def test_write_xyz(component, tmpdir_factory):
wd = tmpdir_factory.mktemp('xyz_test')
xyz_file = os.path.join(wd, f'{component.id}.xyz')
ccd_writer.write_molecule(xyz_file, component)
assert os.path.isfile(xyz_file)
assert os.path.getsize(xyz_file) > 0
with open(xyz_file, 'r') as fp:
lines = fp.read().splitlines()
assert lines[1] == component.id
assert int(lines[0]) == len(lines[2:])
def test_cif_write(component: Component, tmpdir, rem_hs):
path = tmpdir.join(f"{component.id}.cif")
to_check = must_have_categories.copy()
ccd_writer.write_molecule(str(path), component, remove_hs=rem_hs)
json_obj = reader.read(path)
if component.id == "NA": # Na is an atom!
to_check.pop(2) # remove "_chem_comp_bond"
if component.id == "D3O" and rem_hs: # D3O has single heavy atom
to_check.pop(2)
assert json_obj
assert component.id in json_obj
for c in to_check:
assert c in json_obj[component.id]
def test_json_write(component, tmpdir_factory):
wd = tmpdir_factory.mktemp("json_test")
for remove_h in True, False:
suffix = "" if remove_h else "H"
json_file = os.path.join(wd, f"{component.id}{suffix}.json")
ccd_writer.write_molecule(json_file, component, remove_hs=remove_h)
rdkit_mol = component.mol_no_h if remove_h else component.mol
assert os.path.isfile(json_file)
assert os.path.getsize(json_file) > 0
with open(json_file, "r") as fp:
js = json.load(fp)
key = list(js.keys())[0]
assert key == component.id
assert len(js[key]["atoms"]) == rdkit_mol.GetNumAtoms()
assert len(js[key]["bonds"]) == rdkit_mol.GetNumBonds()
def test_write_sdf(component, tmpdir_factory):
wd = tmpdir_factory.mktemp('sdf_test')
for ideal in True, False:
for remove_hs in True, False:
suffix = f'{("" if remove_hs else "H")}'
sdf_file = os.path.join(wd, f'{component.id}_{suffix}.sdf')
conf_type = ConformerType.Ideal if ideal else ConformerType.Model
ccd_writer.write_molecule(path=sdf_file,
component=component,
conf_type=conf_type,
remove_hs=remove_hs)
rdkit_mol = component.mol_no_h if remove_hs else component.mol
assert os.path.isfile(sdf_file)
assert os.path.getsize(sdf_file) > 0
mol = Chem.MolFromMolFile(sdf_file, sanitize=False)
assert isinstance(mol, Chem.rdchem.Mol)
assert mol.GetNumAtoms() == rdkit_mol.GetNumAtoms()
def __write_molecule(self, path, component, alt_names, conformer_type):
"""Write out deemed structure.
Args:
path str: Path where the molecule will be stored.
component (Component): Component to be written.
alt_names (bool): Whether or not molecule will be written with
alternate names.
conformer_type (Component): Conformer to be written.
"""
try:
ccd_writer.write_molecule(path,
component,
remove_hs=False,
alt_names=alt_names,
conf_type=conformer_type)
except Exception:
self.logger.error(f'error writing {path}.')
with open(path, 'w') as f:
f.write('')