def test_init(self):
mol = Molecule(["C", "H", "H", "H", "H"], self.coords)
gau = GaussianInput(mol, charge=1, route_parameters={'SP': "",
"SCF": "Tight"})
self.assertEqual(gau.spin_multiplicity, 2)
mol = Molecule(["C", "H", "H", "H", "H"], self.coords, charge=-1)
gau = GaussianInput(mol, route_parameters={'SP': "", "SCF": "Tight"})
self.assertEqual(gau.spin_multiplicity, 2)
self.assertRaises(ValueError, GaussianInput, mol, spin_multiplicity=1)
def write_mol(mol, filename):
"""
Write a molecule to a file based on file extension. For example, anything
ending in a "xyz" is assumed to be a XYZ file. Supported formats include
xyz, Gaussian input (gjf|g03|g09|com|inp), and pymatgen's JSON serialized
molecules.
Args:
mol (Molecule/IMolecule): Molecule to write
filename (str): A filename to write to.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.xyz*"):
return XYZ(mol).write_file(filename)
elif any([
fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["gjf", "g03", "g09", "com", "inp"]
]):
return GaussianInput(mol).write_file(filename)
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename, "w") as f:
return json.dump(mol, f, cls=PMGJSONEncoder)
else:
m = re.search("\.(pdb|mol|mdl|sdf|sd|ml2|sy2|mol2|cml|mrv)",
filename.lower())
if m:
return BabelMolAdaptor(mol).write_file(filename, m.group(1))
raise ValueError("Unrecognized file extension!")
def setUp(self):
coords = [[0.000000, 0.000000, 0.000000],
[0.000000, 0.000000, 1.089000],
[1.026719, 0.000000, -0.363000],
[-0.513360, -0.889165, -0.363000],
[-0.513360, 0.889165, -0.363000]]
self.coords = coords
mol = Molecule(["C", "H", "H", "H", "H"], coords)
self.gau = GaussianInput(
mol, route_parameters={'SP': "", "SCF": "Tight"},
input_parameters={"EPS": 12})
