def convert_str(str_data, in_format, out_format):
mol = Molecule()
conv = FileFormatManager()
opts = {}
opts['perceiveBonds'] = False
conv.read_string(mol, str_data, in_format, json.dumps(opts))
return conv.write_string(mol, out_format)
def read(self):
str_data = self._file.read()
mol = Molecule()
conv = FileFormatManager()
conv.read_string(mol, str_data, 'json')
cjson_str = conv.write_string(mol, 'cjson')
cjson = json.loads(cjson_str)
return cjson
def molecule_properties(str_data, in_format):
mol = Molecule()
conv = FileFormatManager()
conv.read_string(mol, str_data, in_format)
properties = {
'atomCount': mol.atom_count(),
'heavyAtomCount': mol.atom_count() - mol.atom_count(1),
'mass': mol.mass(),
'spacedFormula': mol.formula(' ', 0),
'formula': mol.formula('', 1)
}
return properties
def read(self):
str_data = self._file.read()
mol = Molecule()
conv = FileFormatManager()
conv.read_string(mol, str_data, 'json')
cjson_str = conv.write_string(mol, 'cjson')
cjson = json.loads(cjson_str)
# Copy some calculated properties
data = json.loads(str_data)
energy = parse(
'simulation.calculations[0].calculationResults.totalEnergy.value'
).find(data)
if len(energy) == 1:
energy = energy[0].value
cjson.setdefault('properties',
{})['totalEnergy'] = energy * HARTREE_TO_J_MOL
return cjson
def calculate_mo(cjson, mo):
mol = Molecule()
conv = FileFormatManager()
conv.read_string(mol, json.dumps(cjson), 'cjson')
# Do some scaling of our spacing based on the size of the molecule.
atom_count = mol.atom_count()
spacing = 0.30
if atom_count > 50:
spacing = 0.5
elif atom_count > 30:
spacing = 0.4
elif atom_count > 10:
spacing = 0.33
cube = mol.add_cube()
# Hard wiring spacing/padding for now, this could be exposed in future too.
cube.set_limits(mol, spacing, 4)
gaussian = GaussianSetTools(mol)
gaussian.calculate_molecular_orbital(cube, mo)
return conv.write_string(mol, "cjson")
def convert_str(str_data, in_format, out_format):
mol = Molecule()
conv = FileFormatManager()
conv.read_string(mol, str_data, in_format)
return conv.write_string(mol, out_format)
def avo_convert_str(str_data, in_format, out_format):
mol = Molecule()
conv = FileFormatManager()
conv.read_string(mol, str_data, in_format)
return conv.write_string(mol, out_format)
def atom_count(str_data, in_format):
mol = Molecule()
conv = FileFormatManager()
conv.read_string(mol, str_data, in_format)
return mol.atom_count()