Reference¶
Components¶
Core libraries¶
- Lib build
ConfLabelsConfMasksare_connected()build_regex_substitutions()create_Coulomb_params_raw()create_LJ_params_raw()create_bonds_apart_mask_for_ij_pairs()create_conformer_labels()create_sidechains_masks_per_residue()extract_ff_params_for_seq()gen_3l_residue_labels_per_atom()gen_atom_pair_connectivity_masks()gen_ij_pairs_upper_diagonal()gen_residue_number_per_atom()get_cycle_bond_type()get_cycle_distances_backbone()get_indexes_from_primer_length()init_conflabels()init_confmasks()make_combined_regex()make_list_atom_labels()populate_dict_with_database()prepare_energy_function()prepare_slice_dict()
- Lib Calculations and math
- Lib Check
- Lib mmCIF
CIFParserCIFParser.altlocCIFParser.atnameCIFParser.chainidCIFParser.chargeCIFParser.elementCIFParser.get_line_elements_for_PDB()CIFParser.get_value()CIFParser.icodeCIFParser.lineCIFParser.occCIFParser.read_cif()CIFParser.recordCIFParser.resnameCIFParser.resseqCIFParser.serialCIFParser.tempfactorCIFParser.xcoordCIFParser.ycoordCIFParser.zcoord
find_cif_atom_site_headers()is_cif()parse_cif_line()populate_cif_dictionary()
- Lib CLI
AllParamArgsToTupleCSV2TupleCheckExt()CustomParserFolderOrTarListOfIntsPositiveSumListOfPositiveIntsParamsToDictReadDictionarySeqOrFastaadd_argument_chunks()add_argument_cif()add_argument_cmd()add_argument_dany()add_argument_db()add_argument_decimals()add_argument_degrees()add_argument_destination_folder()add_argument_dhelix()add_argument_dloopoff()add_argument_dstrand()add_argument_duser()add_argument_idb()add_argument_minimum()add_argument_ncores()add_argument_nohnterm()add_argument_output()add_argument_output_folder()add_argument_pdb_files()add_argument_pdbids()add_argument_plot()add_argument_random_seed()add_argument_record()add_argument_reduced()add_argument_replace()add_argument_seq()add_argument_source()add_argument_update()add_argument_vdWb()add_argument_vdWr()add_argument_vdWt()add_general_arg()add_subparser()add_version()load_args()maincli()minimum_value()parse_doc_params()
- Lib Download
- Lib Energy
- Lib Filter
aligndb()make_any_overlap_regex()make_helix_overlap_regex()make_loop_overlap_regex()make_overlap_regex()make_ranges()make_regex_combinations()make_regex_combinations_from_ranges()make_strand_overlap_regex()regex_forward_no_overlap()regex_forward_with_overlap()regex_has_overlap()regex_range()regex_search()
- Lib Functional
- Lib higher level
bgeo_reduce()cli_helper_calc_bgeo()cli_helper_calc_torsions()cli_helper_calc_torsionsJ()convert_bond_geo_lib()download_pipeline()extract_secondary_structure()get_bond_geos()get_separate_torsions()get_torsions()get_torsionsJ()read_trimer_torsion_planar_angles()validate_backbone_labels_for_torsion()validate_coords_for_backbone_torsions()
- Lib I/O
FileIteratorFileIteratorBaseFileReaderIteratorTarFileIteratoradd_existent_files()concatenate_entries()extract_from_tar()file_exists()glob_folder()has_suffix()has_suffix_fasta()is_valid_fasta_file()list_files_recursively()log_nonexistent()make_destination_folder()make_folder_or_cwd()parse_suffix()paths_from_flist()read_FASTAS_from_file()read_FASTAS_from_file_to_strings()read_PDBID_from_folder()read_PDBID_from_source()read_PDBID_from_tar()read_dict_from_json()read_dict_from_pickle()read_dict_from_tar()read_dictionary_from_disk()read_lines()read_path_bundle()read_text()save_dict_to_json()save_dict_to_pickle()save_dictionary()save_file_to_tar()save_pairs_to_disk()save_pairs_to_files()save_pairs_to_tar()
- Lib Multicore
- Lib Parse
convert_int_float_lines_to_dict()convert_tuples_to_lists()fill_list()get_diff_between_aa1l()get_diff_between_groups()get_mers()get_seq_chunk()get_seq_next_residue()get_trimer_seq()group_by()group_runs()is_valid_fasta()make_list_if_not()mkdssp_w_split()parse_dssp()pop_difference_with_log()remap_sequence()remove_empty_keys()sample_case()split_by_ranges()split_into_chunks()split_pdb_by_dssp()translate_seq_to_3l()values_to_dict()
- Lib PDB
- Lib Structure
- Classes
StructureStructure.add_filter()Structure.add_filter_backbone()Structure.add_filter_chain()Structure.add_filter_record_name()Structure.build()Structure.chain_setStructure.clear_filters()Structure.consecutive_residuesStructure.coordsStructure.data_arrayStructure.fastaStructure.filtered_atomsStructure.filtered_residuesStructure.filtersStructure.get_PDB()Structure.get_sorted_minimal_backbone_coords()Structure.pop_last_filter()Structure.residuesStructure.write_PDB()
concatenate_residue_labels()detect_structure_type()filter_record_lines()gen_empty_structure_data_array()generate_backbone_pairs_labels()generate_residue_labels()get_datastr()is_backbone()parse_cif_to_array()parse_pdb_to_array()populate_structure_array_from_pdb()save_structure_by_chains()structure_to_pdb()write_PDB()
- Lib Timer
- Lib Validate
eval_bb_bond_length_distribution()evaluate_vdw_clash_by_threshold_from_disk()report_sequential_bon_len()report_vdw_clash()validate_bb_bond_len()validate_bb_bonds_len_from_disk()validate_conformer_for_builder()vdw_clash_by_threshold()vdw_clash_by_threshold_calc()vdw_clash_by_threshold_common_preparation()