src
- src package
- Submodules
- src.columns module
- src.dataset_creator module
DatasetCreatorDatasetCreator.dataset_nameDatasetCreator.structure_determination_methodologyDatasetCreator.rcsb_entity_polymer_typeDatasetCreator.dstartDatasetCreator.dendDatasetCreator.download_allDatasetCreator.exptl_methodDatasetCreator.resolutionDatasetCreator.year_rangeDatasetCreator.polymer_entity_instance_countDatasetCreator.polymer_entity_count_RNADatasetCreator.selected_polymer_entity_typesDatasetCreator.pdbx_keywordsDatasetCreator.polymer_typeDatasetCreator.sequence_lengthDatasetCreator.sequence_identityDatasetCreator.auto_downloadDatasetCreator.alignment_toolDatasetCreator.rfam_cm_pathDatasetCreator.e_value_cmscanDatasetCreator.saveDatasetCreator.dataset_filesDatasetCreator.final_fasta_pathDatasetCreator.cmscan_pathDatasetCreator.tbloutDatasetCreator.clean_tblout_pathDatasetCreator.final_fams_pathDatasetCreator.final_pdb_list_pathDatasetCreator.final_chain_ids_pathDatasetCreator.cmdDatasetCreator.dataDatasetCreator.structure_filterDatasetCreator.polymer_level_filterDatasetCreator.save_filtered_data()DatasetCreator.save_pdb_list()DatasetCreator.save_dataframe()DatasetCreator.get_without_filter_df()DatasetCreator.get_structure_filtered_df()DatasetCreator.get_polymer_filtered_df()DatasetCreator.get_final_df()DatasetCreator.create_final_fasta_file()DatasetCreator.run_cmscan()DatasetCreator.get_final_families()DatasetCreator.get_final_pdb_list()DatasetCreator.apply_filters()DatasetCreator.apply_polymer_filters()DatasetCreator.apply_structure_filters()DatasetCreator.create_final_fasta_file()DatasetCreator.run()DatasetCreator.save_dataframe()DatasetCreator.save_pdb_list()
main()
- src.dataset_download module
DatasetDownloadDatasetDownload.SEARCH_API_BASE_URIDatasetDownload.DATA_API_BASE_URI_GRAPHQLDatasetDownload.dstartDatasetDownload.dendDatasetDownload.structure_determination_methodologyDatasetDownload.rcsb_entity_polymer_typeDatasetDownload.data_pathDatasetDownload.dfDatasetDownload.get_search_api_query()DatasetDownload.get_graphql_query()DatasetDownload.get_pdb_list()DatasetDownload.get_data_for_each_pdb()DatasetDownload.get_data_as_df()DatasetDownload.save_data_as_csv()DatasetDownload.DATA_API_BASE_URI_GRAPHQLDatasetDownload.SEARCH_API_BASE_URIDatasetDownload.get_data_as_df()DatasetDownload.get_data_for_each_pdb()DatasetDownload.get_graphql_query()DatasetDownload.get_pdb_list()DatasetDownload.get_search_api_query()DatasetDownload.save_data_as_csv()
- src.pdb_filter module
- src.polymer_level_filter module
PolymerLevelFilterPolymerLevelFilter.polymer_typePolymerLevelFilter.sequence_lengthPolymerLevelFilter.sequence_identityPolymerLevelFilter.auto_downloadPolymerLevelFilter.alignment_toolPolymerLevelFilter.pdb_parserPolymerLevelFilter.DATA_PATHPolymerLevelFilter.sequence_identity_mat_filePolymerLevelFilter.sequence_identity_mat_pathPolymerLevelFilter.apply_filters_on_pdb_id()PolymerLevelFilter.apply_filters_on_list()PolymerLevelFilter.create_combined_fasta_file()PolymerLevelFilter.create_sequence_identity_mat_emboss()PolymerLevelFilter.get_sequence_identity_df_emboss()PolymerLevelFilter.create_sequence_identity_mat_clustal()PolymerLevelFilter.get_sequence_identity_df_clustal()PolymerLevelFilter.apply_filter_on_df()PolymerLevelFilter.create_final_fasta_file()PolymerLevelFilter.apply_filter_on_df()PolymerLevelFilter.apply_filters_on_list()PolymerLevelFilter.apply_filters_on_pdb_id()PolymerLevelFilter.create_combined_fasta_file()PolymerLevelFilter.create_final_fasta_file()PolymerLevelFilter.create_sequence_identity_mat_clustal()PolymerLevelFilter.create_sequence_identity_mat_emboss()PolymerLevelFilter.get_sequence_identity_df_clustal()PolymerLevelFilter.get_sequence_identity_df_emboss()
- src.structure_filter module
StructureLevelFilterStructureLevelFilter.exptl_methodStructureLevelFilter.resolutionStructureLevelFilter.year_rangeStructureLevelFilter.polymer_entity_instance_countStructureLevelFilter.polymer_entity_count_RNAStructureLevelFilter.selected_polymer_entity_typesStructureLevelFilter.pdbx_keywordsStructureLevelFilter._check_dataframe()StructureLevelFilter.apply_exptl_method_filter()StructureLevelFilter.apply_resolution_filter()StructureLevelFilter.apply_year_range_filter()StructureLevelFilter.apply_polymer_entity_instance_count_filter()StructureLevelFilter.apply_polymer_entity_count_RNA_filter()StructureLevelFilter.apply_selected_polymer_entity_types_filter()StructureLevelFilter.apply_pdbx_keywords_filter()StructureLevelFilter.apply_filters()StructureLevelFilter.apply_exptl_method_filter()StructureLevelFilter.apply_filters()StructureLevelFilter.apply_pdbx_keywords_filter()StructureLevelFilter.apply_polymer_entity_count_RNA_filter()StructureLevelFilter.apply_polymer_entity_instance_count_filter()StructureLevelFilter.apply_resolution_filter()StructureLevelFilter.apply_selected_polymer_entity_types_filter()StructureLevelFilter.apply_year_range_filter()
- src.utils module
contacts_from_pdb()download_fasta_file()download_fasta_files()download_pdb_file()download_pdb_files()extract_sequence_from_combined_fasta()extract_sequences_for_pdb_ids()generate_contact_map_from_mmcif_file()generate_contact_map_from_pdb_file()get_final_fam_pdb_chain_csv()parse_fasta()remove_backbone_contacts()save_sequences()write_sequences_to_files()
- Module contents