def test_spherical(self):
a = PointGroupAnalyzer(CH4)
self.assertEqual(a.sch_symbol, "Td")
self.assertEqual(len(a.get_pointgroup()), 24)
a = PointGroupAnalyzer(PF6)
self.assertEqual(a.sch_symbol, "Oh")
self.assertEqual(len(a.get_pointgroup()), 48)
xyz = XYZ.from_file(os.path.join(test_dir, "c60.xyz"))
a = PointGroupAnalyzer(xyz.molecule)
self.assertEqual(a.sch_symbol, "Ih")
def test_dihedral(self):
a = PointGroupAnalyzer(C2H4)
self.assertEqual(a.sch_symbol, "D2h")
self.assertEqual(len(a.get_pointgroup()), 8)
a = PointGroupAnalyzer(BF3)
self.assertEqual(a.sch_symbol, "D3h")
self.assertEqual(len(a.get_pointgroup()), 12)
xyz = XYZ.from_file(os.path.join(test_dir, "b12h12.xyz"))
a = PointGroupAnalyzer(xyz.molecule)
self.assertEqual(a.sch_symbol, "D5d")
def test_spherical(self):
a = PointGroupAnalyzer(CH4)
self.assertEqual(a.sch_symbol, "Td")
self.assertEqual(len(a.get_pointgroup()), 24)
a = PointGroupAnalyzer(PF6)
self.assertEqual(a.sch_symbol, "Oh")
self.assertEqual(len(a.get_pointgroup()), 48)
xyz = XYZ.from_file(os.path.join(test_dir, "c60.xyz"))
a = PointGroupAnalyzer(xyz.molecule)
self.assertEqual(a.sch_symbol, "Ih")
def test_dihedral(self):
a = PointGroupAnalyzer(C2H4)
self.assertEqual(a.sch_symbol, "D2h")
self.assertEqual(len(a.get_pointgroup()), 8)
a = PointGroupAnalyzer(BF3)
self.assertEqual(a.sch_symbol, "D3h")
self.assertEqual(len(a.get_pointgroup()), 12)
xyz = XYZ.from_file(os.path.join(test_dir, "b12h12.xyz"))
a = PointGroupAnalyzer(xyz.molecule)
self.assertEqual(a.sch_symbol, "D5d")
def read_mol(filename):
"""
Reads a molecule 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), Gaussian output (.out|and
pymatgen's JSON serialized molecules. Using openbabel,
many more extensions are supported but requires openbabel to be installed.
Args:
filename:
A filename to read from.
Returns:
A Molecule object.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.xyz*"):
return XYZ.from_file(filename).molecule
elif any([
fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["gjf", "g03", "g09", "com", "inp"]
]):
return GaussianInput.from_file(filename).molecule
elif any([
fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["out", "lis", "log"]
]):
return GaussianOutput(filename).final_structure
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename) as f:
s = json.load(f, cls=PMGJSONDecoder)
if type(s) != Molecule:
raise IOError("File does not contain a valid serialized "
"molecule")
return s
else:
m = re.search("\.(pdb|mol|mdl|sdf|sd|ml2|sy2|mol2|cml|mrv)",
filename.lower())
if m:
return BabelMolAdaptor.from_file(filename, m.group(1)).pymatgen_mol
raise ValueError("Unrecognized file extension!")
def read_mol(filename):
"""
Reads a molecule 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), Gaussian output (.out|and
pymatgen's JSON serialized molecules. Using openbabel,
many more extensions are supported but requires openbabel to be installed.
Args:
filename:
A filename to read from.
Returns:
A Molecule object.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.xyz*"):
return XYZ.from_file(filename).molecule
elif any([fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["gjf", "g03", "g09", "com", "inp"]]):
return GaussianInput.from_file(filename).molecule
elif any([fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["out", "lis", "log"]]):
return GaussianOutput(filename).final_structure
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename) as f:
s = json.load(f, cls=PMGJSONDecoder)
if type(s) != Molecule:
raise IOError("File does not contain a valid serialized "
"molecule")
return s
else:
m = re.search("\.(pdb|mol|mdl|sdf|sd|ml2|sy2|mol2|cml|mrv)",
filename.lower())
if m:
return BabelMolAdaptor.from_file(filename,
m.group(1)).pymatgen_mol
raise ValueError("Unrecognized file extension!")