API reference#
Subpackages#
- pinder.core package
- Subpackages
- pinder.core.index package
- Submodules
- pinder.core.index.id module
- pinder.core.index.system module
FolderNamesunbound_rmsd_with_mask_fallback()PinderSystemPinderSystem.entryPinderSystem.pdbs_pathPinderSystem.mappings_pathPinderSystem.nativePinderSystem.holo_receptorPinderSystem.holo_ligandPinderSystem.aligned_holo_RPinderSystem.aligned_holo_LPinderSystem.apo_receptorPinderSystem.apo_ligandPinderSystem.pred_receptorPinderSystem.pred_ligandPinderSystem.filter_common_uniprot_res()PinderSystem.create_masked_bound_unbound_complexes()PinderSystem.create_complex()PinderSystem.create_apo_complex()PinderSystem.create_pred_complex()PinderSystem.unbound_rmsd()PinderSystem.unbound_difficulty()PinderSystem.apo_monomer_difficulty()PinderSystem.download_entry()PinderSystem.filepathsPinderSystem.metadataPinderSystem.pymol_scriptPinderSystem.load_alt_apo_structure()PinderSystem.load_structure()
- pinder.core.index.utils module
get_pinder_location()get_pinder_bucket_root()get_index_location()get_index()get_metadata()get_extra_metadata()SupplementaryDataSupplementaryData.sequence_databaseSupplementaryData.supplementary_metadataSupplementaryData.entity_metadataSupplementaryData.chain_metadataSupplementaryData.ecod_metadataSupplementaryData.enzyme_classification_metadataSupplementaryData.interface_annotationsSupplementaryData.sabdab_metadataSupplementaryData.monomer_neffSupplementaryData.paired_neffSupplementaryData.transient_interface_metadataSupplementaryData.ialign_split_similarity_labels
get_supplementary_data()get_sequence_database()download_dataset()get_arg_parser_args()download_pinder_cmd()update_index_cmd()get_missing_blobs()sync_pinder_structure_data()IndexEntryIndexEntry.model_configIndexEntry.splitIndexEntry.idIndexEntry.pdb_idIndexEntry.cluster_idIndexEntry.cluster_id_RIndexEntry.cluster_id_LIndexEntry.pinder_sIndexEntry.pinder_xlIndexEntry.pinder_af2IndexEntry.uniprot_RIndexEntry.uniprot_LIndexEntry.holo_R_pdbIndexEntry.holo_L_pdbIndexEntry.predicted_R_pdbIndexEntry.predicted_L_pdbIndexEntry.apo_R_pdbIndexEntry.apo_L_pdbIndexEntry.apo_R_pdbsIndexEntry.apo_L_pdbsIndexEntry.holo_RIndexEntry.holo_LIndexEntry.predicted_RIndexEntry.predicted_LIndexEntry.apo_RIndexEntry.apo_LIndexEntry.apo_R_qualityIndexEntry.apo_L_qualityIndexEntry.chain1_neffIndexEntry.chain2_neffIndexEntry.chain_RIndexEntry.chain_LIndexEntry.contains_antibodyIndexEntry.contains_antigenIndexEntry.contains_enzymeIndexEntry.pdb_path()IndexEntry.mapping_path()IndexEntry.pdb_pathsIndexEntry.mapping_pathsIndexEntry.pinder_idIndexEntry.pinder_pdbIndexEntry.apo_R_altIndexEntry.apo_L_altIndexEntry.homodimerIndexEntry.test_systemIndexEntry.model_computed_fieldsIndexEntry.model_fields
MetadataEntryMetadataEntry.model_configMetadataEntry.idMetadataEntry.entry_idMetadataEntry.methodMetadataEntry.dateMetadataEntry.release_dateMetadataEntry.resolutionMetadataEntry.labelMetadataEntry.probabilityMetadataEntry.chain1_idMetadataEntry.chain2_idMetadataEntry.assemblyMetadataEntry.assembly_detailsMetadataEntry.oligomeric_detailsMetadataEntry.oligomeric_countMetadataEntry.biol_detailsMetadataEntry.complex_typeMetadataEntry.chain_1MetadataEntry.asym_id_1MetadataEntry.chain_2MetadataEntry.asym_id_2MetadataEntry.length1MetadataEntry.length2MetadataEntry.length_resolved_1MetadataEntry.length_resolved_2MetadataEntry.number_of_components_1MetadataEntry.number_of_components_2MetadataEntry.link_densityMetadataEntry.planarityMetadataEntry.max_var_1MetadataEntry.max_var_2MetadataEntry.num_atom_typesMetadataEntry.n_residue_pairsMetadataEntry.n_residuesMetadataEntry.buried_sasaMetadataEntry.intermolecular_contactsMetadataEntry.charged_charged_contactsMetadataEntry.charged_polar_contactsMetadataEntry.charged_apolar_contactsMetadataEntry.polar_polar_contactsMetadataEntry.apolar_polar_contactsMetadataEntry.apolar_apolar_contactsMetadataEntry.interface_atom_gaps_4AMetadataEntry.missing_interface_residues_4AMetadataEntry.interface_atom_gaps_8AMetadataEntry.missing_interface_residues_8AMetadataEntry.entity_id_RMetadataEntry.entity_id_LMetadataEntry.pdb_strand_id_RMetadataEntry.pdb_strand_id_LMetadataEntry.ECOD_names_RMetadataEntry.ECOD_names_LMetadataEntry.pinder_idMetadataEntry.model_computed_fieldsMetadataEntry.model_fields
fix_index()fix_metadata()downcast_dtypes()set_mapping_column_types()
- Module contents
- pinder.core.loader package
- Submodules
- pinder.core.loader.dataset module
structure2tensor_transform()pad_to_max_length()pad_and_stack()collate_complex()collate_batch()PinderDatasetPPIDatasetPPIDataset.raw_file_namesPPIDataset.processed_file_namesPPIDataset.process_single_file()PPIDataset.process_single_file_parallel()PPIDataset.process_parallel()PPIDataset.process()PPIDataset.len()PPIDataset.get()PPIDataset.get_filename()PPIDataset.get_filename_idx()PPIDataset.load_filename()
get_geo_loader()get_torch_loader()
- pinder.core.loader.filters module
PinderFilterBaseStructureFilterMinAtomTypesFilterFilterMetadataFieldsChainQueryDualChainQueryResidueCountAtomTypeCountCompleteBackBoneCheckChainElongationDetachedChainQueryCheckContactsFilterByResidueCountFilterByMissingHoloFilterSubByContactsFilterByHoloElongationFilterDetachedHoloPinderFilterSubBaseFilterSubLengthsFilterSubRmsdsFilterByHoloOverlapFilterByHoloSeqIdentityFilterSubByAtomTypesFilterSubByChainQueryFilterByElongationFilterDetachedSub
- pinder.core.loader.geodata module
- pinder.core.loader.loader module
- pinder.core.loader.structure module
reverse_dict()StructureStructure.filepathStructure.uniprot_mapStructure.pinder_idStructure.atom_arrayStructure.pdb_engineStructure.read_pdb()Structure.to_pdb()Structure.filter()Structure.set_chain()Structure.get_per_chain_seq_alignments()Structure.align_common_sequence()Structure.get_contacts()Structure.get_interface_mask()Structure.get_interface_residues()Structure.superimpose()Structure.uniprot_mappingStructure.resolved_mappingStructure.resolved_pdb2uniprotStructure.resolved_uniprot2pdbStructure.coordsStructure.dataframeStructure.backbone_maskStructure.calpha_maskStructure.n_atomsStructure.chainsStructure.chain_sequenceStructure.sequenceStructure.fastaStructure.tokenized_sequenceStructure.residue_namesStructure.residuesStructure.atom_namesStructure.b_factor
find_potential_interchain_bonded_atoms()mask_common_uniprot()canonical_atom_type_mask()backbone_atom_tensor()
- pinder.core.loader.transforms module
- pinder.core.loader.utils module
- pinder.core.loader.writer module
- Module contents
- pinder.core.structure package
- Submodules
- pinder.core.structure.atoms module
biotite_pdbxfile()biotite_pdbfile()rust_pdbfile()atom_array_from_pdb_file()atom_vdw_radius()backbone_mask()mask_from_res_list()apply_mask()filter_atoms()get_backbone_atom_masks()assign_receptor_ligand()renumber_res_ids()standardize_atom_array()stack_filter_intersect()get_seq_alignments()get_seq_identity()calc_num_mismatches()align_sequences()resn2seq()get_seq_aligned_structures()get_per_chain_seq_alignments()invert_chain_seq_map()get_buried_sasa()get_resolved_resi_from_atom_array()get_resolved_resi()write_pdb()rename_chains()cif_to_pdb()normalize_orientation()
- pinder.core.structure.contacts module
- pinder.core.structure.models module
- pinder.core.structure.superimpose module
- pinder.core.structure.surgery module
- Module contents
- pinder.core.submit package
- pinder.core.utils package
- Submodules
- 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
- Module contents
- pinder.core.index package
- Module contents
- Subpackages
- pinder.data package
- Subpackages
- pinder.data.annotation package
- Submodules
- 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
run_graphql_annotation_query()fetch_entry_annotations()parse_pfam()parse_ec()parse_polymer_entity_instance()cast_entity_info_lists()add_entity_info()parse_annotation_data()csv_format_pfam()csv_format_features()csv_format_annotations()safe_fetch_entry_annotations()populate_rcsb_annotations()split_annotation_types()extract_feature_positions()cast_incompatible_annotation_columns()cast_incompatible_feature_columns()collate_csvs()collect_csvs_by_group()collect_rcsb_annotations()
- pinder.data.annotation.interface_gaps module
- pinder.data.annotation.planarity module
- pinder.data.annotation.sabdab module
- Module contents
- pinder.data.pipeline package
- Submodules
- pinder.data.pipeline.cache module
- pinder.data.pipeline.constants module
- pinder.data.pipeline.data_pipeline module
save_stage_metadata()year_month()task_step()scatter_step()DataIngestPipelineDataIngestPipeline.run()DataIngestPipeline.run_stage()DataIngestPipeline.generate_download_rcsb_files_tasks()DataIngestPipeline.download_rcsb_files()DataIngestPipeline.generate_cif_ingest_tasks()DataIngestPipeline.ingest_rcsb_files()DataIngestPipeline.generate_pisa_annotation_tasks()DataIngestPipeline.get_pisa_annotations()DataIngestPipeline.generate_rcsb_annotation_tasks()DataIngestPipeline.get_rcsb_annotations()DataIngestPipeline.join_rcsb_annotations()DataIngestPipeline.generate_dimer_annotation_tasks()DataIngestPipeline.get_dimer_annotations()DataIngestPipeline.collect_dimer_annotations()DataIngestPipeline.generate_foldseek_contacts_tasks()DataIngestPipeline.get_dimer_contacts()DataIngestPipeline.collect_foldseek_contacts()DataIngestPipeline.generate_populate_entry_tasks()DataIngestPipeline.populate_entries()DataIngestPipeline.generate_populate_predicted_tasks()DataIngestPipeline.populate_predicted()DataIngestPipeline.index_dimers()DataIngestPipeline.add_predicted_monomers()DataIngestPipeline.get_valid_apo_monomers()DataIngestPipeline.generate_apo_pairing_metric_tasks()DataIngestPipeline.get_apo_pairing_metrics()DataIngestPipeline.join_apo_pairing_metrics()DataIngestPipeline.add_apo_pairings_to_index()DataIngestPipeline.create_foldseek_dbs()DataIngestPipeline.generate_foldseek_tasks()DataIngestPipeline.run_foldseek()DataIngestPipeline.join_foldseek()DataIngestPipeline.create_mmseqs_dbs()DataIngestPipeline.generate_mmseqs_tasks()DataIngestPipeline.run_mmseqs()DataIngestPipeline.join_mmseqs()DataIngestPipeline.construct_interface_graph()DataIngestPipeline.construct_foldseek_graph()DataIngestPipeline.construct_mmseqs_graph()DataIngestPipeline.cluster()DataIngestPipeline.generate_find_leakage_tasks()DataIngestPipeline.find_leakage()DataIngestPipeline.get_transitive_hits()DataIngestPipeline.get_af2_hard_difficulty_transitive_hits()DataIngestPipeline.get_splits()DataIngestPipeline.get_alignment_similarity()DataIngestPipeline.construct_final_index()DataIngestPipeline.get_test_set()
- pinder.data.pipeline.scatter module
- pinder.data.pipeline.tasks module
- Module contents
- pinder.data.plot package
- Submodules
- 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
patch_af2mm_monomer_types()get_dockq_metrics()get_ialign_metrics()get_penalized_dockq()select_top_n()remove_af2mm_nonaf2()get_subsampled_train()get_deleaked_sr()get_diffdock_ialign_sr()get_timesplit_pinder_xl_ids()get_af2mm_ialign_sr()get_af2mm_neff_sr()sr_curve()reference_based_violin_plots()main()
- pinder.data.plot.plot module
ColorsColors.whiteColors.grayColors.pinkColors.brightpinkColors.pinderColors.palepurpleColors.whitepurpleColors.purpleColors.redpurpleColors.greenColors.palegreenColors.tealColors.bluish_greenColors.blueColors.cb_blueColors.cb_skyblueColors.iceColors.deepiceColors.paleblueColors.denimColors.navyColors.midnightColors.cb_orangeColors.cb_vermillionColors.cb_yellowColors.palette()Colors.colorsColors.lightColors.darkColors.colorblind_pairedColors.bluesColors.pinksColors.purplesColors.neutralColors.pairedColors.brightColors.pastel
ThemeLightThemeDarkThemeformat_axes()format_text()format_legend()format_facets()apply_formatting()LinePlotBarPlotViolinPlot
- pinder.data.plot.run module
- pinder.data.plot.structure_case_studies module
- pinder.data.plot.validity module
- Module contents
- pinder.data.qc package
- Submodules
- 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
load_data()process_test_table()align_sequences()write_alignment()generate_alignments()get_processed_alignments()load_train_system_id_mapping()get_pdb_chain_uni()system_id_to_alignment()alignments_to_dual_alignment()get_aligned_indices()get_aligned_interface_indices()analyze_leakage()subsample_train()sequence_leakage_main()
- pinder.data.qc.uniprot_leakage module
- pinder.data.qc.utils module
- Module contents
- pinder.data.annotation package
- Submodules
- pinder.data.alignment_utils module
DomainInfoDomainAlignmentAlignment.pdbid1Alignment.pdbid2Alignment.alntmscoreAlignment.qstartAlignment.qendAlignment.qlenAlignment.tstartAlignment.tendAlignment.tlenAlignment.alnlenAlignment.from_line()Alignment.from_foldseek_line()Alignment.from_ecod_info()Alignment.indices1()Alignment.indices2()Alignment.flip_query_and_target()
Interfaceget_foldseek_contacts()get_foldseek_numbering()get_foldseek_dimer_contacts()generate_dimer_foldseek_contacts()populate_foldseek_contacts()safe_read_contact_json()load_contact_info()collect_contact_jsons()load_interface_pkl()write_interface_dict()get_interfaces_from_config()
- pinder.data.apo_utils module
sufficient_atom_types()sufficient_residues()valid_structure()validate_apo_monomer()holo_apo_seq_identity()chain_instance_from_chain()remove_apo_chain_copies()remove_dimer_chain_copies()hybrid_align()get_superimposed_metrics()get_sequence_based_metrics()get_unbound_id()get_apo_pairing_metrics_for_id()calculate_frac_monomer_dimer_overlap()
- pinder.data.config module
PinderDataGenConfigContactConfigTransientInterfaceConfigFoldseekConfigMMSeqsConfigGraphConfigScatterConfigClusterConfigClusterConfig.seedClusterConfig.canonical_methodClusterConfig.edge_weightClusterConfig.foldseek_cluster_edge_thresholdClusterConfig.foldseek_edge_thresholdClusterConfig.foldseek_af2_difficulty_thresholdClusterConfig.mmseqs_edge_thresholdClusterConfig.resolution_thrClusterConfig.min_chain_lengthClusterConfig.min_atom_typesClusterConfig.max_var_thrClusterConfig.oligomeric_countClusterConfig.methodClusterConfig.interface_atom_gaps_4AClusterConfig.prodigy_labelClusterConfig.number_of_componentsClusterConfig.alphafold_cutoff_dateClusterConfig.depth_limitClusterConfig.max_node_degreeClusterConfig.top_nClusterConfig.min_depth_2_hits_with_commClusterConfig.max_depth_2_hits_with_commClusterConfig.max_depth_2_hits
ApoPairingConfigApoPairingConfig.apo_chainApoPairingConfig.contact_radApoPairingConfig.backbone_onlyApoPairingConfig.heavy_onlyApoPairingConfig.min_atom_typesApoPairingConfig.min_residuesApoPairingConfig.min_holo_resolved_fracApoPairingConfig.align_methodApoPairingConfig.max_refine_rmsdApoPairingConfig.min_aligned_apo_res_fracApoPairingConfig.min_seq_identityApoPairingConfig.max_interface_miss_fracApoPairingConfig.max_frac_monomer_dimer_sequenceApoPairingConfig.invalid_coverage_upper_boundApoPairingConfig.invalid_coverage_lower_boundApoPairingConfig.scaled_score_metrics
IalignConfigget_config_hash()
- pinder.data.csv_utils module
- pinder.data.find_transitive_hits module
get_potential_representatives()get_test_conversion_dicts()get_proto_splits_pindex()get_leakage_dict()get_transitive_hits()cluster_leaks()batch_cluster_leaks()get_leak_map_for_id()map_leak_pairs()find_split_leakage()map_systems_to_fsid_pairs()map_fsid_pair_to_systems()deep_merge_dict()intersection_unordered_product()unordered_set_product()len_unordered_set_product()
- pinder.data.foldseek_utils module
fasta2dict()create_fasta_from_systems()extract_fasta_from_pdb()parallel_extract_fasta()create_fasta_from_foldseek_inputs()create_foldseek_input_dir()run_foldseek()run_mmseqs()create_dbs()run_db_vs_db()run_foldseek_db_pair()create_dbs_and_run()setup_foldseek_dbs()collate_foldseek_alignments()collate_mmseqs_alignments()aln_to_df()filter_foldseek_edges()filter_mmseqs_edges()alignment_to_parquet()run_foldseek_on_pinder_chains()run_mmseqs_on_pinder_chains()setup_mmseqs_dbs()run_mmseqs_db_pair()
- 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
ingest_rscb_files()ingest_mmcif_list()generate_bio_assembly()read_mmcif_file()convert_category()replace_with_nan()get_mmcif_category()infer_uniprot_from_mapping()sequence_mapping()get_entities()get_metadata()get_structure_chains()get_interacting_chains()save()save_mapping_checkpoint()process_mmcif()
- pinder.data.get_dimers module
primary_dimer_index_from_dimers()merge_index_and_entities()validate_schemas()summarize_putative_apo_pred_counts()merge_metadata()cast_resi_to_valid_str()load_mapping_chains()collate_chain_info()collate_entity_pqts()populate_predicted()get_pdb_entry_dirs()get_monomers_from_mapping_pqts()get_dimers_from_dimer_pdbs()get_af_monomers_from_monomer_ids()populate_entries()populate_predicted_from_monomers()get_dimers_from_interface_annotations()get_matching_entry_files()split_monomer_dimer_mapping_pqts()split_monomer_dimer_pdbs()get_monomer_index_from_files()get_dimer_index_from_files()get_populated_entries()index_dimers()find_intersection()get_per_chain_ecod_summary()add_ecod_to_metadata()add_enzyme_classification()add_predicted_monomers_to_index()get_dimer_interchain_bond_atom_info()label_potential_transient_interfaces()
- pinder.data.get_splits module
- pinder.data.get_test_set module
- pinder.data.graph_utils module
get_alignment_graph_with_indices()sample_pairs_from_clusters()system_to_pdb_chain_id()system_id_to_fsid_pair()system_monomer_to_fsid()interface_monomer_to_system_monomer()get_interface_graph()cluster_from_graph()get_node_to_cluster_mapping()clean_interface_graph()load_graph_pickle()construct_interface_graph()construct_graph_from_alignment()construct_interface_cleaned_graph()construct_interface_alignment_graph()InterfaceGraphMaxGraph
- pinder.data.rcsb_rsync module
- pinder.data.run module
- pinder.data.system module
- Module contents
- Subpackages
- pinder.eval package
- Subpackages
- pinder.eval.clashes package
- pinder.eval.dockq package
- Submodules
- pinder.eval.dockq.biotite_dockq module
- pinder.eval.dockq.method module
InvalidChainsErrorTooFewChainsErrorExpectedChainsNotFoundErrorvalidate_system_id()get_valid_eval_systems()SubsetIdsget_expected_counts()summarize_valid_systems()download_entry()get_eval_metrics()safe_get_eval_metrics()get_eval_metrics_all_methods()get_method_eval_metrics()add_pinder_set()get_missing_system_penalty_metrics()CapriClassMethodMetricsMethodMetrics.metricsMethodMetrics.add_rank_column()MethodMetrics.get_metrics()MethodMetrics.oracle_median_summary()MethodMetrics.get_leaderboard_entry()MethodMetrics.median_oracle()MethodMetrics.get_hit_rates()MethodMetrics.top_k()MethodMetrics.top_k_oracle()MethodMetrics.top_percentile()MethodMetrics.system_oracle()MethodMetrics.system_median()MethodMetrics.method_median()MethodMetrics.method_oracle()MethodMetrics.system_capri_hit_rate()MethodMetrics.median_capri_hit_rate()MethodMetrics.histogram_plot()
- pinder.eval.dockq.metrics module
- pinder.eval.dockq.unbound module
- Module contents
- Submodules
- pinder.eval.create_submission module
- pinder.eval.run module
- Module contents
- Subpackages
- pinder.methods package
- Subpackages
- Submodules
- pinder.methods.main module
- Module contents