def main(): """ Main method for the script """ args = get_args() file = list(nmrstarlib.read_files(args.restraints))[0] restraints = file["save_CNS/XPLOR_distance_constraints_2"]["loop_1"] for r in restraints[1]: id1 = r[SEQ1] res1 = r[COMP1] atom1 = r[ATOM1] id2 = r[SEQ2] res2 = r[COMP2] atom2 = r[ATOM2] if res1 in COLORS and res2 in COLORS: if (ATOM_EXPR.match(atom1) is not None and ATOM_EXPR.match(atom2) is not None): if res1 == "ILE": label1 = f"I{id1}" else: label1 = f"{res1[0]}{id1}.{atom1[-1]}" if res2 == "ILE": label2 = f"I{id2}" else: label2 = f"{res2[0]}{id2}.{atom2[-1]}" print(label1, label2)
def LoadNMRCS(BMRBID, FOLDER): """Load a file in NMRSTAR 3.1 format and get Chemical shift data.""" # print(FOLDER+BMRBID) starfiles = nmrstarlib.read_files(FOLDER + BMRBID) starfile = starfile = list(starfiles) keyList = list(starfile[0].keys()) indices = [i for i, s in enumerate(keyList) if 'comment' in s] df, iNum = getCS(starfile, keyList, indices) return df, iNum
def test_converter_module(from_path, to_path, from_format, to_format): nmrstar_file_translator = StarFileToStarFile(from_path=from_path, to_path=to_path, from_format=from_format, to_format=to_format) converter = Converter(file_generator=nmrstar_file_translator) converter.convert() starfile_generator = nmrstarlib.read_files(to_path) starfiles_list = list(starfile_generator) starfiles_ids_set = set(sf.id for sf in starfiles_list) assert starfiles_ids_set.issubset({"15000", "18569", "2RPV", "2FRG"})
def test_converter_module(from_path, to_path, from_format, to_format): nmrstar_file_translator = StarFileToStarFile(from_path=from_path, to_path=to_path, from_format=from_format, to_format=to_format) converter = Converter(file_generator=nmrstar_file_translator) converter.convert() starfile_generator = nmrstarlib.read_files(to_path) starfiles_list = list(starfile_generator) starfiles_ids_set = set(sf.id for sf in starfiles_list) assert starfiles_ids_set.issubset({"15000", "18569", "2RPV", "2FRG"})
def test_chem_shifts_by_residue_all(test_input, test_output, amino_acids, atoms, amino_acids_and_atoms): input_file_path1, input_file_path2 = test_input output_file_path1, output_file_path2 = test_output starfile_generator = nmrstarlib.read_files(input_file_path1, input_file_path2) starfile1 = next(starfile_generator) starfile2 = next(starfile_generator) test_chem_shifts1 = starfile1.chem_shifts_by_residue(amino_acids=amino_acids, atoms=atoms, amino_acids_and_atoms=amino_acids_and_atoms, nmrstar_version="3") test_chem_shifts2 = starfile2.chem_shifts_by_residue(amino_acids=amino_acids, atoms=atoms, amino_acids_and_atoms=amino_acids_and_atoms, nmrstar_version="2") with open(output_file_path1, "r") as infile: model_chem_shifts1 = json.load(infile, object_pairs_hook=collections.OrderedDict) with open(output_file_path2, "r") as infile: model_chem_shifts2 = json.load(infile, object_pairs_hook=collections.OrderedDict) assert repr(test_chem_shifts1) == repr(model_chem_shifts1) assert repr(test_chem_shifts2) == repr(model_chem_shifts2)
def test_from_local_file(source): starfile_generator = nmrstarlib.read_files(*source) starfiles_list = list(starfile_generator) starfiles_ids_set = set(sf.id for sf in starfiles_list) assert starfiles_ids_set.issubset({"18569", "2RPV"})
def test_reading(source): starfile_generator = nmrstarlib.read_files(source) starfiles_list = list(starfile_generator) starfiles_ids_set = set(sf.id for sf in starfiles_list) assert starfiles_ids_set.issubset({"15000", "18569", "2RPV", "2FRG"})
def test_from_url(source): starfile_generator = nmrstarlib.read_files(*source) starfile1 = next(starfile_generator) starfile2 = next(starfile_generator) assert starfile1.id in ("15000", "18569") and starfile2.id in ("15000", "18569")
def test_from_local_file(source): starfile_generator = nmrstarlib.read_files(*source) starfiles_list = list(starfile_generator) starfiles_ids_set = set(sf.id for sf in starfiles_list) assert starfiles_ids_set.issubset({"18569", "2RPV"})
def test_reading(source): starfile_generator = nmrstarlib.read_files(source) starfiles_list = list(starfile_generator) starfiles_ids_set = set(sf.id for sf in starfiles_list) assert starfiles_ids_set.issubset({"15000", "18569", "2RPV", "2FRG"})
def test_from_url(source): starfile_generator = nmrstarlib.read_files(*source) starfile1 = next(starfile_generator) starfile2 = next(starfile_generator) assert starfile1.id in ("15000", "18569") and starfile2.id in ("15000", "18569")