pinder.core package#
Subpackages#
- pinder.core.index package
- Submodules
- pinder.core.index.id module
- pinder.core.index.system module
FolderNamesPinderSystemPinderSystem.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
Module contents#
Namespace package for pinder-core.