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")