Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W A add_ligand_hydrogens (plinder.core.structure.structure.Structure attribute) add_missing_atoms() (in module plinder.core.structure.ccd_template) add_sequence_ids_to_aligned_pocket_residues() (in module plinder.core.scores.custom) adjacency (plinder.data.annotations.ccd_ligand_dbs.ResidueGraph attribute) aggregate_scores() (plinder.data.annotations.get_similarity_scores.Scorer method) align_molecules() (in module plinder.data.annotations.get_similarity_scores) align_sequences() (in module plinder.core.structure.atoms) aligned_pocket_residues (plinder.core.scores.custom.CustomScoringResult attribute) (plinder.core.scores.custom.CustomSequenceScoringResult attribute) alignment_chain_lookup (plinder.core.scores.custom.CustomScoringAssets attribute) (plinder.data.annotations.get_similarity_scores.Scorer attribute) alternatives (plinder.core.structure.smallmols_similarity.RascalParityMatch attribute) annotate_cofactor_similarity() (in module plinder.data.annotations.get_similarity_scores) annotate_custom_cif_files() (in module plinder.core.scores.custom) annotate_ligand_3d_score_ability() (in module plinder.data.annotations.get_similarity_scores) annotate_ligand_similarity() (in module plinder.data.annotations.get_similarity_scores) annotate_prodigy_crystal_interface() (in module plinder.data.annotations.interface_utils) annotation (plinder.core.index.interface.PlinderInterface property) annotation_table (plinder.core.scores.custom.CustomScoringAssets attribute) (plinder.core.scores.custom.CustomStructureAnnotations attribute) AnnotationRow (class in plinder.data.annotations.save_utils) apolar_apolar_contacts (plinder.data.annotations.interface_utils.ProdigyCrystalAnnotation attribute) apolar_polar_contacts (plinder.data.annotations.interface_utils.ProdigyCrystalAnnotation attribute) apply_mask() (in module plinder.core.structure.atoms) arbitrary_types_allowed (plinder.core.structure.structure.Structure.Config attribute) archive (plinder.core.index.system.PlinderSystem property) assign_bond_orders_from_smiles() (in module plinder.data.annotations.cif_utils) asym_id (plinder.core.scores.entries.ChainView attribute) (plinder.core.scores.entries.LigandView attribute) atom_array (plinder.core.index.interface.PlinderInterface property) atom_array_from_cif_file() (in module plinder.core.structure.atoms) atom_array_summary_markdown_repr() (in module plinder.core.utils.dataclass) atoms (plinder.core.structure.smallmols_similarity.RascalParityMatch attribute) (plinder.data.annotations.ccd_ligand_dbs.ResidueGraph attribute) atoms_to_rdkit_mol() (in module plinder.data.annotations.cif_utils) auth_id (plinder.core.scores.entries.ChainView attribute) author_to_asym (plinder.core.scores.entries.EntryView attribute) B backend (plinder.core.scores.custom.SearchDatabaseBundle attribute) best_sequence_links (plinder.core.scores.custom.CustomSequenceScoringResult attribute) biotite_ciffile() (in module plinder.core.structure.atoms) biounit (plinder.data.annotations.save_utils.ReconstructedSystem attribute) biounit_chains (plinder.core.index.system.PlinderSystem property) biounit_id (plinder.core.index.interface.PlinderInterface property) (plinder.core.scores.entries.InterfaceView attribute) (plinder.data.annotations.interface_utils.ProteinInterface attribute) bonds (plinder.core.structure.ccd_template.ComponentTemplate attribute) (plinder.core.structure.smallmols_similarity.RascalParityMatch attribute) build_apo_candidate_manifest() (in module plinder.data.linked_apo) build_biounit() (in module plinder.data.annotations.cif_utils) build_ccd_ecfp_db() (in module plinder.data.annotations.ccd_ligand_dbs) build_ccd_mmp_db() (in module plinder.data.annotations.ccd_ligand_dbs) build_ccd_parity_scores() (in module plinder.data.annotations.ccd_ligand_dbs) build_ccd_tanimoto_scores() (in module plinder.data.annotations.ccd_ligand_dbs) build_interface_apo_candidate_manifest() (in module plinder.data.interface_apo) build_interface_apo_query_manifest() (in module plinder.data.interface_apo) build_ligand_affinity_table() (in module plinder.data.annotations.affinity) build_ligand_ccd_match() (in module plinder.data.annotations.ccd_ligand_dbs) build_ligand_similarity_annotations() (in module plinder.data.annotations.get_similarity_scores) C calculate_custom_interface_similarity_scores() (in module plinder.core.scores.custom) calculate_custom_protein_similarity_scores() (in module plinder.core.scores.custom) calculate_custom_similarity_scores() (in module plinder.core.scores.custom) calculate_interface_similarity_scores() (in module plinder.core.scores.reconstruct) candidate_map() (in module plinder.data.annotations.affinity) canonical_ligand_sdf_path() (in module plinder.data.annotations.get_similarity_scores) canonical_ligand_sdfs (plinder.core.index.system.PlinderSystem property) canonical_smiles() (in module plinder.data.annotations.ccd_ligand_dbs) ccd_code_residue_graph() (in module plinder.data.annotations.ccd_ligand_dbs) ccd_code_sequence() (in module plinder.data.annotations.ccd_ligand_dbs) ccd_component_table() (in module plinder.data.annotations.ccd_ligand_dbs) ccd_component_template() (in module plinder.core.structure.ccd_template) ccd_dbs_dir() (in module plinder.data.annotations.ccd_ligand_dbs) ccd_fingerprint_path() (in module plinder.data.annotations.ccd_ligand_dbs) ccd_heavy_atom_names() (in module plinder.core.structure.ccd_template) ccd_ids (plinder.data.annotations.ccd_ligand_dbs.CcdIndex attribute) ccd_index() (in module plinder.data.annotations.ccd_ligand_dbs) ccd_node_similarity() (in module plinder.data.annotations.ccd_ligand_dbs) ccd_parity_path() (in module plinder.data.annotations.ccd_ligand_dbs) ccd_universe_signature() (in module plinder.data.annotations.ccd_ligand_dbs) CcdIndex (class in plinder.data.annotations.ccd_ligand_dbs) CcdMatch (class in plinder.data.annotations.ccd_ligand_dbs) CcdParityTable (class in plinder.data.annotations.ccd_ligand_dbs) chain_1 (plinder.core.scores.entries.InterfaceView attribute) (plinder.data.annotations.interface_utils.ProteinInterface attribute) chain_1_residue_indices (plinder.data.annotations.interface_utils.ProteinInterface attribute) chain_1_residue_number_to_index (plinder.core.scores.entries.InterfaceView attribute) chain_1_residue_numbers (plinder.data.annotations.interface_utils.ProteinInterface attribute) chain_2 (plinder.core.scores.entries.InterfaceView attribute) (plinder.data.annotations.interface_utils.ProteinInterface attribute) chain_2_residue_indices (plinder.data.annotations.interface_utils.ProteinInterface attribute) chain_2_residue_number_to_index (plinder.core.scores.entries.InterfaceView attribute) chain_2_residue_numbers (plinder.data.annotations.interface_utils.ProteinInterface attribute) chain_cif_dir (plinder.core.scores.custom.CustomQueryInputs attribute) chain_manifest (plinder.core.scores.custom.CustomQueryInputs attribute) chain_pair_contact_areas() (in module plinder.data.annotations.contact_areas) chain_similarity_scores (plinder.core.scores.custom.CustomScoringResult attribute) (plinder.core.scores.custom.CustomSequenceScoringResult attribute) chain_structures (plinder.core.index.interface.PlinderInterface property) chain_type (plinder.core.scores.entries.ChainView attribute) chains (plinder.core.index.interface.PlinderInterface property) (plinder.core.scores.entries.EntryView attribute) (plinder.core.scores.entries.InterfaceView property) chains_for_alignment() (plinder.core.scores.entries.EntryView method) ChainView (class in plinder.core.scores.entries) charged_apolar_contacts (plinder.data.annotations.interface_utils.ProdigyCrystalAnnotation attribute) charged_charged_contacts (plinder.data.annotations.interface_utils.ProdigyCrystalAnnotation attribute) charged_polar_contacts (plinder.data.annotations.interface_utils.ProdigyCrystalAnnotation attribute) check_cif_bond_orders() (in module plinder.data.annotations.cif_utils) check_custom_mmcif_fields() (in module plinder.data.annotations.cif_utils) checked_key() (in module plinder.core.utils.http) cigar_alignment_sql() (in module plinder.core.scores.mapping) CloudPath() (plinder.core.utils.http.ReleaseClient method) cluster_alignments (plinder.core.scores.custom.SearchDatabaseBundle attribute) column_description_text() (in module plinder.data.annotations.utils) combine_scores() (in module plinder.data.annotations.get_similarity_scores) compare_stereo_to_template() (in module plinder.core.structure.smallmols_utils) complete_missing_atoms (plinder.core.structure.structure.Structure attribute) component_ccd_ids (plinder.data.annotations.ccd_ligand_dbs.CcdMatch attribute) component_sequence_identity() (in module plinder.data.annotations.ccd_ligand_dbs) ComponentTemplate (class in plinder.core.structure.ccd_template) composite_parity() (in module plinder.data.annotations.ccd_ligand_dbs) composite_similarity() (in module plinder.data.annotations.ccd_ligand_dbs) compute() (plinder.data.annotations.ccd_ligand_dbs.CcdParityTable class method) compute_ligand_fingerprints() (in module plinder.data.annotations.get_similarity_scores) contact_area (plinder.data.annotations.interface_utils.ProteinInterface attribute) ContextConfig (class in plinder.core.utils.config) conversion_target (plinder.core.scores.custom.SearchDatabaseBundle attribute) coordinates (plinder.core.structure.inputs.StructureInput attribute) coverage (plinder.core.scores.custom.CustomProteinSearchConfig attribute) coverage() (plinder.core.structure.smallmols_similarity.RascalParityMatch method) (plinder.data.annotations.ccd_ligand_dbs.CcdParityTable method) create_custom_query_databases() (in module plinder.core.scores.custom) create_db() (in module plinder.data.databases) create_db_index() (in module plinder.data.databases) created_database_is_complete() (in module plinder.data.databases) cross_ligand_chemical_similarity() (in module plinder.core.scores.ligand) CustomProteinSearchConfig (class in plinder.core.scores.custom) CustomQueryDatabases (class in plinder.core.scores.custom) CustomQueryInputs (class in plinder.core.scores.custom) CustomScoringAssets (class in plinder.core.scores.custom) CustomScoringResult (class in plinder.core.scores.custom) CustomSequenceScoringResult (class in plinder.core.scores.custom) CustomStructureAnnotations (class in plinder.core.scores.custom) D data_dir (plinder.core.release.PlinderRelease attribute) database_identifiers() (in module plinder.data.databases) databases (plinder.core.scores.custom.CustomQueryDatabases attribute) DataConfig (class in plinder.core.utils.config) db_dir (plinder.data.annotations.get_similarity_scores.Scorer attribute) decode_cigar_residue_positions() (in module plinder.core.scores.mapping) DEFAULT_PROBE_RADIUS (in module plinder.data.annotations.contact_areas) departed_leaving_atoms() (in module plinder.core.structure.ccd_template) description_excluded_from_column_docs() (in module plinder.data.annotations.utils) description_excluded_from_flat_export() (in module plinder.data.annotations.utils) detect_protein_interfaces() (in module plinder.data.annotations.interface_utils) directed() (plinder.data.annotations.ccd_ligand_dbs.CcdParityTable method) DocBaseModel (class in plinder.data.annotations.utils) document_properties() (plinder.data.annotations.utils.DocBaseModel class method) document_properties_to_tsv() (plinder.data.annotations.utils.DocBaseModel class method) donors (plinder.data.annotations.ccd_ligand_dbs.ResidueGraph attribute) donors_of() (plinder.data.annotations.ccd_ligand_dbs.ResidueGraph method) download_alphafold_cif_file() (in module plinder.core.utils.io) download_paths() (in module plinder.core.utils.cpl) download_pdb_mmcifs() (in module plinder.core.utils.io) download_plinder_cmd() (in module plinder.core.index.utils) drop_self_clashing_symmetry_copies() (in module plinder.data.annotations.cif_utils) E elements (plinder.core.structure.ccd_template.ComponentTemplate attribute) enrich_cif_with_ccd_bonds() (in module plinder.data.annotations.cif_utils) enrich_cif_with_smiles_bonds() (in module plinder.data.annotations.cif_utils) entity_id (plinder.core.scores.entries.ChainView attribute) entries (plinder.data.annotations.get_similarity_scores.Scorer attribute) entries_by_structure (plinder.core.scores.custom.CustomStructureAnnotations attribute) entry (plinder.core.index.system.PlinderSystem property) entry_chains (plinder.core.scores.custom.CustomScoringAssets attribute) (plinder.core.scores.custom.CustomStructureAnnotations attribute) entry_pdb_id (plinder.core.index.interface.PlinderInterface property) entry_views_from_df() (in module plinder.core.scores.entries) EntryTaxonomy (class in plinder.data.annotations.cif_utils) EntryView (class in plinder.core.scores.entries) evaluate_predictions() (in module plinder.eval.batch) evalue (plinder.core.scores.custom.CustomProteinSearchConfig attribute) evalue_for() (plinder.core.scores.custom.CustomProteinSearchConfig method) exact_search_database_paths() (in module plinder.data.databases) expand_alignment_cigar() (in module plinder.core.scores.alignment) expand_residue_positions() (in module plinder.core.scores.mapping) extract_ligand_links_to_neighbouring_chains() (in module plinder.data.annotations.interaction_utils) F fetch() (plinder.core.release.PlinderRelease method) file_sha256() (in module plinder.core.utils.files) FileMetadata (class in plinder.core.utils.http) filter() (plinder.core.structure.structure.Structure method) finalize_monomer_similarity_scores() (in module plinder.data.monomer_similarity) find_metal_bridges() (in module plinder.data.annotations.interaction_utils) find_ph_mentions() (in module plinder.data.annotations.cif_utils) find_protein_chain_contacts() (in module plinder.data.annotations.interface_utils) find_structure_files() (in module plinder.core.structure.inputs) find_water_bridges() (in module plinder.data.annotations.interaction_utils) fingerprint_basis_sha256() (in module plinder.data.annotations.get_similarity_scores) foldseek_config (plinder.data.annotations.get_similarity_scores.Scorer attribute) foldseek_evalue (plinder.core.scores.custom.CustomProteinSearchConfig attribute) force_update (plinder.core.utils.config.DataConfig attribute) from_path() (plinder.core.structure.inputs.StructureInput class method) G generate_input_conformer() (in module plinder.core.structure.smallmols_utils) get() (plinder.data.annotations.save_utils.AnnotationRow method) get_chain_external_mappings() (in module plinder.data.annotations.cif_utils) get_cluster_column_descriptions() (in module plinder.data.docs) get_column_descriptions() (in module plinder.data.docs) get_column_mapr() (plinder.data.annotations.get_similarity_scores.Scorer method) get_config() (plinder.data.annotations.get_similarity_scores.Scorer method) get_config_hash() (in module plinder.core.utils.config) get_covalent_connections() (in module plinder.data.annotations.interaction_utils) get_db_ids() (in module plinder.data.databases) get_descriptions_and_types() (plinder.data.annotations.utils.DocBaseModel class method) get_entry_info() (in module plinder.data.annotations.cif_utils) get_entry_ph_range() (in module plinder.data.annotations.cif_utils) get_entry_taxonomy() (in module plinder.data.annotations.cif_utils) get_feature_map_score() (in module plinder.data.annotations.get_similarity_scores) get_label_asym_sequences() (in module plinder.data.annotations.cif_utils) get_legacy_chain_instance_mapping() (in module plinder.data.annotations.cif_utils) get_ligand_of_interest() (in module plinder.data.annotations.cif_utils) get_ligand_pair_pocket_pli_scores() (plinder.data.annotations.get_similarity_scores.Scorer method) get_ligand_pair_shape_scores() (plinder.data.annotations.get_similarity_scores.Scorer method) get_ligand_pocket_scores() (plinder.data.annotations.get_similarity_scores.Scorer method) get_matched_template() (in module plinder.core.structure.smallmols_utils) get_mmcif_revision() (in module plinder.data.annotations.cif_utils) get_model_count() (in module plinder.data.annotations.cif_utils) get_pdb_mmcif() (in module plinder.core.utils.io) get_pdb_revision() (in module plinder.core.utils.io) get_per_residue_atoms() (in module plinder.core.structure.atoms) get_per_residue_mask() (in module plinder.core.structure.atoms) get_plinder_path() (in module plinder.core.utils.cpl) get_pocket_pli_scores() (plinder.data.annotations.get_similarity_scores.Scorer method) get_properties() (plinder.core.structure.structure.Structure class method) get_protein_chain_length() (plinder.data.annotations.get_similarity_scores.Scorer method) get_protein_receptor_chains() (plinder.data.annotations.get_similarity_scores.Scorer method) get_protein_scores() (plinder.data.annotations.get_similarity_scores.Scorer method) get_protein_scores_pair() (plinder.data.annotations.get_similarity_scores.Scorer method) get_residue_index_mapping_mask() (in module plinder.core.structure.atoms) get_score_df() (plinder.data.annotations.get_similarity_scores.Scorer method) get_scores() (plinder.data.annotations.get_similarity_scores.Scorer method) get_scores_apo_pred() (plinder.data.annotations.get_similarity_scores.Scorer method) get_scores_holo() (plinder.data.annotations.get_similarity_scores.Scorer method) get_sequence_similarity() (in module plinder.data.annotations.get_similarity_scores) get_sequence_similarity_helper() (in module plinder.data.annotations.get_similarity_scores) get_structure_with_altloc() (in module plinder.data.annotations.cif_utils) get_sucos_score() (in module plinder.data.annotations.get_similarity_scores) get_symmetry_mate_contacts() (in module plinder.data.annotations.interaction_utils) get_table_column_descriptions() (in module plinder.data.docs) get_template_to_mol_matches() (in module plinder.core.structure.smallmols_utils) get_unit_cell_with_altloc() (in module plinder.data.annotations.cif_utils) get_unknown_ligand_ids() (in module plinder.data.annotations.cif_utils) H heavy (plinder.core.structure.ccd_template.ComponentTemplate attribute) holo (plinder.core.scores.entries.ChainView attribute) holo_structure (plinder.core.index.system.PlinderSystem property) host_organism_names (plinder.data.annotations.cif_utils.EntryTaxonomy attribute) host_taxonomy_ids (plinder.data.annotations.cif_utils.EntryTaxonomy attribute) I id (plinder.core.scores.entries.InterfaceView attribute) (plinder.core.scores.entries.LigandView attribute) (plinder.core.scores.entries.SystemView attribute) (plinder.core.structure.structure.Structure attribute) identifier_map (plinder.core.scores.custom.CustomQueryDatabases attribute) include_pli_fident (plinder.data.annotations.get_similarity_scores.Scorer attribute) initialize() (plinder.core.structure.structure.Structure method) input_ligand_conformer_atom_array (plinder.core.structure.structure.Structure property) input_ligand_conformers (plinder.core.structure.structure.Structure property) input_ligand_conformers_coords (plinder.core.structure.structure.Structure property) input_ligand_templates (plinder.core.structure.structure.Structure property) input_sequence_full_atom_feat (plinder.core.structure.structure.Structure property) input_sequence_list_ordered_by_chain (plinder.core.structure.structure.Structure property) input_sequence_residue_mask_stacked (plinder.core.structure.structure.Structure property) inputs (plinder.core.scores.custom.CustomQueryDatabases attribute) install_database_directory() (in module plinder.data.databases) instance_chain (plinder.core.scores.entries.LigandView attribute) interactions_counter (plinder.core.scores.entries.LigandView attribute) (plinder.core.scores.entries.SystemView attribute) interface_annotations (plinder.core.scores.custom.CustomScoringAssets attribute) (plinder.core.scores.custom.CustomStructureAnnotations attribute) interface_cif (plinder.core.index.interface.PlinderInterface property) interface_residue_masks (plinder.core.index.interface.PlinderInterface property) interface_scores (plinder.core.scores.custom.CustomScoringResult attribute) interface_structure (plinder.core.index.interface.PlinderInterface property) interface_system_id() (in module plinder.data.annotations.interface_utils) InterfaceApoSelectionConfig (class in plinder.data.interface_apo) interfaces (plinder.core.scores.entries.EntryView attribute) InterfaceView (class in plinder.core.scores.entries) intermolecular_contacts (plinder.data.annotations.interface_utils.ProdigyCrystalAnnotation attribute) is_chemical_cluster_metric() (in module plinder.core.scores.metrics) is_connected (plinder.data.annotations.ccd_ligand_dbs.ResidueGraph property) is_dir (plinder.core.utils.http.FileMetadata attribute) is_ligand_level_metric() (in module plinder.core.scores.metrics) is_ligand_shape_comparable() (in module plinder.data.annotations.get_similarity_scores) is_offline() (in module plinder.core.utils.cpl) is_polypeptide (plinder.core.scores.entries.ChainView property) is_proper (plinder.core.scores.entries.LigandView attribute) is_shape_comparable (plinder.core.scores.entries.LigandView attribute) is_tree (plinder.data.annotations.ccd_ligand_dbs.ResidueGraph property) K key() (plinder.core.utils.http.ReleaseClient method) L label (plinder.data.annotations.interface_utils.ProdigyCrystalAnnotation attribute) labels (plinder.data.annotations.ccd_ligand_dbs.ResidueGraph attribute) leaving (plinder.core.structure.ccd_template.ComponentTemplate attribute) length (plinder.core.scores.entries.ChainView attribute) ligand_archives (plinder.core.scores.custom.CustomScoringAssets attribute) ligand_atom_array (plinder.core.structure.structure.Structure property) ligand_atom_features() (in module plinder.core.structure.smallmols_utils) ligand_chain_ordered (plinder.core.structure.structure.Structure property) ligand_features() (in module plinder.data.annotations.ccd_ligand_dbs) ligand_holo_chain_keys() (in module plinder.data.linked_apo) ligand_mols (plinder.core.index.system.PlinderSystem property) (plinder.core.structure.structure.Structure attribute) ligand_parity() (in module plinder.data.annotations.ccd_ligand_dbs) ligand_pharmacophore_records() (in module plinder.data.annotations.get_similarity_scores) ligand_score_manifest_payload() (in module plinder.data.annotations.get_similarity_scores) ligand_scores (plinder.core.scores.custom.CustomScoringResult attribute) ligand_scores() (in module plinder.data.annotations.get_similarity_scores) ligand_sdf_resolver (plinder.data.annotations.get_similarity_scores.Scorer attribute) ligand_sdf_root (plinder.core.scores.custom.CustomStructureAnnotations attribute) ligand_sdfs (plinder.core.index.system.PlinderSystem property) (plinder.core.structure.inputs.StructureInput attribute) (plinder.core.structure.structure.Structure attribute) ligand_similarity() (in module plinder.data.annotations.ccd_ligand_dbs) ligand_smiles (plinder.core.structure.structure.Structure attribute) ligand_structures (plinder.core.index.system.PlinderSystem property) ligand_template2resolved_atom_order_stacks (plinder.core.structure.structure.Structure property) ligands (plinder.core.scores.entries.SystemView attribute) (plinder.eval.inputs.PreparedPrediction attribute) LigandView (class in plinder.core.scores.entries) link_density (plinder.data.annotations.interface_utils.ProdigyCrystalAnnotation attribute) link_or_copy_file() (in module plinder.core.utils.files) linked_apo_structures (plinder.core.index.system.PlinderSystem property) linked_atoms_by_residue() (in module plinder.core.structure.ccd_template) LinkedApoSelectionConfig (class in plinder.data.linked_apo) links (plinder.data.annotations.ccd_ligand_dbs.ResidueGraph attribute) load() (plinder.data.annotations.ccd_ligand_dbs.CcdParityTable class method) load_alignment_entry_views() (in module plinder.core.scores.entries) load_alignments() (plinder.data.annotations.get_similarity_scores.Scorer method) load_ccd_components() (in module plinder.data.annotations.ccd_ligand_dbs) load_entry_views() (in module plinder.core.scores.entries) load_ligands() (plinder.core.structure.structure.Structure method) load_ligands_from_annotation_table() (in module plinder.data.annotations.get_similarity_scores) load_ligands_from_index() (in module plinder.data.annotations.get_similarity_scores) load_protein() (plinder.core.structure.structure.Structure method) load_sdf_molecule() (in module plinder.data.annotations.get_similarity_scores) load_sdf_molecule_block() (in module plinder.data.annotations.get_similarity_scores) load_sequence() (plinder.core.structure.structure.Structure method) M main() (in module plinder.data.monomer_similarity) (in module plinder.eval.cli) make_atom_mask() (in module plinder.core.structure.atoms) make_ccd_ligand_dbs() (in module plinder.data.annotations.ccd_ligand_dbs) make_db() (in module plinder.data.databases) make_dbs() (plinder.data.annotations.get_similarity_scores.Scorer method) make_exact_search_db() (in module plinder.data.databases) make_ligand_ccd_match() (in module plinder.data.annotations.ccd_ligand_dbs) make_ligand_mmp_pairs() (in module plinder.data.annotations.mmpdb_utils) make_protein_sequence_clusters() (in module plinder.data.protein_clusters) make_protein_structure_clusters() (in module plinder.data.protein_clusters) make_sub_db() (in module plinder.data.databases) make_sub_dbs() (in module plinder.data.databases) manifest (plinder.core.scores.custom.SearchDatabaseBundle attribute) map_alignment_df() (plinder.data.annotations.get_similarity_scores.Scorer method) map_alignment_files() (plinder.data.annotations.get_similarity_scores.Scorer method) map_chain_alignment() (in module plinder.core.scores.alignment) map_custom_alignment_hits() (in module plinder.core.scores.custom) map_row() (plinder.data.annotations.get_similarity_scores.Scorer method) mapped_alignment_schema() (in module plinder.core.utils.schemas) mapped_alignment_schema_is_current() (in module plinder.core.utils.schemas) mapping() (plinder.data.annotations.ccd_ligand_dbs.CcdParityTable method) mappings() (plinder.data.annotations.ccd_ligand_dbs.CcdParityTable method) match_composite_by_sequence() (in module plinder.data.annotations.ccd_ligand_dbs) match_kind (plinder.data.annotations.ccd_ligand_dbs.CcdMatch attribute) match_ligand_to_ccd() (in module plinder.data.annotations.ccd_ligand_dbs) match_ligands() (in module plinder.core.structure.smallmols_utils) matched_affinity() (in module plinder.data.annotations.affinity) matched_ccd_ids (plinder.data.annotations.ccd_ligand_dbs.CcdMatch attribute) max_per_side (plinder.data.interface_apo.InterfaceApoSelectionConfig attribute) max_per_system (plinder.data.linked_apo.LinkedApoSelectionConfig attribute) max_query_proper_ligand_chains (plinder.data.annotations.get_similarity_scores.Scorer attribute) max_query_protein_chains (plinder.data.annotations.get_similarity_scores.Scorer attribute) max_seqs (plinder.core.scores.custom.CustomProteinSearchConfig attribute) maximum_weight_bipartite_assignment() (in module plinder.core.scores.metrics) metadata() (plinder.core.utils.http.ReleaseClient method) mhfp6_bulk_jaccard() (in module plinder.core.structure.smallmols_similarity) mhfp6_ligand_scores() (in module plinder.data.annotations.get_similarity_scores) min_interface_residues_from_schema() (in module plinder.data.annotations.interface_utils) min_pocket_fident (plinder.data.linked_apo.LinkedApoSelectionConfig attribute) min_protein_fident_qcov_weighted_sum (plinder.data.linked_apo.LinkedApoSelectionConfig attribute) min_protein_fident_weighted_sum (plinder.data.linked_apo.LinkedApoSelectionConfig attribute) min_protein_lddt_weighted_sum (plinder.data.linked_apo.LinkedApoSelectionConfig attribute) min_query_coverage (plinder.data.interface_apo.InterfaceApoSelectionConfig attribute) min_seq_id (plinder.core.scores.custom.CustomProteinSearchConfig attribute) min_sequence_identity (plinder.data.interface_apo.InterfaceApoSelectionConfig attribute) min_target_coverage (plinder.data.interface_apo.InterfaceApoSelectionConfig attribute) minimum_threshold (plinder.data.annotations.get_similarity_scores.Scorer attribute) minimum_thresholds (plinder.data.annotations.get_similarity_scores.Scorer attribute) MissingBondOrderError mmseqs_config (plinder.data.annotations.get_similarity_scores.Scorer attribute) mmseqs_evalue (plinder.core.scores.custom.CustomProteinSearchConfig attribute) model_config (plinder.core.structure.structure.Structure attribute) (plinder.data.annotations.utils.DocBaseModel attribute) modified (plinder.core.utils.http.FileMetadata attribute) module plinder.core.index.interface plinder.core.index.query plinder.core.index.system plinder.core.index.utils plinder.core.release plinder.core.scores.alignment plinder.core.scores.custom plinder.core.scores.entries plinder.core.scores.interface plinder.core.scores.ligand plinder.core.scores.mapping plinder.core.scores.metrics plinder.core.scores.protein plinder.core.scores.query plinder.core.scores.reconstruct plinder.core.scores.search plinder.core.structure.atoms plinder.core.structure.ccd_template plinder.core.structure.inputs plinder.core.structure.smallmols_similarity plinder.core.structure.smallmols_utils plinder.core.structure.structure plinder.core.structure.superimpose plinder.core.utils.config plinder.core.utils.constants plinder.core.utils.cpl plinder.core.utils.dataclass plinder.core.utils.dec plinder.core.utils.files plinder.core.utils.http plinder.core.utils.io plinder.core.utils.log plinder.core.utils.sanitize plinder.core.utils.schemas plinder.data.annotations.affinity plinder.data.annotations.ccd_ligand_dbs plinder.data.annotations.cif_utils plinder.data.annotations.contact_areas plinder.data.annotations.get_similarity_scores plinder.data.annotations.interaction_utils plinder.data.annotations.interface_utils plinder.data.annotations.mmpdb_utils plinder.data.annotations.save_utils plinder.data.annotations.utils plinder.data.databases plinder.data.docs plinder.data.interface_apo plinder.data.linked_apo plinder.data.monomer_similarity plinder.data.protein_clusters plinder.eval.batch plinder.eval.cli plinder.eval.commands plinder.eval.inputs mol2mhfp6() (in module plinder.core.structure.smallmols_similarity) mol2morgan_fp() (in module plinder.core.structure.smallmols_similarity) mol_assigned_bond_orders_by_template() (in module plinder.core.structure.smallmols_utils) mol_from_smiles() (in module plinder.core.utils.sanitize) monomer_search_databases (plinder.core.scores.custom.CustomScoringAssets attribute) N num_contact_residue_pairs (plinder.core.scores.entries.InterfaceView attribute) (plinder.data.annotations.interface_utils.ProteinInterface attribute) num_interactions (plinder.core.scores.entries.LigandView attribute) num_ligands (plinder.core.index.system.PlinderSystem property) num_pocket_residues (plinder.core.scores.entries.LigandView attribute) num_proteins (plinder.core.index.system.PlinderSystem property) num_unique_interactions (plinder.core.scores.entries.LigandView attribute) O opposed (plinder.core.structure.smallmols_similarity.RascalParityMatch attribute) overlay_monomer_search_databases (plinder.core.scores.custom.CustomScoringAssets attribute) overlay_search_databases (plinder.core.scores.custom.CustomScoringAssets attribute) P pack_residue_identities() (in module plinder.core.scores.mapping) parity_similarity() (in module plinder.core.structure.smallmols_similarity) parse_ph_range() (in module plinder.data.annotations.cif_utils) parse_struct_conn() (in module plinder.data.annotations.cif_utils) partner_contact_areas() (in module plinder.data.annotations.contact_areas) path() (plinder.core.release.PlinderRelease method) (plinder.core.utils.http.ReleaseClient method) pdb_id (plinder.core.scores.entries.EntryView attribute) (plinder.core.scores.entries.InterfaceView attribute) (plinder.core.scores.entries.LigandView attribute) (plinder.core.scores.entries.SystemView attribute) (plinder.data.annotations.interface_utils.ProteinInterface attribute) pdb_ids (plinder.core.utils.config.ContextConfig attribute) pdb_mmcif_cache_path() (in module plinder.core.utils.io) plinder.core.index.interface module plinder.core.index.query module plinder.core.index.system module plinder.core.index.utils module plinder.core.release module plinder.core.scores.alignment module plinder.core.scores.custom module plinder.core.scores.entries module plinder.core.scores.interface module plinder.core.scores.ligand module plinder.core.scores.mapping module plinder.core.scores.metrics module plinder.core.scores.protein module plinder.core.scores.query module plinder.core.scores.reconstruct module plinder.core.scores.search module plinder.core.structure.atoms module plinder.core.structure.ccd_template module plinder.core.structure.inputs module plinder.core.structure.smallmols_similarity module plinder.core.structure.smallmols_utils module plinder.core.structure.structure module plinder.core.structure.superimpose module plinder.core.utils.config module plinder.core.utils.constants module plinder.core.utils.cpl module plinder.core.utils.dataclass module plinder.core.utils.dec module plinder.core.utils.files module plinder.core.utils.http module plinder.core.utils.io module plinder.core.utils.log module plinder.core.utils.sanitize module plinder.core.utils.schemas module plinder.data.annotations.affinity module plinder.data.annotations.ccd_ligand_dbs module plinder.data.annotations.cif_utils module plinder.data.annotations.contact_areas module plinder.data.annotations.get_similarity_scores module plinder.data.annotations.interaction_utils module plinder.data.annotations.interface_utils module plinder.data.annotations.mmpdb_utils module plinder.data.annotations.save_utils module plinder.data.annotations.utils module plinder.data.databases module plinder.data.docs module plinder.data.interface_apo module plinder.data.linked_apo module plinder.data.monomer_similarity module plinder.data.protein_clusters module plinder.eval.batch module plinder.eval.cli module plinder.eval.commands module plinder.eval.inputs module plinder_bucket (plinder.core.utils.config.DataConfig attribute) plinder_dir (plinder.core.utils.config.DataConfig attribute) plinder_mount (plinder.core.utils.config.DataConfig attribute) plinder_release (plinder.core.utils.config.DataConfig attribute) plinder_release_number (plinder.core.utils.config.DataConfig attribute) plinder_remote (plinder.core.utils.config.DataConfig attribute) PlinderInterface (class in plinder.core.index.interface) PlinderRelease (class in plinder.core.release) PlinderSystem (class in plinder.core.index.system) pocket_index_to_number_per_chain (plinder.core.scores.entries.EntryView property) pocket_residue_index_to_number (plinder.core.scores.entries.SystemView property) pocket_residue_number_to_index (plinder.core.scores.entries.LigandView attribute) (plinder.core.scores.entries.SystemView attribute) polar_polar_contacts (plinder.data.annotations.interface_utils.ProdigyCrystalAnnotation attribute) prefetch_similarity_alignments() (in module plinder.core.scores.reconstruct) prepare_custom_protein_score_alignments() (in module plinder.core.scores.custom) prepare_custom_score_alignments() (in module plinder.core.scores.custom) prepare_ligand_for_3d_scoring() (in module plinder.data.annotations.get_similarity_scores) prepare_prediction() (in module plinder.eval.inputs) PreparedPrediction (class in plinder.eval.inputs) probability_bio (plinder.data.annotations.interface_utils.ProdigyCrystalAnnotation attribute) prodigy (plinder.data.annotations.interface_utils.ProteinInterface attribute) ProdigyCrystalAnnotation (class in plinder.data.annotations.interface_utils) proper_num_interactions (plinder.core.scores.entries.SystemView attribute) proper_num_pocket_residues (plinder.core.scores.entries.SystemView attribute) proper_num_unique_interactions (plinder.core.scores.entries.SystemView attribute) protein_atom_array (plinder.core.structure.structure.Structure attribute) protein_backbone_mask (plinder.core.structure.structure.Structure property) protein_calpha_coords (plinder.core.structure.structure.Structure property) protein_calpha_mask (plinder.core.structure.structure.Structure property) protein_chain_mappers (plinder.data.annotations.get_similarity_scores.Scorer attribute) protein_chain_ordered (plinder.core.structure.structure.Structure property) protein_chains (plinder.core.structure.structure.Structure property) protein_chains_asym_id (plinder.core.scores.entries.LigandView attribute) (plinder.core.scores.entries.SystemView attribute) protein_coords (plinder.core.structure.structure.Structure property) protein_hits (plinder.core.scores.custom.CustomScoringResult attribute) (plinder.core.scores.custom.CustomSequenceScoringResult attribute) protein_interfaces_to_table() (in module plinder.data.annotations.interface_utils) protein_n_atoms (plinder.core.structure.structure.Structure property) protein_path (plinder.core.structure.structure.Structure attribute) protein_score_alignments (plinder.core.scores.custom.CustomScoringResult attribute) (plinder.core.scores.custom.CustomSequenceScoringResult attribute) protein_scores (plinder.core.scores.custom.CustomScoringResult attribute) (plinder.core.scores.custom.CustomSequenceScoringResult attribute) protein_sequence (plinder.core.structure.structure.Structure attribute) protein_sequence_from_structure (plinder.core.structure.structure.Structure property) protein_structure_b_factor (plinder.core.structure.structure.Structure property) protein_structure_tokenized_sequence (plinder.core.structure.structure.Structure property) protein_unique_atom_names (plinder.core.structure.structure.Structure property) protein_unique_residue_ids (plinder.core.structure.structure.Structure property) protein_unique_residue_names (plinder.core.structure.structure.Structure property) protein_unresolved_atom_mask (plinder.core.structure.structure.Structure property) ProteinInterface (class in plinder.data.annotations.interface_utils) publish_affinity_tables() (in module plinder.data.annotations.affinity) publish_search_database_bundle() (in module plinder.data.databases) Q query_ccd_mmp_pairs() (in module plinder.data.annotations.ccd_ligand_dbs) query_ccd_parity() (in module plinder.data.annotations.ccd_ligand_dbs) query_ccd_tanimoto() (in module plinder.data.annotations.ccd_ligand_dbs) query_chain_overlap() (in module plinder.core.scores.protein) query_databases (plinder.core.scores.custom.CustomScoringResult attribute) (plinder.core.scores.custom.CustomSequenceScoringResult attribute) query_half_interface_similarity() (in module plinder.core.scores.interface) query_inputs (plinder.core.scores.custom.CustomScoringResult attribute) (plinder.core.scores.custom.CustomSequenceScoringResult attribute) query_interface_similarity() (in module plinder.core.scores.interface) query_ligand_chemical_similarity() (in module plinder.core.scores.ligand) query_ligand_similarity() (in module plinder.core.scores.ligand) query_protein_similarity() (in module plinder.core.scores.protein) query_table() (in module plinder.core.index.query) R rascal_parity_coverage() (in module plinder.core.structure.smallmols_similarity) rascal_parity_match() (in module plinder.core.structure.smallmols_similarity) rascal_parity_score() (in module plinder.core.structure.smallmols_similarity) RascalParityMatch (class in plinder.core.structure.smallmols_similarity) read_input_structure() (in module plinder.core.structure.inputs) read_json_cache() (in module plinder.core.utils.files) read_ligand_sdf() (in module plinder.core.structure.inputs) read_mmcif_container() (in module plinder.data.annotations.cif_utils) read_mmcif_file() (in module plinder.data.annotations.cif_utils) read_score_table() (in module plinder.core.scores.query) read_structure_table() (in module plinder.core.structure.inputs) receptor (plinder.data.annotations.save_utils.ReconstructedSystem attribute) (plinder.eval.inputs.PreparedPrediction attribute) receptor_chain_types (plinder.core.index.system.PlinderSystem property) receptor_cif (plinder.core.index.system.PlinderSystem property) (plinder.data.annotations.save_utils.SystemReconstructionOutputs attribute) receptor_include_other_protein_chains (plinder.data.annotations.save_utils.SystemReconstructionOptions attribute) receptor_molecule (plinder.eval.inputs.PreparedPrediction attribute) receptor_structure (plinder.core.index.system.PlinderSystem property) receptor_type (plinder.core.index.system.PlinderSystem property) (plinder.core.scores.entries.ChainView property) (plinder.core.scores.entries.SystemView attribute) receptor_waters (plinder.data.annotations.save_utils.SystemReconstructionOptions attribute) reconstruct() (plinder.core.index.interface.PlinderInterface method) (plinder.core.index.system.PlinderSystem method) reconstruct_interface() (in module plinder.data.annotations.save_utils) reconstruct_interface_similarity_scores() (in module plinder.core.scores.reconstruct) reconstruct_linked_apo() (plinder.core.index.system.PlinderSystem method) reconstruct_similarity_scores() (in module plinder.core.scores.reconstruct) reconstruct_system() (in module plinder.data.annotations.save_utils) reconstructed (plinder.core.index.system.PlinderSystem property) ReconstructedSystem (class in plinder.data.annotations.save_utils) reference_id (plinder.core.structure.inputs.StructureInput attribute) reference_ligands() (in module plinder.eval.inputs) release_alignment_mapping_schema() (in module plinder.core.utils.schemas) release_alignment_mapping_schema_is_current() (in module plinder.core.utils.schemas) ReleaseClient (class in plinder.core.utils.http) released_ids (plinder.data.annotations.ccd_ligand_dbs.CcdIndex attribute) remove_nonphysical_bonds() (in module plinder.data.annotations.cif_utils) repair_score_df_targets() (plinder.data.annotations.get_similarity_scores.Scorer method) residue_address() (in module plinder.data.annotations.cif_utils) residue_graph_features() (in module plinder.data.annotations.ccd_ligand_dbs) residue_graph_from_atoms() (in module plinder.data.annotations.ccd_ligand_dbs) residue_number_to_index (plinder.core.scores.entries.InterfaceView property) ResidueGraph (class in plinder.data.annotations.ccd_ligand_dbs) resn2seq() (in module plinder.core.structure.atoms) resolve_custom_scoring_assets() (in module plinder.core.scores.custom) resolve_ligand_archives() (in module plinder.core.scores.custom) resolve_ligand_sdf() (plinder.data.annotations.get_similarity_scores.Scorer method) resolve_search_database() (in module plinder.core.scores.custom) resolved_ligand_mols (plinder.core.structure.structure.Structure property) resolved_ligand_mols_coords (plinder.core.structure.structure.Structure property) retry() (in module plinder.core.utils.io) root (plinder.core.scores.custom.CustomQueryDatabases attribute) (plinder.core.scores.custom.CustomQueryInputs attribute) (plinder.core.scores.custom.CustomStructureAnnotations attribute) (plinder.core.scores.custom.SearchDatabaseBundle attribute) roots (plinder.data.annotations.ccd_ligand_dbs.ResidueGraph attribute) run() (in module plinder.data.databases) run_alignment() (in module plinder.data.annotations.get_similarity_scores) run_alignments() (plinder.data.annotations.get_similarity_scores.Scorer method) run_custom_monomer_searches() (in module plinder.core.scores.custom) run_custom_protein_searches() (in module plinder.core.scores.custom) run_openstructure() (in module plinder.eval.commands) run_peppr_interactions() (in module plinder.data.annotations.interaction_utils) run_posebusters() (in module plinder.eval.commands) S sanitize() (in module plinder.core.utils.sanitize) save_cif_file() (in module plinder.data.annotations.save_utils) save_ligands() (in module plinder.data.annotations.save_utils) save_reconstructed_chain() (in module plinder.data.annotations.save_utils) save_reconstructed_interface() (in module plinder.data.annotations.save_utils) save_reconstructed_system() (in module plinder.data.annotations.save_utils) save_to_disk() (plinder.core.structure.structure.Structure method) score() (plinder.core.structure.smallmols_similarity.RascalParityMatch method) score_alignments (plinder.core.scores.custom.CustomScoringResult attribute) score_cache_is_current() (in module plinder.data.annotations.get_similarity_scores) score_canonical_ligand_pairs() (plinder.data.annotations.get_similarity_scores.Scorer method) score_custom_cif_files() (in module plinder.core.scores.custom) score_custom_sequence_file() (in module plinder.core.scores.custom) score_metrics_metadata() (in module plinder.data.annotations.get_similarity_scores) score_monomer_pairs() (in module plinder.data.monomer_similarity) score_thresholds_metadata() (in module plinder.data.annotations.get_similarity_scores) Scorer (class in plinder.data.annotations.get_similarity_scores) scores (plinder.core.utils.config.DataConfig attribute) scores_dir (plinder.data.annotations.get_similarity_scores.Scorer attribute) search() (in module plinder.core.scores.search) search_databases (plinder.core.scores.custom.CustomScoringAssets attribute) search_target (plinder.core.scores.custom.SearchDatabaseBundle attribute) SearchDatabaseBundle (class in plinder.core.scores.custom) select_assembly_ids() (in module plinder.data.annotations.cif_utils) select_linked_apo_structures() (in module plinder.data.linked_apo) selected_index_to_number_per_chain (plinder.core.scores.entries.EntryView property) sensitivity (plinder.core.scores.custom.CustomProteinSearchConfig attribute) sequence_atom_mask (plinder.core.structure.structure.Structure property) sequence_fasta (plinder.core.scores.custom.CustomQueryInputs attribute) sequence_links (plinder.core.scores.custom.CustomSequenceScoringResult attribute) sequences (plinder.core.index.interface.PlinderInterface property) (plinder.core.index.system.PlinderSystem property) sequences_fasta (plinder.core.index.system.PlinderSystem property) (plinder.data.annotations.save_utils.SystemReconstructionOutputs attribute) set_chain() (plinder.core.structure.structure.Structure method) setup_logger() (in module plinder.core.utils.log) shadowed_entries (plinder.core.scores.custom.CustomScoringAssets attribute) shape_score_threads (plinder.data.annotations.get_similarity_scores.Scorer attribute) similarity() (plinder.data.annotations.ccd_ligand_dbs.CcdParityTable method) size (plinder.core.utils.http.FileMetadata attribute) skip_3d_confgen (plinder.core.structure.structure.Structure attribute) smiles (plinder.core.index.system.PlinderSystem property) smiles2nonstereo() (in module plinder.core.structure.smallmols_similarity) smiles_to_ccd_ids (plinder.data.annotations.ccd_ligand_dbs.CcdIndex attribute) source_mmcif_path (plinder.core.index.interface.PlinderInterface property) (plinder.core.index.system.PlinderSystem property) source_mmcifs (plinder.core.utils.config.DataConfig attribute) source_organism_names (plinder.data.annotations.cif_utils.EntryTaxonomy attribute) source_taxonomy_ids (plinder.data.annotations.cif_utils.EntryTaxonomy attribute) source_to_full_db_file (plinder.data.annotations.get_similarity_scores.Scorer attribute) steam_evalue (plinder.core.scores.custom.CustomProteinSearchConfig attribute) stringify_dataclass() (in module plinder.core.utils.dataclass) Structure (class in plinder.core.structure.structure) Structure.Config (class in plinder.core.structure.structure) structure_type (plinder.core.structure.structure.Structure attribute) StructureInput (class in plinder.core.structure.inputs) structures (plinder.core.index.system.PlinderSystem property) superimpose() (plinder.core.structure.structure.Structure method) superimpose_chain() (in module plinder.core.structure.superimpose) superpose_linked_apo() (plinder.core.index.system.PlinderSystem method) system (plinder.core.index.system.PlinderSystem property) (plinder.data.annotations.save_utils.ReconstructedSystem attribute) system_cif (plinder.core.index.system.PlinderSystem property) (plinder.data.annotations.save_utils.SystemReconstructionOutputs attribute) system_id (plinder.core.scores.entries.LigandView attribute) (plinder.data.annotations.interface_utils.ProteinInterface property) system_ids (plinder.core.utils.config.ContextConfig attribute) system_include_ligands (plinder.data.annotations.save_utils.SystemReconstructionOptions attribute) system_include_other_ligand_chains (plinder.data.annotations.save_utils.SystemReconstructionOptions attribute) system_include_other_protein_chains (plinder.data.annotations.save_utils.SystemReconstructionOptions attribute) system_is_query_scoreable() (plinder.data.annotations.get_similarity_scores.Scorer method) system_is_target_scoreable() (plinder.data.annotations.get_similarity_scores.Scorer static method) system_type (plinder.core.scores.entries.SystemView attribute) system_waters (plinder.data.annotations.save_utils.SystemReconstructionOptions attribute) SystemReconstructionOptions (class in plinder.data.annotations.save_utils) SystemReconstructionOutputs (class in plinder.data.annotations.save_utils) systems (plinder.core.scores.entries.EntryView attribute) SystemView (class in plinder.core.scores.entries) T table() (plinder.core.release.PlinderRelease method) tessellation_atom_mask() (in module plinder.data.annotations.contact_areas) thread_pool() (in module plinder.core.utils.cpl) timeit() (in module plinder.core.utils.dec) to_row() (plinder.data.annotations.interface_utils.ProteinInterface method) two_char_codes (plinder.core.utils.config.ContextConfig attribute) U uniprot_ids (plinder.core.scores.entries.ChainView attribute) unpack_residue_identities() (in module plinder.core.scores.mapping) unresolved_atoms_from_template() (in module plinder.core.structure.ccd_template) update_letters() (in module plinder.core.utils.constants) V validate_biounit_chain_ids (plinder.data.annotations.save_utils.SystemReconstructionOptions attribute) W write_cif() (in module plinder.core.structure.atoms) write_column_descriptions() (in module plinder.data.docs) write_custom_aligned_pocket_residues() (in module plinder.core.scores.custom) write_custom_chain_similarity_scores() (in module plinder.core.scores.custom) write_custom_query_files() (in module plinder.core.scores.custom) write_custom_sequence_link_tables() (in module plinder.core.scores.custom) write_custom_sequence_query_files() (in module plinder.core.scores.custom) write_ecfp4_fingerprint_table() (in module plinder.data.annotations.get_similarity_scores) write_interface_apo_structure_table() (in module plinder.data.interface_apo) write_json_atomic() (in module plinder.core.utils.files) write_linked_apo_structure_table() (in module plinder.data.linked_apo) write_mhfp6_fingerprints() (in module plinder.data.annotations.get_similarity_scores) write_search_structure() (in module plinder.core.structure.inputs)
