eval.dockq.method) add_predicted_monomers() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) add_predicted_monomers_to_index() (in module pinder.data.get_dimers) add_rank_column() (pinder.eval.dockq.method.MethodMetrics static method) add_sabdab_annotations() (in module pinder.data.annotation.sabdab) add_weighted_apo_score() (in module pinder.data.get_apo) add_xaxis_title() (in module pinder.data.plot.figure_utils) add_xtal_dummy_dockq() (in module pinder.data.plot.validity) add_yaxis_title() (in module pinder.data.plot.figure_utils) af2 (pinder.core.index.system.FolderNames attribute) agg_field (pinder.data.graph_utils.MaxGraph attribute) align_common_sequence() (pinder.core.loader.structure.Structure method) align_method (pinder.data.config.ApoPairingConfig attribute) align_sequences() (in module pinder.core.structure.atoms) (in module pinder.data.qc.similarity_check) aligned_holo_L (pinder.core.index.system.PinderSystem property) aligned_holo_R (pinder.core.index.system.PinderSystem property) Alignment (class in pinder.data.alignment_utils) alignment_filename (pinder.data.config.FoldseekConfig attribute) (pinder.data.config.MMSeqsConfig attribute) alignment_printout (pinder.data.config.IalignConfig attribute) alignment_to_parquet() (in module pinder.data.foldseek_utils) alignment_type (pinder.data.config.FoldseekConfig attribute) alignments1 (pinder.data.alignment_utils.Interface attribute) alignments2 (pinder.data.alignment_utils.Interface attribute) alignments_to_dual_alignment() (in module pinder.data.qc.similarity_check) ALL (pinder.methods.SUPPORTED_PAIRS attribute) aln_to_df() (in module pinder.data.foldseek_utils) alnlen (pinder.data.alignment_utils.Alignment attribute) alntmscore (pinder.data.alignment_utils.Alignment attribute) alphafold (pinder.core.index.system.FolderNames attribute) alphafold_cutoff_date (pinder.data.config.ClusterConfig attribute) analyze_leakage() (in module pinder.data.qc.similarity_check) annotate_complex() (in module pinder.data.get_annotations) annotate_interface_gaps() (in module pinder.data.annotation.interface_gaps) annotate_longest_intersecting_ecod_domain() (in module pinder.data.qc.annotation_check) annotate_pisalite() (in module pinder.data.get_annotations) annotation_hit_rate_barplot() (in module pinder.data.plot.categories) apo (pinder.core.index.system.FolderNames attribute) (pinder.core.structure.models.MonomerName attribute) APO (pinder.methods.SUPPORTED_PAIRS attribute) apo_chain (pinder.data.config.ApoPairingConfig attribute) apo_L (pinder.core.index.utils.IndexEntry attribute) apo_L_alt (pinder.core.index.utils.IndexEntry property) apo_L_pdb (pinder.core.index.utils.IndexEntry attribute) apo_L_pdbs (pinder.core.index.utils.IndexEntry attribute) apo_L_quality (pinder.core.index.utils.IndexEntry attribute) apo_ligand (pinder.core.index.system.PinderSystem property) apo_monomer_difficulty() (pinder.core.index.system.PinderSystem method) apo_pairing_id_batch_size (pinder.data.config.ScatterConfig attribute) apo_R (pinder.core.index.utils.IndexEntry attribute) apo_R_alt (pinder.core.index.utils.IndexEntry property) apo_R_pdb (pinder.core.index.utils.IndexEntry attribute) apo_R_pdbs (pinder.core.index.utils.IndexEntry attribute) apo_R_quality (pinder.core.index.utils.IndexEntry attribute) apo_receptor (pinder.core.index.system.PinderSystem property) apolar_apolar_contacts (pinder.core.index.utils.MetadataEntry attribute) apolar_polar_contacts (pinder.core.index.utils.MetadataEntry attribute) ApoPairingConfig (class in pinder.data.config) apply_dimer_filters() (pinder.core.loader.loader.PinderLoader static method) apply_formatting() (in module pinder.data.plot.plot) apply_mask() (in module pinder.core.structure.atoms) apply_structure_filters() (pinder.core.loader.loader.PinderLoader method) area_fill_color (pinder.data.plot.plot.Theme attribute) assembly (pinder.core.index.utils.MetadataEntry attribute) assembly_details (pinder.core.index.utils.MetadataEntry attribute) assign_pinder_s_subset() (in module pinder.data.get_test_set) assign_receptor_ligand() (in module pinder.core.structure.atoms) assign_test_subsets() (in module pinder.data.get_test_set) asym_id_1 (pinder.core.index.utils.MetadataEntry attribute) asym_id_2 (pinder.core.index.utils.MetadataEntry attribute) Atom (pinder.core.loader.geodata.NodeRepresentation attribute) atom_array (pinder.core.loader.structure.Structure attribute) atom_array_from_pdb_file() (in module pinder.core.structure.atoms) atom_array_summary_markdown_repr() (in module pinder.core.utils.dataclass) atom_contacts (pinder.core.structure.contacts.ContactPairs attribute) atom_names (pinder.core.loader.structure.Structure property) atom_vdw_radius() (in module pinder.core.structure.atoms) AtomTypeCount (class in pinder.core.loader.filters) axis_line_color (pinder.data.plot.plot.DarkTheme attribute) (pinder.data.plot.plot.LightTheme attribute) (pinder.data.plot.plot.Theme attribute) axis_linewidth (pinder.data.plot.plot.Theme attribute) axis_title_color (pinder.data.plot.plot.DarkTheme attribute) (pinder.data.plot.plot.LightTheme attribute) (pinder.data.plot.plot.Theme attribute) B b_factor (pinder.core.loader.structure.Structure property) backbone_atom_tensor() (in module pinder.core.loader.structure) backbone_definition (pinder.data.config.ContactConfig attribute) backbone_mask (pinder.core.loader.structure.Structure property) backbone_mask() (in module pinder.core.structure.atoms) backbone_only (pinder.data.config.ApoPairingConfig attribute) (pinder.data.config.ContactConfig attribute) BackboneDefinition (class in pinder.core.structure.models) BarPlot (class in pinder.data.plot.plot) barplot() (pinder.data.plot.plot.BarPlot method) Base (class in pinder.core.structure.models) batch_cluster_leaks() (in module pinder.data.find_transitive_hits) bin_annotation() (in module pinder.data.plot.categories) binding_leakage_main() (in module pinder.data.qc.annotation_check) biol_details (pinder.core.index.utils.MetadataEntry attribute) biotite (pinder.core.structure.models.BackboneDefinition attribute) biotite_pdbfile() (in module pinder.core.structure.atoms) biotite_pdbxfile() (in module pinder.core.structure.atoms) BiotiteDockQ (class in pinder.eval.dockq.biotite_dockq) blob_tree() (in module pinder.core.utils.paths) blob_tree_cmd() (in module pinder.core.utils.paths) blue (pinder.data.plot.plot.Colors attribute) blues (pinder.data.plot.plot.Colors property) bluish_green (pinder.data.plot.plot.Colors attribute) bold_annotations() (in module pinder.data.plot.figure_utils) bold_trace_name() (in module pinder.data.plot.figure_utils) box_fill_color (pinder.data.plot.plot.DarkTheme attribute) (pinder.data.plot.plot.LightTheme attribute) (pinder.data.plot.plot.Theme attribute) bright (pinder.data.plot.plot.Colors property) brightpink (pinder.data.plot.plot.Colors attribute) bucket_process_many() (in module pinder.core.utils.cloud) (pinder.core.utils.cloud.Gsutil static method) buried_sasa (pinder.core.index.utils.MetadataEntry attribute) C calc_fnat() (in module pinder.eval.dockq.metrics) calc_irmsd() (in module pinder.eval.dockq.metrics) calc_lrmsd() (in module pinder.eval.dockq.metrics) calc_num_mismatches() (in module pinder.core.structure.atoms) calculate() (pinder.eval.dockq.biotite_dockq.BiotiteDockQ method) calculate_elongation() (in module pinder.data.annotation.elongation) calculate_frac_monomer_dimer_overlap() (in module pinder.data.apo_utils) calpha_mask (pinder.core.loader.structure.Structure property) canonical_atom_type_mask() (in module pinder.core.loader.structure) canonical_method (pinder.data.config.ClusterConfig attribute) capri_class() (in module pinder.eval.dockq.metrics) CapriClass (class in pinder.eval.dockq.method) cast_entity_info_lists() (in module pinder.data.annotation.graphql) cast_incompatible_annotation_columns() (in module pinder.data.annotation.graphql) cast_incompatible_feature_columns() (in module pinder.data.annotation.graphql) cast_resi_to_valid_str() (in module pinder.data.get_dimers) cb_blue (pinder.data.plot.plot.Colors attribute) cb_orange (pinder.data.plot.plot.Colors attribute) cb_skyblue (pinder.data.plot.plot.Colors attribute) cb_vermillion (pinder.data.plot.plot.Colors attribute) cb_yellow (pinder.data.plot.plot.Colors attribute) chain (pinder.core.index.id.Protein attribute) (pinder.data.alignment_utils.Domain attribute) (pinder.data.alignment_utils.DomainInfo attribute) chain1_id (pinder.core.index.utils.MetadataEntry attribute) chain1_neff (pinder.core.index.utils.IndexEntry attribute) chain2_id (pinder.core.index.utils.MetadataEntry attribute) chain2_neff (pinder.core.index.utils.IndexEntry attribute) chain_1 (pinder.core.index.utils.MetadataEntry attribute) chain_2 (pinder.core.index.utils.MetadataEntry attribute) chain_instance_from_chain() (in module pinder.data.apo_utils) chain_L (pinder.core.index.utils.IndexEntry attribute) chain_metadata (pinder.core.index.utils.SupplementaryData attribute) chain_R (pinder.core.index.utils.IndexEntry attribute) chain_sequence (pinder.core.loader.structure.Structure property) ChainConfig (class in pinder.core.structure.models) ChainQuery (class in pinder.core.loader.filters) chains (pinder.core.loader.structure.Structure property) charged_apolar_contacts (pinder.core.index.utils.MetadataEntry attribute) charged_charged_contacts (pinder.core.index.utils.MetadataEntry attribute) charged_polar_contacts (pinder.core.index.utils.MetadataEntry attribute) check_backbone() (pinder.core.loader.filters.CompleteBackBone method) check_length() (pinder.core.loader.filters.AtomTypeCount method) (pinder.core.loader.filters.ResidueCount method) CheckChainElongation (class in pinder.core.loader.filters) CheckContacts (class in pinder.core.loader.filters) choose_final_clusters() (in module pinder.data.get_clusters) chunk_all_vs_all_indices() (in module pinder.data.pipeline.scatter) chunk_apo_pairing_ids() (in module pinder.data.pipeline.scatter) chunk_collection() (in module pinder.data.pipeline.scatter) chunk_dataframe() (in module pinder.data.pipeline.scatter) chunk_dict() (in module pinder.data.pipeline.scatter) chunk_dict_with_indices() (in module pinder.data.pipeline.scatter) cif_glob() (in module pinder.data.pipeline.tasks) cif_to_pdb() (in module pinder.core.structure.atoms) clamp_rgb_value() (in module pinder.data.plot.structure_case_studies) clean_interface_graph() (in module pinder.data.graph_utils) cluster() (in module pinder.data.get_clusters) (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) cluster_from_graph() (in module pinder.data.graph_utils) cluster_id (pinder.core.index.utils.IndexEntry attribute) cluster_id_L (pinder.core.index.utils.IndexEntry attribute) cluster_id_R (pinder.core.index.utils.IndexEntry attribute) cluster_leaks() (in module pinder.data.find_transitive_hits) ClusterConfig (class in pinder.data.config) code (pinder.core.utils.cloud.Error attribute) (pinder.core.utils.cloud.GCPError attribute) (pinder.core.utils.cloud.GCPTimeOutError attribute) collate_apo_metrics() (in module pinder.data.get_apo) collate_batch() (in module pinder.core.loader.dataset) collate_chain_info() (in module pinder.data.get_dimers) collate_complex() (in module pinder.core.loader.dataset) collate_csvs() (in module pinder.data.annotation.graphql) collate_entity_pqts() (in module pinder.data.get_dimers) collate_foldseek_alignments() (in module pinder.data.foldseek_utils) collate_mmseqs_alignments() (in module pinder.data.foldseek_utils) collect() (in module pinder.data.get_annotations) collect_annotations() (in module pinder.data.get_annotations) collect_contact_jsons() (in module pinder.data.alignment_utils) collect_csvs_by_group() (in module pinder.data.annotation.graphql) collect_dimer_annotations() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) collect_foldseek_contacts() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) collect_interacting_chains() (in module pinder.data.get_annotations) collect_metadata() (in module pinder.data.get_annotations) collect_rcsb_annotations() (in module pinder.data.annotation.graphql) colorblind_paired (pinder.data.plot.plot.Colors property) Colors (class in pinder.data.plot.plot) colors (pinder.data.plot.plot.Colors property) combine_native_and_predicted() (in module pinder.data.plot.validity) complete_rcsb_annotation() (in module pinder.data.pipeline.cache) CompleteBackBone (class in pinder.core.loader.filters) complex_type (pinder.core.index.utils.MetadataEntry attribute) connected_component_radius (pinder.data.config.PinderDataGenConfig attribute) construct_final_index() (in module pinder.data.get_splits) (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) construct_foldseek_graph() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) construct_graph_from_alignment() (in module pinder.data.graph_utils) construct_interface_alignment_graph() (in module pinder.data.graph_utils) construct_interface_cleaned_graph() (in module pinder.data.graph_utils) construct_interface_graph() (in module pinder.data.graph_utils) (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) construct_mmseqs_graph() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) construct_sequence_database() (in module pinder.data.get_test_set) contact_rad (pinder.data.config.ApoPairingConfig attribute) ContactConfig (class in pinder.data.config) ContactPairs (class in pinder.core.structure.contacts) contains_antibody (pinder.core.index.utils.IndexEntry attribute) contains_antigen (pinder.core.index.utils.IndexEntry attribute) contains_enzyme (pinder.core.index.utils.IndexEntry attribute) convert_category() (in module pinder.data.get_data) coords (pinder.core.loader.structure.Structure property) copy_pinder_set() (in module pinder.data.plot.families) copy_xtal_apo_pred_metrics() (in module pinder.data.plot.validity) count (pinder.eval.dockq.method.SubsetIds attribute) count_clashes() (in module pinder.eval.clashes) count_pinder_clashes() (in module pinder.eval.clashes) coverage_threshold (pinder.data.config.GraphConfig attribute) cp_dir() (pinder.core.utils.cloud.Gsutil method) cp_paired_paths() (pinder.core.utils.cloud.Gsutil method) cp_paths() (pinder.core.utils.cloud.Gsutil method) create_apo_complex() (pinder.core.index.system.PinderSystem method) create_complex() (pinder.core.index.system.PinderSystem method) create_dbs() (in module pinder.data.foldseek_utils) create_dbs_and_run() (in module pinder.data.foldseek_utils) create_decoy_stack() (pinder.eval.dockq.biotite_dockq.BiotiteDockQ static method) create_fasta_from_foldseek_inputs() (in module pinder.data.foldseek_utils) create_fasta_from_systems() (in module pinder.data.foldseek_utils) create_foldseek_dbs() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) create_foldseek_input_dir() (in module pinder.data.foldseek_utils) create_masked_bound_unbound_complexes() (pinder.core.index.system.PinderSystem method) create_mmseqs_dbs() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) create_normalized_test_monomers() (in module pinder.data.get_test_set) create_nx_radius_graph() (in module pinder.core.loader.utils) create_pred_complex() (pinder.core.index.system.PinderSystem method) create_transformed_holo_monomer() (in module pinder.data.get_test_set) csv_format_annotations() (in module pinder.data.annotation.graphql) csv_format_features() (in module pinder.data.annotation.graphql) csv_format_pfam() (in module pinder.data.annotation.graphql) curate_test_split() (in module pinder.data.get_test_set) D dark (pinder.data.plot.plot.Colors property) DarkTheme (class in pinder.data.plot.plot) dataframe (pinder.core.loader.structure.Structure property) DataIngestPipeline (class in pinder.data.pipeline.data_pipeline) dataset_difficulty_barplot() (in module pinder.data.plot.difficulty) DatasetName (class in pinder.core.structure.models) date (pinder.core.index.utils.MetadataEntry attribute) decoy_ligand (pinder.core.structure.models.ChainConfig attribute) decoy_receptor (pinder.core.structure.models.ChainConfig attribute) DecoyDockQ (class in pinder.eval.dockq.biotite_dockq) deep_merge_dict() (in module pinder.data.find_transitive_hits) deepice (pinder.data.plot.plot.Colors attribute) default_val (pinder.data.graph_utils.MaxGraph attribute) denim (pinder.data.plot.plot.Colors attribute) depth_limit (pinder.data.config.ClusterConfig attribute) DetachedChainQuery (class in pinder.core.loader.filters) detect_disulfide_bonds() (in module pinder.data.annotation.contact_classification) Dimer (class in pinder.core.index.id) dimer_batch_size (pinder.data.config.ScatterConfig attribute) dimer_glob() (in module pinder.data.pipeline.tasks) distance_cutoff (pinder.data.config.IalignConfig attribute) disulfide_bond_dihedral (pinder.data.config.TransientInterfaceConfig attribute) disulfide_bond_dihedral_tol (pinder.data.config.TransientInterfaceConfig attribute) disulfide_bond_distance (pinder.data.config.TransientInterfaceConfig attribute) disulfide_bond_distance_tol (pinder.data.config.TransientInterfaceConfig attribute) dockq (pinder.core.structure.models.BackboneDefinition attribute) Domain (class in pinder.data.alignment_utils) domain_id (pinder.data.alignment_utils.Domain attribute) DomainInfo (class in pinder.data.alignment_utils) downcast_dtypes() (in module pinder.core.index.utils) DOWNLOAD (pinder.core.utils.cloud.Gsutil attribute) download_dataset() (in module pinder.core.index.utils) download_entry() (in module pinder.eval.dockq.method) (pinder.core.index.system.PinderSystem method) download_pdbfam_db() (in module pinder.data.qc.utils) download_pinder_cmd() (in module pinder.core.index.utils) download_rcsb_files() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) download_rscb_files() (in module pinder.data.rcsb_rsync) download_sabdab() (in module pinder.data.annotation.sabdab) download_two_char_codes() (in module pinder.data.rcsb_rsync) DualChainQuery (class in pinder.core.loader.filters) E ecod_domain_id (pinder.data.alignment_utils.DomainInfo attribute) ecod_metadata (pinder.core.index.utils.SupplementaryData attribute) ECOD_names_L (pinder.core.index.utils.MetadataEntry attribute) ECOD_names_R (pinder.core.index.utils.MetadataEntry attribute) edge_weight (pinder.data.config.ClusterConfig attribute) empty_file() (in module pinder.core.utils.paths) entity_id_L (pinder.core.index.utils.MetadataEntry attribute) entity_id_R (pinder.core.index.utils.MetadataEntry attribute) entity_metadata (pinder.core.index.utils.SupplementaryData attribute) entry (pinder.core.index.system.PinderSystem attribute) entry_glob() (in module pinder.data.pipeline.tasks) entry_id (pinder.core.index.utils.MetadataEntry attribute) enzyme_classification_metadata (pinder.core.index.utils.SupplementaryData attribute) Error evalue (pinder.data.config.FoldseekConfig attribute) (pinder.data.config.MMSeqsConfig attribute) expand_local_path() (in module pinder.core.utils.paths) ExpectedChainsNotFoundError explode_sabdab_per_chain() (in module pinder.data.annotation.sabdab) exponential_retry() (in module pinder.core.utils.retry) extract_fasta_from_pdb() (in module pinder.data.foldseek_utils) extract_feature_positions() (in module pinder.data.annotation.graphql) extract_pdb_seq_from_pdb_file() (in module pinder.core.utils.pdb_utils) extract_sequence() (in module pinder.data.get_test_set) F family_diversity_bar_plot() (in module pinder.data.plot.families) family_grid_plot() (in module pinder.data.plot.families) fasta (pinder.core.loader.structure.Structure property) fasta2dict() (in module pinder.data.foldseek_utils) fetch_entry_annotations() (in module pinder.data.annotation.graphql) fetch_panther_ids() (in module pinder.data.plot.families) filepath (pinder.core.loader.structure.Structure attribute) filepaths (pinder.core.index.system.PinderSystem property) filter() (pinder.core.loader.filters.FilterByElongation method) (pinder.core.loader.filters.FilterByHoloElongation method) (pinder.core.loader.filters.FilterByHoloOverlap method) (pinder.core.loader.filters.FilterByHoloSeqIdentity method) (pinder.core.loader.filters.FilterByMissingHolo method) (pinder.core.loader.filters.FilterByResidueCount method) (pinder.core.loader.filters.FilterDetachedHolo method) (pinder.core.loader.filters.FilterDetachedSub method) (pinder.core.loader.filters.FilterMetadataFields method) (pinder.core.loader.filters.FilterSubByAtomTypes method) (pinder.core.loader.filters.FilterSubByChainQuery method) (pinder.core.loader.filters.FilterSubByContacts method) (pinder.core.loader.filters.FilterSubLengths method) (pinder.core.loader.filters.FilterSubRmsds method) (pinder.core.loader.filters.MinAtomTypesFilter method) (pinder.core.loader.filters.PinderFilterBase method) (pinder.core.loader.filters.PinderFilterSubBase method) (pinder.core.loader.filters.StructureFilter method) (pinder.core.loader.structure.Structure method) filter_atoms() (in module pinder.core.structure.atoms) filter_by_chain_query() (pinder.core.loader.filters.PinderFilterSubBase static method) filter_common_uniprot_res() (pinder.core.index.system.PinderSystem method) filter_foldseek_edges() (in module pinder.data.foldseek_utils) filter_interface_intersect() (in module pinder.core.utils.unbound) (in module pinder.eval.dockq.unbound) filter_mmseqs_edges() (in module pinder.data.foldseek_utils) FilterByElongation (class in pinder.core.loader.filters) FilterByHoloElongation (class in pinder.core.loader.filters) FilterByHoloOverlap (class in pinder.core.loader.filters) FilterByHoloSeqIdentity (class in pinder.core.loader.filters) FilterByMissingHolo (class in pinder.core.loader.filters) FilterByResidueCount (class in pinder.core.loader.filters) FilterDetachedHolo (class in pinder.core.loader.filters) FilterDetachedSub (class in pinder.core.loader.filters) FilterMetadataFields (class in pinder.core.loader.filters) FilterSubByAtomTypes (class in pinder.core.loader.filters) FilterSubByChainQuery (class in pinder.core.loader.filters) FilterSubByContacts (class in pinder.core.loader.filters) FilterSubLengths (class in pinder.core.loader.filters) FilterSubRmsds (class in pinder.core.loader.filters) find_intersection() (in module pinder.data.get_dimers) find_leakage() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) find_potential_interchain_bonded_atoms() (in module pinder.core.loader.structure) find_potential_leaks() (in module pinder.data.get_alignment_similarity) find_split_leakage() (in module pinder.data.find_transitive_hits) fix_annotation_mismatch() (in module pinder.core.structure.surgery) fix_index() (in module pinder.core.index.utils) fix_metadata() (in module pinder.core.index.utils) fix_mismatched_atoms() (in module pinder.core.structure.surgery) flip_interface() (pinder.data.alignment_utils.Interface method) flip_query_and_target() (pinder.data.alignment_utils.Alignment method) fnat_unbound_summary() (in module pinder.core.utils.unbound) (in module pinder.eval.dockq.unbound) FolderNames (class in pinder.core.index.system) foldseek_af2_difficulty_threshold (pinder.data.config.ClusterConfig attribute) foldseek_cluster_edge_threshold (pinder.data.config.ClusterConfig attribute) foldseek_db_size (pinder.data.config.ScatterConfig attribute) foldseek_edge_threshold (pinder.data.config.ClusterConfig attribute) foldseek_pdb_glob() (in module pinder.data.pipeline.tasks) FoldseekConfig (class in pinder.data.config) format_axes() (in module pinder.data.plot.plot) format_facets() (in module pinder.data.plot.plot) format_legend() (in module pinder.data.plot.plot) format_text() (in module pinder.data.plot.plot) format_text_template() (in module pinder.data.plot.figure_utils) frodock() (in module pinder.methods.run.frodock.predict) from_contact_info() (pinder.data.alignment_utils.Interface class method) from_domain_info() (pinder.data.alignment_utils.Domain class method) from_ecod_info() (pinder.data.alignment_utils.Alignment class method) from_foldseek_line() (pinder.data.alignment_utils.Alignment class method) from_line() (pinder.data.alignment_utils.Alignment class method) (pinder.data.alignment_utils.Interface class method) from_pinder_system() (pinder.core.loader.geodata.PairedPDB class method) from_residue (pinder.core.index.id.Protein attribute) from_string() (pinder.core.index.id.Dimer class method) (pinder.core.index.id.Monomer class method) from_structure_pair() (pinder.core.loader.geodata.PairedPDB class method) from_system() (pinder.data.alignment_utils.Interface class method) G GCPError GCPTimeOutError gcs_read_dataframe() (in module pinder.core.utils.cloud) generate_alignments() (in module pinder.data.qc.similarity_check) generate_apo_pairing_metric_tasks() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) generate_bio_assembly() (in module pinder.data.get_data) generate_case_image_grids() (in module pinder.data.plot.structure_case_studies) generate_case_scripts() (in module pinder.data.plot.structure_case_studies) generate_chimera_grid_scripts() (in module pinder.data.plot.structure_case_studies) generate_chimerax_native_pred_overlay() (in module pinder.data.plot.structure_case_studies) generate_cif_ingest_tasks() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) generate_color_palette() (in module pinder.data.plot.structure_case_studies) generate_dimer_annotation_tasks() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) generate_dimer_foldseek_contacts() (in module pinder.data.alignment_utils) generate_download_rcsb_files_tasks() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) generate_find_leakage_tasks() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) generate_foldseek_contacts_tasks() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) generate_foldseek_tasks() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) generate_latex_rows() (in module pinder.data.plot.leaderboards) generate_latex_rows_all() (in module pinder.data.plot.leaderboards) generate_latex_table() (in module pinder.data.plot.leaderboards) generate_latex_table_all() (in module pinder.data.plot.leaderboards) generate_mmseqs_tasks() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) generate_per_monomer_leaderboard_tables() (in module pinder.data.plot.leaderboards) generate_per_subset_leaderboard_tables() (in module pinder.data.plot.leaderboards) generate_pisa_annotation_tasks() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) generate_populate_entry_tasks() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) generate_populate_predicted_tasks() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) generate_rcsb_annotation_tasks() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) get() (pinder.core.loader.dataset.PPIDataset method) get_af2_hard_difficulty_transitive_hits() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) get_af2mm_ialign_sr() (in module pinder.data.plot.performance) get_af2mm_neff_sr() (in module pinder.data.plot.performance) get_af_monomers_from_monomer_ids() (in module pinder.data.get_dimers) get_aligned_indices() (in module pinder.data.qc.similarity_check) get_aligned_interface_indices() (in module pinder.data.qc.similarity_check) get_alignment_graph_with_indices() (in module pinder.data.graph_utils) get_alignment_similarity() (in module pinder.data.get_alignment_similarity) (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) get_all_rsync_entries() (in module pinder.data.rcsb_rsync) get_alternate_apo_codes() (in module pinder.core.loader.loader) get_annotation_metadata() (in module pinder.data.plot.annotations) get_annotations() (in module pinder.data.get_annotations) get_apo_monomer_difficulty() (in module pinder.core.utils.unbound) (in module pinder.eval.dockq.unbound) get_apo_monomer_weighted_score() (in module pinder.data.annotation.canonical_apo) (in module pinder.data.get_apo) get_apo_pairing_metrics() (in module pinder.data.get_apo) (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) get_apo_pairing_metrics_for_id() (in module pinder.data.apo_utils) get_arg_parser_args() (in module pinder.core.index.utils) get_atom_neighbors() (in module pinder.core.structure.contacts) get_atoms_within_coordinate() (in module pinder.core.structure.contacts) get_available_monomers() (in module pinder.core.loader.loader) get_backbone_atom_masks() (in module pinder.core.structure.atoms) get_binding_leakage() (in module pinder.data.qc.annotation_check) get_bucket() (pinder.core.utils.cloud.Gsutil method) get_buried_sasa() (in module pinder.core.structure.atoms) get_cache_delta() (in module pinder.data.pipeline.tasks) get_canonical_apo_codes() (in module pinder.data.annotation.canonical_apo) get_case_data() (in module pinder.data.plot.structure_case_studies) get_case_subset() (in module pinder.data.plot.structure_case_studies) get_categorical_annotation_hit_rate() (in module pinder.data.plot.categories) get_cluster_diversity() (in module pinder.data.qc.pfam_diversity) get_config_hash() (in module pinder.data.config) get_contacts() (pinder.core.loader.structure.Structure method) get_container_cpu_frac() (in module pinder.core.utils.cloud) get_corresponding_residues() (in module pinder.core.utils.unbound) (in module pinder.eval.dockq.unbound) get_cpu_limit() (in module pinder.core.utils.cloud) get_crystal_contact_classification() (in module pinder.data.annotation.contact_classification) get_dataset_indices() (in module pinder.data.plot.datasets) get_db4_difficulty() (in module pinder.core.utils.unbound) (in module pinder.eval.dockq.unbound) get_decoy_contacts() (pinder.eval.dockq.biotite_dockq.DecoyDockQ method) get_deleaked_sr() (in module pinder.data.plot.performance) get_dev_systems() (in module pinder.data.system) get_diff() (in module pinder.data.plot.difficulty) get_diffdock_ialign_sr() (in module pinder.data.plot.performance) get_difficulties() (in module pinder.data.plot.difficulty) get_dimer_annotations() (in module pinder.data.get_annotations) (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) get_dimer_contacts() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) get_dimer_index_from_files() (in module pinder.data.get_dimers) get_dimer_interchain_bond_atom_info() (in module pinder.data.get_dimers) get_dimer_pdbs_missing_foldseek_contacts() (in module pinder.data.pipeline.cache) get_dimer_to_cluster_pair() (in module pinder.data.get_clusters) get_dimers_from_dimer_pdbs() (in module pinder.data.get_dimers) get_dimers_from_interface_annotations() (in module pinder.data.get_dimers) get_dockq_metrics() (in module pinder.data.plot.performance) get_dockq_score() (in module pinder.eval.dockq.metrics) get_ecod_annotations() (in module pinder.data.qc.pfam_diversity) get_ecod_paired_leakage() (in module pinder.data.qc.annotation_check) get_entities() (in module pinder.data.get_data) get_eval_metrics() (in module pinder.eval.dockq.method) get_eval_metrics_all_methods() (in module pinder.eval.dockq.method) get_expected_counts() (in module pinder.eval.dockq.method) get_extra_metadata() (in module pinder.core.index.utils) get_filename() (pinder.core.loader.dataset.PPIDataset method) get_filename_idx() (pinder.core.loader.dataset.PPIDataset method) get_foldseek_contacts() (in module pinder.data.alignment_utils) get_foldseek_dimer_contacts() (in module pinder.data.alignment_utils) get_foldseek_numbering() (in module pinder.data.alignment_utils) get_geo_loader() (in module pinder.core.loader.dataset) get_hit_interfaces() (in module pinder.data.get_alignment_similarity) get_hit_rates() (pinder.eval.dockq.method.MethodMetrics method) get_ialign_leakage() (in module pinder.data.plot.leakage) get_ialign_metrics() (in module pinder.data.plot.performance) get_index() (in module pinder.core.index.utils) get_index_location() (in module pinder.core.index.utils) get_interacting_chains() (in module pinder.data.get_data) get_interface_graph() (in module pinder.data.graph_utils) get_interface_mask() (in module pinder.eval.dockq.metrics) (pinder.core.loader.structure.Structure method) get_interface_residues() (pinder.core.loader.structure.Structure method) get_interfaces_from_config() (in module pinder.data.alignment_utils) get_irmsd() (pinder.eval.dockq.biotite_dockq.DecoyDockQ method) get_irmsd_interface() (in module pinder.eval.dockq.biotite_dockq) get_leaderboard_dict() (in module pinder.data.plot.leaderboards) get_leaderboard_entry() (pinder.eval.dockq.method.MethodMetrics method) get_leaderboard_table() (in module pinder.data.plot.leaderboards) get_leak_map_for_id() (in module pinder.data.find_transitive_hits) get_leakage_dict() (in module pinder.data.find_transitive_hits) get_lrmsd() (pinder.eval.dockq.biotite_dockq.DecoyDockQ method) get_matching_entry_files() (in module pinder.data.get_dimers) get_max_var() (in module pinder.data.annotation.elongation) (pinder.core.loader.filters.CheckChainElongation static method) get_merged_metadata() (in module pinder.data.qc.pfam_diversity) get_metadata() (in module pinder.core.index.utils) (in module pinder.data.get_data) get_method_color_palette() (in module pinder.data.plot.structure_case_studies) get_method_eval_metrics() (in module pinder.eval.dockq.method) get_metrics() (pinder.eval.dockq.biotite_dockq.DecoyDockQ method) (pinder.eval.dockq.method.MethodMetrics method) get_missing_blobs() (in module pinder.core.index.utils) get_missing_system_penalty_metrics() (in module pinder.eval.dockq.method) get_mmcif_category() (in module pinder.data.get_data) get_monomer_counts() (in module pinder.data.plot.leaderboards) get_monomer_index_from_files() (in module pinder.data.get_dimers) get_monomers_from_mapping_pqts() (in module pinder.data.get_dimers) get_native_contacts() (pinder.eval.dockq.biotite_dockq.BiotiteDockQ method) get_node_to_cluster_mapping() (in module pinder.data.graph_utils) get_num_connected_components() (in module pinder.data.annotation.detached_components) get_oracle_per_id_monomer_method() (in module pinder.data.plot.structure_case_studies) get_paired_difficulties() (in module pinder.data.plot.difficulty) get_paired_hits() (in module pinder.data.get_alignment_similarity) get_paired_uniprot_intersection() (in module pinder.data.qc.annotation_check) get_panther_id() (in module pinder.data.plot.families) get_panther_metadata() (in module pinder.data.plot.families) get_pdb_chain_uni() (in module pinder.data.qc.similarity_check) get_pdb_entry_dirs() (in module pinder.data.get_dimers) get_penalized_dockq() (in module pinder.data.plot.performance) get_per_chain_ecod_summary() (in module pinder.data.get_dimers) get_per_chain_seq_alignments() (in module pinder.core.structure.atoms) (pinder.core.loader.structure.Structure method) get_pfam_diversity() (in module pinder.data.qc.pfam_diversity) get_pfam_metadata() (in module pinder.data.plot.families) get_pinder_bucket_root() (in module pinder.core.index.utils) get_pinder_location() (in module pinder.core.index.utils) get_pisa_annotations() (in module pinder.data.get_annotations) (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) get_pisa_unannotated() (in module pinder.data.pipeline.cache) get_planarity() (in module pinder.data.annotation.planarity) get_populated_entries() (in module pinder.data.get_dimers) get_potential_representatives() (in module pinder.data.find_transitive_hits) get_processed_alignments() (in module pinder.data.qc.similarity_check) get_proto_splits_pindex() (in module pinder.data.find_transitive_hits) get_putative_pairings() (in module pinder.data.get_apo) get_rcsb_annotations() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) get_rcsb_unannotated() (in module pinder.data.pipeline.cache) get_receptor_masks() (in module pinder.eval.dockq.metrics) get_ref_alignment_hits() (in module pinder.data.get_alignment_similarity) get_ref_free_metrics() (in module pinder.data.plot.validity) get_resolved_resi() (in module pinder.core.structure.atoms) get_resolved_resi_from_atom_array() (in module pinder.core.structure.atoms) get_rsync_directories() (in module pinder.data.rcsb_rsync) get_rsync_two_char_pdb_entries() (in module pinder.data.rcsb_rsync) get_seq_aligned_structures() (in module pinder.core.structure.atoms) get_seq_alignments() (in module pinder.core.structure.atoms) get_seq_identity() (in module pinder.core.structure.atoms) get_sequence_based_metrics() (in module pinder.data.apo_utils) get_sequence_based_oligomer_state() (in module pinder.data.plot.datasets) get_sequence_database() (in module pinder.core.index.utils) get_split_subsets() (in module pinder.data.get_splits) get_splits() (in module pinder.data.get_splits) (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) get_stack_contacts() (in module pinder.core.structure.contacts) get_stage_inputs() (in module pinder.data.pipeline.tasks) get_stage_tasks() (in module pinder.data.pipeline.tasks) get_stratified_sample() (in module pinder.data.get_test_set) get_structure_chains() (in module pinder.data.get_data) get_subsampled_train() (in module pinder.data.plot.performance) get_subset_hits() (in module pinder.data.get_alignment_similarity) get_subset_interfaces() (in module pinder.data.get_alignment_similarity) get_success_rate() (in module pinder.data.plot.validity) get_summary_diversity_and_leakage_stats() (in module pinder.data.plot.leakage) get_superimposed_metrics() (in module pinder.data.apo_utils) get_supplementary_data() (in module pinder.core.index.utils) get_system_monomer_difficulty() (in module pinder.data.annotation.canonical_apo) get_systems() (in module pinder.core.loader.loader) get_test_conversion_dicts() (in module pinder.data.find_transitive_hits) get_test_set() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) get_test_val_splits() (in module pinder.data.get_splits) get_timesplit_pinder_xl_ids() (in module pinder.data.plot.performance) get_torch_loader() (in module pinder.core.loader.dataset) get_train_noisy_apo() (in module pinder.data.get_splits) get_transitive_hits() (in module pinder.data.find_transitive_hits) (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) get_two_char_codes_not_downloaded() (in module pinder.data.rcsb_rsync) get_unannotated_dimer_pdbs() (in module pinder.data.pipeline.cache) get_unbound_difficulty() (in module pinder.core.utils.unbound) (in module pinder.eval.dockq.unbound) get_unbound_id() (in module pinder.data.apo_utils) get_unbound_interface_metrics() (in module pinder.core.utils.unbound) (in module pinder.eval.dockq.unbound) get_uningested_mmcif() (in module pinder.data.pipeline.cache) get_valid_apo_monomer_ids() (in module pinder.data.get_apo) get_valid_apo_monomers() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) get_valid_eval_systems() (in module pinder.eval.dockq.method) graph_type_glob() (in module pinder.data.pipeline.tasks) GraphConfig (class in pinder.data.config) graphql_batch_size (pinder.data.config.ScatterConfig attribute) gray (pinder.data.plot.plot.Colors attribute) green (pinder.data.plot.plot.Colors attribute) grouped_stacked_bar() (pinder.data.plot.plot.BarPlot method) Gsutil (class in pinder.core.utils.cloud) H hdock() (in module pinder.methods.run.hdock.predict) heavy_only (pinder.data.config.ApoPairingConfig attribute) (pinder.data.config.ContactConfig attribute) histogram_plot() (pinder.eval.dockq.method.MethodMetrics method) holo (pinder.core.index.system.FolderNames attribute) (pinder.core.structure.models.MonomerName attribute) HOLO (pinder.methods.SUPPORTED_PAIRS attribute) holo_apo_seq_identity() (in module pinder.data.apo_utils) holo_L (pinder.core.index.utils.IndexEntry attribute) holo_L_pdb (pinder.core.index.utils.IndexEntry attribute) holo_ligand (pinder.core.index.system.PinderSystem property) holo_R (pinder.core.index.utils.IndexEntry attribute) holo_R_pdb (pinder.core.index.utils.IndexEntry attribute) holo_receptor (pinder.core.index.system.PinderSystem property) homodimer (pinder.core.index.utils.IndexEntry property) hybrid_align() (in module pinder.data.apo_utils) I ialign() (in module pinder.data.qc.ialign) ialign_all() (in module pinder.data.qc.ialign) ialign_split_similarity_labels (pinder.core.index.utils.SupplementaryData attribute) ialign_vs_idist_density() (in module pinder.data.plot.leakage) IalignConfig (class in pinder.data.config) ice (pinder.data.plot.plot.Colors attribute) id (pinder.core.index.utils.IndexEntry attribute) (pinder.core.index.utils.MetadataEntry attribute) ids (pinder.eval.dockq.method.SubsetIds attribute) image_grid() (in module pinder.data.plot.image) index_dimers() (in module pinder.data.get_dimers) (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) IndexEntry (class in pinder.core.index.utils) indices1 (pinder.data.alignment_utils.Interface attribute) indices1() (pinder.data.alignment_utils.Alignment method) indices2 (pinder.data.alignment_utils.Interface attribute) indices2() (pinder.data.alignment_utils.Alignment method) infer_uniprot_from_mapping() (in module pinder.data.get_data) ingest_mmcif_list() (in module pinder.data.get_data) ingest_rcsb_files() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) ingest_rscb_files() (in module pinder.data.get_data) inject_logger() (in module pinder.core.utils.log) interacting_chains_backbone_only (pinder.data.config.PinderDataGenConfig attribute) interacting_chains_radius (pinder.data.config.PinderDataGenConfig attribute) Interface (class in pinder.data.alignment_utils) interface_annotations (pinder.core.index.utils.SupplementaryData attribute) interface_atom_gaps_4A (pinder.core.index.utils.MetadataEntry attribute) (pinder.data.config.ClusterConfig attribute) interface_atom_gaps_8A (pinder.core.index.utils.MetadataEntry attribute) interface_monomer_to_system_monomer() (in module pinder.data.graph_utils) InterfaceGraph (class in pinder.data.graph_utils) intermolecular_contacts (pinder.core.index.utils.MetadataEntry attribute) intersection_unordered_product() (in module pinder.data.find_transitive_hits) invalid_coverage_lower_bound (pinder.data.config.ApoPairingConfig attribute) invalid_coverage_upper_bound (pinder.data.config.ApoPairingConfig attribute) InvalidChainsError invert_chain_seq_map() (in module pinder.core.structure.atoms) is_homodimer() (in module pinder.core.utils.pdb_utils) is_local_path() (in module pinder.core.utils.paths) is_score_threshold (pinder.data.config.IalignConfig attribute) J join_apo_pairing_metrics() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) join_foldseek() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) join_mmseqs() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) join_rcsb_annotations() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) json_reader() (in module pinder.methods.main) L label (pinder.core.index.utils.MetadataEntry attribute) label_potential_transient_interfaces() (in module pinder.data.get_dimers) label_structure_gaps() (in module pinder.core.structure.contacts) len() (pinder.core.loader.dataset.PPIDataset method) len_unordered_set_product() (in module pinder.data.find_transitive_hits) length1 (pinder.core.index.utils.MetadataEntry attribute) length2 (pinder.core.index.utils.MetadataEntry attribute) length_resolved_1 (pinder.core.index.utils.MetadataEntry attribute) length_resolved_2 (pinder.core.index.utils.MetadataEntry attribute) light (pinder.data.plot.plot.Colors property) LightTheme (class in pinder.data.plot.plot) LinePlot (class in pinder.data.plot.plot) lineplot() (pinder.data.plot.plot.LinePlot method) link_density (pinder.core.index.utils.MetadataEntry attribute) load_alt_apo_structure() (pinder.core.index.system.PinderSystem method) load_cluster_cache() (in module pinder.data.get_clusters) load_contact_info() (in module pinder.data.alignment_utils) load_data() (in module pinder.data.qc.pfam_diversity) (in module pinder.data.qc.similarity_check) load_entity_metadata() (in module pinder.data.qc.utils) load_fasta_file() (in module pinder.core.utils.pdb_utils) load_filename() (pinder.core.loader.dataset.PPIDataset static method) load_graph_pickle() (in module pinder.data.graph_utils) load_index() (in module pinder.data.qc.utils) load_interface_pkl() (in module pinder.data.alignment_utils) load_mapping_chains() (in module pinder.data.get_dimers) load_metadata() (in module pinder.data.qc.utils) load_pfam_db() (in module pinder.data.qc.utils) load_structure() (pinder.core.index.system.PinderSystem static method) load_train_system_id_mapping() (in module pinder.data.qc.similarity_check) log_pvalue_threshold (pinder.data.config.IalignConfig attribute) ls() (pinder.core.utils.cloud.Gsutil method) ls_blobs() (pinder.core.utils.cloud.Gsutil method) M main() (in module pinder.data.plot.annotations) (in module pinder.data.plot.categories) (in module pinder.data.plot.datasets) (in module pinder.data.plot.difficulty) (in module pinder.data.plot.families) (in module pinder.data.plot.leaderboards) (in module pinder.data.plot.leakage) (in module pinder.data.plot.performance) (in module pinder.data.plot.run) (in module pinder.data.plot.structure_case_studies) (in module pinder.data.plot.validity) (in module pinder.data.qc.run) (in module pinder.data.run) (in module pinder.eval.create_submission) (in module pinder.eval.run) (in module pinder.methods.main) make_path_pairs() (in module pinder.core.utils.cloud) map_fsid_pair_to_systems() (in module pinder.data.find_transitive_hits) map_leak_pairs() (in module pinder.data.find_transitive_hits) map_systems_to_fsid_pairs() (in module pinder.data.find_transitive_hits) map_to_pinder_chains() (in module pinder.data.annotation.sabdab) map_to_sabdab_db() (in module pinder.data.annotation.sabdab) mapping_path() (pinder.core.index.utils.IndexEntry method) mapping_paths (pinder.core.index.utils.IndexEntry property) mappings_path (pinder.core.index.system.PinderSystem attribute) marker_line_color (pinder.data.plot.plot.DarkTheme attribute) (pinder.data.plot.plot.LightTheme attribute) (pinder.data.plot.plot.Theme attribute) marker_pattern_bgcolor (pinder.data.plot.plot.DarkTheme attribute) (pinder.data.plot.plot.LightTheme attribute) (pinder.data.plot.plot.Theme attribute) mask_common_uniprot() (in module pinder.core.loader.structure) mask_from_res_list() (in module pinder.core.structure.atoms) max_assembly_chains (pinder.data.config.PinderDataGenConfig attribute) max_depth_2_hits (pinder.data.config.ClusterConfig attribute) max_depth_2_hits_with_comm (pinder.data.config.ClusterConfig attribute) max_frac_monomer_dimer_sequence (pinder.data.config.ApoPairingConfig attribute) max_interface_miss_frac (pinder.data.config.ApoPairingConfig attribute) max_node_degree (pinder.data.config.ClusterConfig attribute) max_refine_rmsd (pinder.data.config.ApoPairingConfig attribute) max_seqs (pinder.data.config.FoldseekConfig attribute) (pinder.data.config.MMSeqsConfig attribute) max_var_1 (pinder.core.index.utils.MetadataEntry attribute) max_var_2 (pinder.core.index.utils.MetadataEntry attribute) max_var_thr (pinder.data.config.ClusterConfig attribute) MaxGraph (class in pinder.data.graph_utils) meanline_color (pinder.data.plot.plot.DarkTheme attribute) (pinder.data.plot.plot.LightTheme attribute) (pinder.data.plot.plot.Theme attribute) median_capri_hit_rate() (pinder.eval.dockq.method.MethodMetrics method) median_oracle() (pinder.eval.dockq.method.MethodMetrics method) merge_annotated_interfaces_with_pindex() (in module pinder.data.qc.annotation_check) merge_index_and_entities() (in module pinder.data.get_dimers) merge_metadata() (in module pinder.data.get_dimers) message_format (pinder.core.utils.cloud.Error attribute) (pinder.core.utils.cloud.GCPError attribute) (pinder.core.utils.cloud.GCPTimeOutError attribute) metadata (pinder.core.index.system.PinderSystem property) metadata_to_ecod_pairs() (in module pinder.data.qc.annotation_check) MetadataEntry (class in pinder.core.index.utils) method (pinder.core.index.utils.MetadataEntry attribute) (pinder.data.config.ClusterConfig attribute) method_context() (in module pinder.core.utils.cloud) method_main() (in module pinder.data.run) method_median() (pinder.eval.dockq.method.MethodMetrics method) method_oracle() (pinder.eval.dockq.method.MethodMetrics method) MethodMetrics (class in pinder.eval.dockq.method) metrics (pinder.eval.dockq.method.MethodMetrics property) midnight (pinder.data.plot.plot.Colors attribute) min_aligned_apo_res_frac (pinder.data.config.ApoPairingConfig attribute) min_alignment_length (pinder.data.config.GraphConfig attribute) min_atom_types (pinder.data.config.ApoPairingConfig attribute) (pinder.data.config.ClusterConfig attribute) min_buried_sasa (pinder.data.config.TransientInterfaceConfig attribute) min_chain_length (pinder.data.config.ClusterConfig attribute) min_depth_2_hits_with_comm (pinder.data.config.ClusterConfig attribute) min_holo_resolved_frac (pinder.data.config.ApoPairingConfig attribute) min_interface (pinder.data.config.IalignConfig attribute) min_interface_length (pinder.data.config.GraphConfig attribute) min_length (pinder.data.config.ContactConfig attribute) min_residues (pinder.data.config.ApoPairingConfig attribute) (pinder.data.config.IalignConfig attribute) min_seq_id (pinder.data.config.MMSeqsConfig attribute) min_seq_identity (pinder.data.config.ApoPairingConfig attribute) MinAtomTypesFilter (class in pinder.core.loader.filters) missing_interface_residues_4A (pinder.core.index.utils.MetadataEntry attribute) missing_interface_residues_8A (pinder.core.index.utils.MetadataEntry attribute) mmcif_batch_size (pinder.data.config.ScatterConfig attribute) mmseqs_edge_threshold (pinder.data.config.ClusterConfig attribute) mmseqs_score_threshold (pinder.data.config.GraphConfig attribute) mmseqs_upper_threshold (pinder.data.config.GraphConfig attribute) MMSeqsConfig (class in pinder.data.config) model_computed_fields (pinder.core.index.utils.IndexEntry attribute) (pinder.core.index.utils.MetadataEntry attribute) (pinder.core.structure.models.Base attribute) (pinder.core.structure.models.ChainConfig attribute) model_config (pinder.core.index.utils.IndexEntry attribute) (pinder.core.index.utils.MetadataEntry attribute) (pinder.core.structure.models.Base attribute) (pinder.core.structure.models.ChainConfig attribute) model_fields (pinder.core.index.utils.IndexEntry attribute) (pinder.core.index.utils.MetadataEntry attribute) (pinder.core.structure.models.Base attribute) (pinder.core.structure.models.ChainConfig attribute) module pinder, [1] pinder.core pinder.core.index pinder.core.index.id pinder.core.index.system pinder.core.index.utils pinder.core.loader pinder.core.loader.dataset pinder.core.loader.filters pinder.core.loader.geodata pinder.core.loader.loader pinder.core.loader.structure pinder.core.loader.transforms pinder.core.loader.utils pinder.core.loader.writer pinder.core.structure pinder.core.structure.atoms pinder.core.structure.contacts pinder.core.structure.models pinder.core.structure.superimpose pinder.core.structure.surgery pinder.core.submit pinder.core.utils pinder.core.utils.cloud pinder.core.utils.constants pinder.core.utils.dataclass pinder.core.utils.log pinder.core.utils.paths pinder.core.utils.pdb_utils pinder.core.utils.process pinder.core.utils.retry pinder.core.utils.string pinder.core.utils.timer pinder.core.utils.unbound pinder.data pinder.data.alignment_utils pinder.data.annotation pinder.data.annotation.canonical_apo pinder.data.annotation.constants pinder.data.annotation.contact_classification pinder.data.annotation.detached_components pinder.data.annotation.elongation pinder.data.annotation.graphql pinder.data.annotation.interface_gaps pinder.data.annotation.planarity pinder.data.annotation.sabdab pinder.data.apo_utils pinder.data.config pinder.data.csv_utils pinder.data.find_transitive_hits pinder.data.foldseek_utils pinder.data.get_alignment_similarity pinder.data.get_annotations pinder.data.get_apo pinder.data.get_clusters pinder.data.get_data pinder.data.get_dimers pinder.data.get_splits pinder.data.get_test_set pinder.data.graph_utils pinder.data.pipeline pinder.data.pipeline.cache pinder.data.pipeline.constants pinder.data.pipeline.data_pipeline pinder.data.pipeline.scatter pinder.data.pipeline.tasks pinder.data.plot pinder.data.plot.annotations pinder.data.plot.categories pinder.data.plot.constants pinder.data.plot.datasets pinder.data.plot.difficulty pinder.data.plot.families pinder.data.plot.figure_utils pinder.data.plot.image pinder.data.plot.leaderboards pinder.data.plot.leakage pinder.data.plot.performance pinder.data.plot.plot pinder.data.plot.run pinder.data.plot.structure_case_studies pinder.data.plot.validity pinder.data.qc pinder.data.qc.annotation_check pinder.data.qc.ialign pinder.data.qc.pfam_diversity pinder.data.qc.run pinder.data.qc.similarity_check pinder.data.qc.uniprot_leakage pinder.data.qc.utils pinder.data.rcsb_rsync pinder.data.run pinder.data.system pinder.eval pinder.eval.clashes pinder.eval.create_submission pinder.eval.dockq pinder.eval.dockq.biotite_dockq pinder.eval.dockq.method pinder.eval.dockq.metrics pinder.eval.dockq.unbound pinder.eval.run pinder.methods pinder.methods.main pinder.methods.preprocess pinder.methods.run pinder.methods.run.af2mm pinder.methods.run.frodock pinder.methods.run.frodock.predict pinder.methods.run.hdock pinder.methods.run.hdock.predict pinder.methods.run.patchdock pinder.methods.run.patchdock.predict pinder.methods.train Monomer (class in pinder.core.index.id) monomer1 (pinder.core.index.id.Dimer attribute) monomer2 (pinder.core.index.id.Dimer attribute) monomer_neff (pinder.core.index.utils.SupplementaryData attribute) MonomerName (class in pinder.core.structure.models) mp_annotate_interface_gaps() (in module pinder.data.annotation.interface_gaps) multi_level_leakage_diversity_bar_plots() (in module pinder.data.plot.leakage) N n_atoms (pinder.core.loader.structure.Structure property) n_residue_pairs (pinder.core.index.utils.MetadataEntry attribute) n_residues (pinder.core.index.utils.MetadataEntry attribute) native (pinder.core.index.system.PinderSystem attribute) native_ligand (pinder.core.structure.models.ChainConfig attribute) native_receptor (pinder.core.structure.models.ChainConfig attribute) natural_sort() (in module pinder.core.utils.string) navy (pinder.data.plot.plot.Colors attribute) neutral (pinder.data.plot.plot.Colors property) NodeRepresentation (class in pinder.core.loader.geodata) normalize_orientation() (in module pinder.core.structure.atoms) num_atom_types (pinder.core.index.utils.MetadataEntry attribute) number_of_components (pinder.data.config.ClusterConfig attribute) number_of_components_1 (pinder.core.index.utils.MetadataEntry attribute) number_of_components_2 (pinder.core.index.utils.MetadataEntry attribute) O oligomer_barplot() (in module pinder.data.plot.datasets) oligomeric_count (pinder.core.index.utils.MetadataEntry attribute) (pinder.data.config.ClusterConfig attribute) oligomeric_details (pinder.core.index.utils.MetadataEntry attribute) only_unique_resi (pinder.data.config.ContactConfig attribute) oracle_median_summary() (pinder.eval.dockq.method.MethodMetrics method) output_prefix (pinder.data.config.IalignConfig attribute) P pad_and_stack() (in module pinder.core.loader.dataset) pad_to_max_length() (in module pinder.core.loader.dataset) paired (pinder.data.plot.plot.Colors property) paired_neff (pinder.core.index.utils.SupplementaryData attribute) PairedPDB (class in pinder.core.loader.geodata) pairwise_chain_contacts() (in module pinder.core.structure.contacts) pairwise_clashes() (in module pinder.core.structure.contacts) pairwise_contacts() (in module pinder.core.structure.contacts) paleblue (pinder.data.plot.plot.Colors attribute) palegreen (pinder.data.plot.plot.Colors attribute) palepurple (pinder.data.plot.plot.Colors attribute) palette() (pinder.data.plot.plot.Colors method) parallel_copy_files() (in module pinder.core.utils.paths) parallel_extract_fasta() (in module pinder.data.foldseek_utils) parallel_read_csvs() (in module pinder.data.csv_utils) parse_annotation_data() (in module pinder.data.annotation.graphql) parse_ec() (in module pinder.data.annotation.graphql) parse_pfam() (in module pinder.data.annotation.graphql) parse_polymer_entity_instance() (in module pinder.data.annotation.graphql) pastel (pinder.data.plot.plot.Colors property) patch_af2mm_monomer_types() (in module pinder.data.plot.performance) patchdock() (in module pinder.methods.run.patchdock.predict) pdb (pinder.data.alignment_utils.DomainInfo attribute) pdb_engine (pinder.core.loader.structure.Structure attribute) pdb_from (pinder.data.alignment_utils.Domain attribute) pdb_id (pinder.core.index.utils.IndexEntry attribute) (pinder.data.alignment_utils.Domain attribute) pdb_id_glob() (in module pinder.data.pipeline.tasks) pdb_path() (pinder.core.index.utils.IndexEntry method) pdb_paths (pinder.core.index.utils.IndexEntry property) pdb_strand_id_L (pinder.core.index.utils.MetadataEntry attribute) pdb_strand_id_R (pinder.core.index.utils.MetadataEntry attribute) pdb_to (pinder.data.alignment_utils.Domain attribute) pdbid1 (pinder.data.alignment_utils.Alignment attribute) (pinder.data.alignment_utils.Interface attribute) pdbid2 (pinder.data.alignment_utils.Alignment attribute) (pinder.data.alignment_utils.Interface attribute) pdbs_path (pinder.core.index.system.PinderSystem attribute) pfam_diversity_main() (in module pinder.data.qc.pfam_diversity) pinder module, [1] pinder (pinder.data.plot.plot.Colors attribute) pinder.core module pinder.core.index module pinder.core.index.id module pinder.core.index.system module pinder.core.index.utils module pinder.core.loader module pinder.core.loader.dataset module pinder.core.loader.filters module pinder.core.loader.geodata module pinder.core.loader.loader module pinder.core.loader.structure module pinder.core.loader.transforms module pinder.core.loader.utils module pinder.core.loader.writer module pinder.core.structure module pinder.core.structure.atoms module pinder.core.structure.contacts module pinder.core.structure.models module pinder.core.structure.superimpose module pinder.core.structure.surgery module pinder.core.submit module pinder.core.utils module pinder.core.utils.cloud module pinder.core.utils.constants module pinder.core.utils.dataclass module pinder.core.utils.log module pinder.core.utils.paths module pinder.core.utils.pdb_utils module pinder.core.utils.process module pinder.core.utils.retry module pinder.core.utils.string module pinder.core.utils.timer module pinder.core.utils.unbound module pinder.data module pinder.data.alignment_utils module pinder.data.annotation module pinder.data.annotation.canonical_apo module pinder.data.annotation.constants module pinder.data.annotation.contact_classification module pinder.data.annotation.detached_components module pinder.data.annotation.elongation module pinder.data.annotation.graphql module pinder.data.annotation.interface_gaps module pinder.data.annotation.planarity module pinder.data.annotation.sabdab module pinder.data.apo_utils module pinder.data.config module pinder.data.csv_utils module pinder.data.find_transitive_hits module pinder.data.foldseek_utils module pinder.data.get_alignment_similarity module pinder.data.get_annotations module pinder.data.get_apo module pinder.data.get_clusters module pinder.data.get_data module pinder.data.get_dimers module pinder.data.get_splits module pinder.data.get_test_set module pinder.data.graph_utils module pinder.data.pipeline module pinder.data.pipeline.cache module pinder.data.pipeline.constants module pinder.data.pipeline.data_pipeline module pinder.data.pipeline.scatter module pinder.data.pipeline.tasks module pinder.data.plot module pinder.data.plot.annotations module pinder.data.plot.categories module pinder.data.plot.constants module pinder.data.plot.datasets module pinder.data.plot.difficulty module pinder.data.plot.families module pinder.data.plot.figure_utils module pinder.data.plot.image module pinder.data.plot.leaderboards module pinder.data.plot.leakage module pinder.data.plot.performance module pinder.data.plot.plot module pinder.data.plot.run module pinder.data.plot.structure_case_studies module pinder.data.plot.validity module pinder.data.qc module pinder.data.qc.annotation_check module pinder.data.qc.ialign module pinder.data.qc.pfam_diversity module pinder.data.qc.run module pinder.data.qc.similarity_check module pinder.data.qc.uniprot_leakage module pinder.data.qc.utils module pinder.data.rcsb_rsync module pinder.data.run module pinder.data.system module pinder.eval module pinder.eval.clashes module pinder.eval.create_submission module pinder.eval.dockq module pinder.eval.dockq.biotite_dockq module pinder.eval.dockq.method module pinder.eval.dockq.metrics module pinder.eval.dockq.unbound module pinder.eval.run module pinder.methods module pinder.methods.main module pinder.methods.preprocess module pinder.methods.run module pinder.methods.run.af2mm module pinder.methods.run.frodock module pinder.methods.run.frodock.predict module pinder.methods.run.hdock module pinder.methods.run.hdock.predict module pinder.methods.run.patchdock module pinder.methods.run.patchdock.predict module pinder.methods.train module pinder_af2 (pinder.core.index.utils.IndexEntry attribute) (pinder.core.structure.models.DatasetName attribute) pinder_id (pinder.core.index.utils.IndexEntry property) (pinder.core.index.utils.MetadataEntry property) (pinder.core.loader.structure.Structure attribute) pinder_pdb (pinder.core.index.utils.IndexEntry property) pinder_s (pinder.core.index.utils.IndexEntry attribute) (pinder.core.structure.models.DatasetName attribute) pinder_xl (pinder.core.index.utils.IndexEntry attribute) (pinder.core.structure.models.DatasetName attribute) PinderClusteredWriter (class in pinder.core.loader.writer) PinderDataGenConfig (class in pinder.data.config) PinderDataset (class in pinder.core.loader.dataset) PinderDefaultWriter (class in pinder.core.loader.writer) PinderFilterBase (class in pinder.core.loader.filters) PinderFilterSubBase (class in pinder.core.loader.filters) PinderLoader (class in pinder.core.loader.loader) PinderLoggingError PinderSystem (class in pinder.core.index.system) PinderWriterBase (class in pinder.core.loader.writer) pink (pinder.data.plot.plot.Colors attribute) pinks (pinder.data.plot.plot.Colors property) pisa_json_to_dataframe() (in module pinder.data.get_annotations) planarity (pinder.core.index.utils.MetadataEntry attribute) plot_ecod_family_distribution() (in module pinder.data.qc.pfam_diversity) plot_merged_metadata_distributions() (in module pinder.data.qc.pfam_diversity) plot_pfam_clan_distribution() (in module pinder.data.qc.pfam_diversity) polar_polar_contacts (pinder.core.index.utils.MetadataEntry attribute) populate_entries() (in module pinder.data.get_dimers) (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) populate_foldseek_contacts() (in module pinder.data.alignment_utils) populate_predicted() (in module pinder.data.get_dimers) (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) populate_predicted_from_monomers() (in module pinder.data.get_dimers) populate_rcsb_annotations() (in module pinder.data.annotation.graphql) PPIDataset (class in pinder.core.loader.dataset) pred_ligand (pinder.core.index.system.PinderSystem property) pred_receptor (pinder.core.index.system.PinderSystem property) PREDICT (pinder.methods.SUPPORTED_ACTIONS attribute) predict() (in module pinder.methods.main) predict_frodock() (in module pinder.methods.run.frodock.predict) predict_hdock() (in module pinder.methods.run.hdock.predict) predict_patchdock() (in module pinder.methods.run.patchdock.predict) predicted (pinder.core.index.system.FolderNames attribute) (pinder.core.structure.models.MonomerName attribute) PREDICTED (pinder.methods.SUPPORTED_PAIRS attribute) predicted_batch_size (pinder.data.config.ScatterConfig attribute) predicted_L (pinder.core.index.utils.IndexEntry attribute) predicted_L_pdb (pinder.core.index.utils.IndexEntry attribute) predicted_R (pinder.core.index.utils.IndexEntry attribute) predicted_R_pdb (pinder.core.index.utils.IndexEntry attribute) prepare_inference_inputs() (in module pinder.methods.preprocess) prepare_inputs() (pinder.eval.dockq.biotite_dockq.BiotiteDockQ method) PREPROCESS (pinder.methods.SUPPORTED_ACTIONS attribute) preprocess() (in module pinder.methods.main) primary_dimer_index_from_dimers() (in module pinder.data.get_dimers) print_test_meta_details() (in module pinder.data.get_splits) probability (pinder.core.index.utils.MetadataEntry attribute) process() (pinder.core.loader.dataset.PPIDataset method) process_in_batches() (in module pinder.data.qc.ialign) process_many() (in module pinder.core.utils.cloud) (pinder.core.utils.cloud.Gsutil static method) process_map() (in module pinder.core.utils.process) process_mmcif() (in module pinder.data.get_data) process_parallel() (pinder.core.loader.dataset.PPIDataset method) process_pfam_data() (in module pinder.data.qc.pfam_diversity) process_single_file() (pinder.core.loader.dataset.PPIDataset static method) process_single_file_parallel() (pinder.core.loader.dataset.PPIDataset static method) process_starmap() (in module pinder.core.utils.process) process_test_table() (in module pinder.data.qc.similarity_check) processed_file_names (pinder.core.loader.dataset.PPIDataset property) prodigy_label (pinder.data.config.ClusterConfig attribute) Protein (class in pinder.core.index.id) proteins (pinder.core.index.id.Monomer attribute) purple (pinder.data.plot.plot.Colors attribute) purples (pinder.data.plot.plot.Colors property) putative_apo_pairings() (in module pinder.data.pipeline.tasks) pymol_script (pinder.core.index.system.PinderSystem property) Q qend (pinder.data.alignment_utils.Alignment attribute) qlen (pinder.data.alignment_utils.Alignment attribute) qstart (pinder.data.alignment_utils.Alignment attribute) query() (pinder.core.loader.filters.AtomTypeCount method) (pinder.core.loader.filters.ChainQuery method) (pinder.core.loader.filters.CheckContacts method) (pinder.core.loader.filters.CompleteBackBone method) (pinder.core.loader.filters.DetachedChainQuery method) (pinder.core.loader.filters.DualChainQuery method) (pinder.core.loader.filters.ResidueCount method) R radius (pinder.data.config.ContactConfig attribute) (pinder.data.config.TransientInterfaceConfig attribute) RandomLigandTransform (class in pinder.core.loader.transforms) raw_file_names (pinder.core.loader.dataset.PPIDataset property) read_csv_non_default_na() (in module pinder.data.csv_utils) read_decoys() (pinder.eval.dockq.biotite_dockq.BiotiteDockQ static method) read_mmcif_file() (in module pinder.data.get_data) read_pdb() (pinder.core.loader.structure.Structure static method) redpurple (pinder.data.plot.plot.Colors attribute) ref_free_violin_plot() (in module pinder.data.plot.validity) reference_based_violin_plots() (in module pinder.data.plot.performance) reformat_hits() (in module pinder.data.get_alignment_similarity) release_date (pinder.core.index.utils.MetadataEntry attribute) REMOTE_COPY (pinder.core.utils.cloud.Gsutil attribute) remote_cp() (pinder.core.utils.cloud.Gsutil method) remote_key() (in module pinder.core.utils.paths) remove_af2mm_nonaf2() (in module pinder.data.plot.performance) remove_annotations() (in module pinder.core.structure.surgery) remove_apo_chain_copies() (in module pinder.data.apo_utils) remove_dimer_chain_copies() (in module pinder.data.apo_utils) remove_duplicate_calpha() (in module pinder.core.structure.surgery) remove_legend_title() (in module pinder.data.plot.figure_utils) remove_xaxis_titles() (in module pinder.data.plot.figure_utils) remove_yaxis_titles() (in module pinder.data.plot.figure_utils) rename_chains() (in module pinder.core.structure.atoms) rename_peptide_cluster_ids() (in module pinder.data.get_splits) renumber_res_ids() (in module pinder.core.structure.atoms) replace_with_nan() (in module pinder.data.get_data) report_ecod_diversity() (in module pinder.data.qc.pfam_diversity) report_uniprot_test_val_leakage() (in module pinder.data.qc.uniprot_leakage) Residue (pinder.core.loader.geodata.NodeRepresentation attribute) residue_contacts (pinder.core.structure.contacts.ContactPairs attribute) residue_names (pinder.core.loader.structure.Structure property) ResidueCount (class in pinder.core.loader.filters) residues (pinder.core.loader.structure.Structure property) resize_img_to_array() (in module pinder.data.plot.image) resn2seq() (in module pinder.core.structure.atoms) resolution (pinder.core.index.utils.MetadataEntry attribute) resolution_thr (pinder.data.config.ClusterConfig attribute) resolved_mapping (pinder.core.loader.structure.Structure property) resolved_pdb2uniprot (pinder.core.loader.structure.Structure property) resolved_uniprot2pdb (pinder.core.loader.structure.Structure property) retry_blob_method() (in module pinder.core.utils.cloud) retry_bucket_method() (in module pinder.core.utils.cloud) reverse_dict() (in module pinder.core.loader.structure) rmdir() (in module pinder.core.utils.paths) rmsd_threshold (pinder.data.config.IalignConfig attribute) run() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) run_db_vs_db() (in module pinder.data.foldseek_utils) run_foldseek() (in module pinder.data.foldseek_utils) (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) run_foldseek_db_pair() (in module pinder.data.foldseek_utils) run_foldseek_on_pinder_chains() (in module pinder.data.foldseek_utils) run_graphql_annotation_query() (in module pinder.data.annotation.graphql) run_mmseqs() (in module pinder.data.foldseek_utils) (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) run_mmseqs_db_pair() (in module pinder.data.foldseek_utils) run_mmseqs_on_pinder_chains() (in module pinder.data.foldseek_utils) run_monomer_dimer_mmseqs() (in module pinder.data.get_apo) run_stage() (pinder.data.pipeline.data_pipeline.DataIngestPipeline method) run_task() (in module pinder.data.pipeline.tasks) rust_pdbfile() (in module pinder.core.structure.atoms) S sabdab_metadata (pinder.core.index.utils.SupplementaryData attribute) safe_fetch_entry_annotations() (in module pinder.data.annotation.graphql) safe_get_eval_metrics() (in module pinder.eval.dockq.method) safe_load_sequence() (in module pinder.core.utils.pdb_utils) safe_read_contact_json() (in module pinder.data.alignment_utils) safe_read_csv() (in module pinder.data.csv_utils) sample_pairs_from_clusters() (in module pinder.data.graph_utils) save() (in module pinder.data.get_data) save_cluster_cache() (in module pinder.data.get_clusters) save_mapping_checkpoint() (in module pinder.data.get_data) save_stage_metadata() (in module pinder.data.pipeline.data_pipeline) scaled_score_metrics (pinder.data.config.ApoPairingConfig attribute) scatter_step() (in module pinder.data.pipeline.data_pipeline) ScatterConfig (class in pinder.data.config) score_threshold (pinder.data.config.GraphConfig attribute) score_type (pinder.data.config.FoldseekConfig attribute) (pinder.data.config.MMSeqsConfig attribute) seed (pinder.data.config.ClusterConfig attribute) select_monomer() (in module pinder.core.loader.loader) select_potential_apo() (in module pinder.data.get_apo) select_top_n() (in module pinder.data.plot.performance) SelectAtomTypes (class in pinder.core.loader.transforms) sensitivity (pinder.data.config.FoldseekConfig attribute) (pinder.data.config.MMSeqsConfig attribute) sequence (pinder.core.loader.structure.Structure property) sequence_database (pinder.core.index.utils.SupplementaryData attribute) sequence_leakage_main() (in module pinder.data.qc.similarity_check) sequence_mapping() (in module pinder.data.get_data) set_canonical_chain_order() (in module pinder.core.structure.surgery) set_chain() (pinder.core.loader.structure.Structure method) set_common() (pinder.eval.dockq.biotite_dockq.BiotiteDockQ method) set_mapping_column_types() (in module pinder.core.index.utils) setup_foldseek_dbs() (in module pinder.data.foldseek_utils) setup_logger() (in module pinder.core.utils.log) setup_mmseqs_dbs() (in module pinder.data.foldseek_utils) side (pinder.core.index.id.Monomer attribute) skip_step() (in module pinder.data.pipeline.cache) source (pinder.core.index.id.Protein attribute) speed_mode (pinder.data.config.IalignConfig attribute) split (pinder.core.index.utils.IndexEntry attribute) split_annotation_types() (in module pinder.data.annotation.graphql) split_annotation_violins() (in module pinder.data.plot.annotations) split_monomer_dimer_mapping_pqts() (in module pinder.data.get_dimers) split_monomer_dimer_pdbs() (in module pinder.data.get_dimers) split_pinder_masked_unmasked() (in module pinder.data.plot.validity) sr_curve() (in module pinder.data.plot.performance) stack_filter_intersect() (in module pinder.core.structure.atoms) standardize_atom_array() (in module pinder.core.structure.atoms) stringify_dataclass() (in module pinder.core.utils.dataclass) strip_glob() (in module pinder.core.utils.paths) Structure (class in pinder.core.loader.structure) structure2tensor() (in module pinder.core.loader.geodata) structure2tensor_transform() (in module pinder.core.loader.dataset) StructureFilter (class in pinder.core.loader.filters) StructureTransform (class in pinder.core.loader.transforms) subsample_train() (in module pinder.data.qc.similarity_check) SubsetIds (class in pinder.eval.dockq.method) success_rate_by_annotation() (in module pinder.data.plot.categories) success_rate_by_chain_novelty() (in module pinder.data.plot.categories) success_rate_by_flexibility() (in module pinder.data.plot.categories) success_rate_by_neff() (in module pinder.data.plot.categories) sufficient_atom_types() (in module pinder.data.apo_utils) sufficient_residues() (in module pinder.data.apo_utils) summarize_putative_apo_pred_counts() (in module pinder.data.get_dimers) summarize_valid_systems() (in module pinder.eval.dockq.method) superimpose() (pinder.core.loader.structure.Structure method) superimpose_chain() (in module pinder.core.structure.superimpose) SuperposeToReference (class in pinder.core.loader.transforms) supplementary_metadata (pinder.core.index.utils.SupplementaryData attribute) SupplementaryData (class in pinder.core.index.utils) SUPPORTED_ACTIONS (class in pinder.methods) SUPPORTED_PAIRS (class in pinder.methods) Surface (pinder.core.loader.geodata.NodeRepresentation attribute) sync_pinder_structure_data() (in module pinder.core.index.utils) system_capri_hit_rate() (pinder.eval.dockq.method.MethodMetrics method) system_id_to_alignment() (in module pinder.data.qc.similarity_check) system_id_to_fsid_pair() (in module pinder.data.graph_utils) system_median() (pinder.eval.dockq.method.MethodMetrics method) system_monomer_to_fsid() (in module pinder.data.graph_utils) system_oracle() (pinder.eval.dockq.method.MethodMetrics method) system_to_pdb_chain_id() (in module pinder.data.graph_utils) T t_name (pinder.data.alignment_utils.Domain attribute) (pinder.data.alignment_utils.DomainInfo attribute) task_step() (in module pinder.data.pipeline.data_pipeline) teal (pinder.data.plot.plot.Colors attribute) template (pinder.data.plot.plot.DarkTheme attribute) (pinder.data.plot.plot.LightTheme attribute) (pinder.data.plot.plot.Theme attribute) tend (pinder.data.alignment_utils.Alignment attribute) test_system (pinder.core.index.utils.IndexEntry property) text_marker_line_color (pinder.data.plot.plot.DarkTheme attribute) (pinder.data.plot.plot.LightTheme attribute) (pinder.data.plot.plot.Theme attribute) Theme (class in pinder.data.plot.plot) three_to_one() (in module pinder.core.utils.pdb_utils) tick_color (pinder.data.plot.plot.DarkTheme attribute) (pinder.data.plot.plot.LightTheme attribute) (pinder.data.plot.plot.Theme attribute) timeit() (in module pinder.core.utils.timer) title (pinder.core.utils.cloud.Error attribute) (pinder.core.utils.cloud.GCPError attribute) (pinder.core.utils.cloud.GCPTimeOutError attribute) tlen (pinder.data.alignment_utils.Alignment attribute) to_pdb() (pinder.core.loader.structure.Structure method) to_residue (pinder.core.index.id.Protein attribute) to_undirected_class() (pinder.data.graph_utils.InterfaceGraph method) tokenized_sequence (pinder.core.loader.structure.Structure property) TooFewChainsError top_k() (pinder.eval.dockq.method.MethodMetrics method) top_k_oracle() (pinder.eval.dockq.method.MethodMetrics method) top_n (pinder.data.config.ClusterConfig attribute) top_percentile() (pinder.eval.dockq.method.MethodMetrics method) TRAIN (pinder.methods.SUPPORTED_ACTIONS attribute) train() (in module pinder.methods.main) transform() (pinder.core.loader.transforms.RandomLigandTransform method) (pinder.core.loader.transforms.SelectAtomTypes method) (pinder.core.loader.transforms.StructureTransform method) (pinder.core.loader.transforms.SuperposeToReference method) (pinder.core.loader.transforms.TransformBase method) transform_struct() (pinder.core.loader.transforms.RandomLigandTransform static method) TransformBase (class in pinder.core.loader.transforms) transient_interface_metadata (pinder.core.index.utils.SupplementaryData attribute) TransientInterfaceConfig (class in pinder.data.config) tree() (in module pinder.core.utils.paths) tstart (pinder.data.alignment_utils.Alignment attribute) two_char_batch_size (pinder.data.config.ScatterConfig attribute) two_char_code_rsync() (in module pinder.data.pipeline.tasks) U unbound_difficulty() (pinder.core.index.system.PinderSystem method) unbound_rmsd() (pinder.core.index.system.PinderSystem method) unbound_rmsd_with_mask_fallback() (in module pinder.core.index.system) uniprot (pinder.core.index.id.Protein attribute) uniprot_L (pinder.core.index.utils.IndexEntry attribute) uniprot_leakage_main() (in module pinder.data.qc.uniprot_leakage) uniprot_map (pinder.core.loader.structure.Structure attribute) uniprot_mapping (pinder.core.loader.structure.Structure property) uniprot_R (pinder.core.index.utils.IndexEntry attribute) unordered_set_product() (in module pinder.data.find_transitive_hits) update_axes() (in module pinder.data.plot.figure_utils) update_index_cmd() (in module pinder.core.index.utils) update_layout() (in module pinder.data.plot.figure_utils) update_letters() (in module pinder.core.utils.constants) UPLOAD (pinder.core.utils.cloud.Gsutil attribute) upper_threshold (pinder.data.config.GraphConfig attribute) V valid_structure() (in module pinder.data.apo_utils) validate_apo_monomer() (in module pinder.data.apo_utils) validate_schemas() (in module pinder.data.get_dimers) validate_system_id() (in module pinder.eval.dockq.method) validity_bar_plot() (in module pinder.data.plot.validity) view_potential_leaks() (in module pinder.data.qc.utils) violin_marker_line_color (pinder.data.plot.plot.DarkTheme attribute) (pinder.data.plot.plot.LightTheme attribute) ViolinPlot (class in pinder.data.plot.plot) violinplot() (pinder.data.plot.plot.ViolinPlot method) visualize_data() (in module pinder.data.qc.pfam_diversity) W white (pinder.data.plot.plot.Colors attribute) whitepurple (pinder.data.plot.plot.Colors attribute) write() (pinder.core.loader.writer.PinderClusteredWriter method) (pinder.core.loader.writer.PinderDefaultWriter method) (pinder.core.loader.writer.PinderWriterBase method) write_alignment() (in module pinder.data.qc.similarity_check) write_fig() (in module pinder.data.plot.figure_utils) write_interface_dict() (in module pinder.data.alignment_utils) write_pdb() (in module pinder.core.structure.atoms) Y yaml_reader() (in module pinder.methods.main) year_month() (in module pinder.data.pipeline.data_pipeline)
