def check_symmetry(met_filename):
""" Function that checks if the given metabolite is symmetric.
Uses pymatgen package for symmetry related operations, and
RDKit for Molfile conversion to XYZ format. Requires Molfiles
of the metabolites to be present in the working_dir/metabolites
folder.
Current criterion for symmetricity is for every carbon except one
(central, if molecule consists of odd number of carbons) to have
at least one equivalent carbon in the structure.
Parameters
----------
met_filename : str
Filename of the specific Molfile
Returns
-------
symmetrical : bool
True if metabolite is symmetric, False if not.
"""
symmetrical = False
# Disable RDKit warnings
RDLogger.DisableLog('rdApp.*')
# Counter for non symmetrical carbon atoms
non_eq_carbons = 0
carbons = 0
# Convert Molfile to XYZ string
molecule = Chem.MolFromMolFile(f'metabolites/{met_filename}')
molecule_xyz = Chem.rdmolfiles.MolToXYZBlock(molecule)
# Create IMolecule object to analyze its' symmetricity
try:
molecule_obj = structure.IMolecule.from_str(molecule_xyz, fmt='xyz')
if len(molecule_obj) == 1:
return symmetrical
# Initialize point group analyzer
pg_analyzer = analyzer.PointGroupAnalyzer(molecule_obj)
except (IndexError, ValueError):
# '*' is unrecognized in particular
print(f'{met_filename} contains unrecognized symbols')
return symmetrical
# Extract equal atom sets
eq_atoms = pg_analyzer.get_equivalent_atoms()
for i in eq_atoms['eq_sets'].keys():
if str(molecule_obj[i].specie) == 'C':
carbons += 1
if len(eq_atoms['eq_sets'].get(i)) == 1:
non_eq_carbons += 1
if non_eq_carbons > 1:
return symmetrical
# Molecule has more than 1 carbon, and at most 1 non-symmetrical carbon
if carbons > 1:
symmetrical = True
return symmetrical
def get_pointgroup(atoms: ase.Atoms) -> str:
"""
uses pymatgen.symmetry.analyzer
"""
atoms.center()
symbs = atoms.get_chemical_symbols()
pos = atoms.get_positions()
mol = pmg.Molecule(symbs, pos)
return pysym.PointGroupAnalyzer(mol).sch_symbol
def getPointgroup(kind, storagepath):
if kind != 'molecule': return None
import pymatgen
import pymatgen.io.ase as pmgase
import pymatgen.symmetry.analyzer as psa
atoms = getAtoms(storagepath)
cm = atoms.get_center_of_mass()
m = pymatgen.Molecule(atoms.get_chemical_symbols(),
atoms.get_positions() - cm)
return psa.PointGroupAnalyzer(m).sch_symbol
def getPointgroup(kind,inittraj): if kind == 'molecule': atoms = pickle.loads(inittraj) cm = atoms.get_center_of_mass() m = pymatgen.Molecule(atoms.get_chemical_symbols(),atoms.get_positions()-cm) try: return psa.PointGroupAnalyzer(m).sch_symbol except ValueError: viz.view(atoms) sys.exit() else: return None
def structure_symmetry():
if is_pbc():
struct = readstructure(crystal=True, molecule=False)
ast = analyzer.SpacegroupAnalyzer(struct)
print("{} : {}".format('Structure Type', 'periodicity'))
print("{} : {}".format('Lattice Type', ast.get_lattice_type()))
print("{} : {}".format('Space Group ID', ast.get_space_group_number()))
print("{} : {}".format('International Symbol',
ast.get_space_group_symbol()))
print("{} : {}".format('Hall Symbol', ast.get_hall()))
return
else:
struct = readstructure(crystal=False, molecule=True)
ast = analyzer.PointGroupAnalyzer(struct)
print("{} : {}".format('Structure Type', 'non-periodicity'))
print("{} : {}".format('International Symbol', ast.get_pointgroup()))
return