Reference¶
Components¶
Core libraries¶
- Lib build
ConfLabels
ConfMasks
are_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
CIFParser
CIFParser.altloc
CIFParser.atname
CIFParser.chainid
CIFParser.charge
CIFParser.element
CIFParser.get_line_elements_for_PDB()
CIFParser.get_value()
CIFParser.icode
CIFParser.line
CIFParser.occ
CIFParser.read_cif()
CIFParser.record
CIFParser.resname
CIFParser.resseq
CIFParser.serial
CIFParser.tempfactor
CIFParser.xcoord
CIFParser.ycoord
CIFParser.zcoord
find_cif_atom_site_headers()
is_cif()
parse_cif_line()
populate_cif_dictionary()
- Lib CLI
AllParam
ArgsToTuple
CSV2Tuple
CheckExt()
CustomParser
FolderOrTar
ListOfIntsPositiveSum
ListOfPositiveInts
ParamsToDict
ReadDictionary
SeqOrFasta
add_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
FileIterator
FileIteratorBase
FileReaderIterator
TarFileIterator
add_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
Structure
Structure.add_filter()
Structure.add_filter_backbone()
Structure.add_filter_chain()
Structure.add_filter_record_name()
Structure.build()
Structure.chain_set
Structure.clear_filters()
Structure.consecutive_residues
Structure.coords
Structure.data_array
Structure.fasta
Structure.filtered_atoms
Structure.filtered_residues
Structure.filters
Structure.get_PDB()
Structure.get_sorted_minimal_backbone_coords()
Structure.pop_last_filter()
Structure.residues
Structure.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()