infile = FileReader(("from stdin", args.input_format, f))
else:
if len(sys.argv) >= 1:
infile = FileReader(("from stdin", "xyz", f))
geom = Geometry(infile)
target_list = []
for sub in args.targets:
ndx_targets = sub.split("=")[0]
target_list.append(geom.find(ndx_targets))
for i, target in enumerate(target_list):
element = args.targets[i].split("=")[1]
# changeElement will only change one at a time
for single_target in target:
geom.change_element(
single_target,
element,
adjust_bonds=fix_bonds,
adjust_hydrogens=adjust_structure
)
if args.outfile:
outfile = args.outfile
if "$INFILE" in outfile:
outfile = outfile.replace("$INFILE", get_filename(f))
geom.write(append=True, outfile=outfile)
else:
print(geom.write(outfile=False))
def test_change_element(self):
mol = Geometry(TestGeometry.benzene)
ref = Geometry(TestGeometry.pyridine)
mol.change_element("1", "N", adjust_hydrogens=True)
self.assertTrue(validate(mol, ref, thresh="loose"))
