def __init__(self, mol=None, symmetrize=True, tm=Tol_matrix(prototype="molecular")):
mo = None
self.smile = None
self.torsionlist = None
if type(mol) == str:
# Parse molecules: either file or molecule name
tmp = mol.split(".")
self.name = tmp[0]
if len(tmp) > 1:
# Load the molecule from the given file
if tmp[-1] in ["xyz", "gjf", "g03", "json"]:
if os.path.exists(mol):
mo = Molecule.from_file(mol)
else:
raise NameError("{:s} is not a valid path".format(mol))
elif tmp[-1] == 'smi':
self.smile = tmp[0]
symbols, xyz, self.torsionlist = self.rdkit_mol_init(tmp[0])
mo = Molecule(symbols, xyz)
symmetrize = False
else:
raise NameError("{:s} is not a supported format".format(tmp[-1]))
else:
# print('\nLoad the molecule {:s} from collections'.format(mol))
mo = molecule_collection[mol]
elif hasattr(mol, "sites"): # pymatgen molecule
self.name = str(mol.formula)
mo = mol
if mo is None:
msg = "Could not create molecules from given input: {:s}".format(mol)
raise NameError(msg)
self.props = mo.site_properties
if len(mo) > 1:
if symmetrize:
pga = PointGroupAnalyzer(mo)
mo = pga.symmetrize_molecule()["sym_mol"]
mo = self.add_site_props(mo)
self.mol = mo
self.tm = tm
self.get_box()
self.volume = self.box.volume
self.get_radius()
self.get_symbols()
self.get_tols_matrix()
xyz = self.mol.cart_coords
self.reset_positions(xyz-self.get_center(xyz))
#Testing water
mol = deepcopy(c60)
print("Original molecule:")
print(mol)
print()
#Apply random rotation to avoid lucky results
R = aa2matrix(1, 1, random=True)
R_op = SymmOp.from_rotation_and_translation(R, [0, 0, 0])
mol.apply_operation(R_op)
print("Rotated molecule:")
print(mol)
print("============================================")
pga = PointGroupAnalyzer(mol)
mol = pga.symmetrize_molecule()['sym_mol']
#orientation_in_wyckoff_position(mol, sg, WP's index in sg)
#returns a list of orientations consistent with the WP's symmetry.
#We can choose any of these orientations at random using np.random.choice
#To use an orientation, do mol.apply_operation(orientation)
#Spacegroup WP 24l (index 2) in sg 221 has m.. symmetry
allowed = orientation_in_wyckoff_position(mol, 221, 2, randomize=True)
print("Found " + str(len(allowed)) + " orientations:")
print("------------------------------")
for op in allowed:
mo = deepcopy(mol)
mo.apply_operation(op)
print()
print(mo)