def CreateEmptyGroupDecomposition(self) -> GroupDecomposition:
"""Create and empty group decomposition object."""
emptymol = Molecule.FromSmiles("")
decomposition = self.Decompose(
emptymol, ignore_protonations=True, raise_exception=False
)
for i, (group, _) in enumerate(decomposition.groups):
decomposition.groups[i] = (group, [])
return decomposition
mol_formula):
if count == '':
count = 1
else:
count = int(count)
atom_bag[atom] = atom_bag.get(atom, 0) + count * times
n_protons = sum([
c * periodic_table.GetAtomicNumber(str(elem))
for (elem, c) in atom_bag.items()
])
atom_bag['e-'] = n_protons - formal_charge
return atom_bag, formal_charge
if __name__ == "__main__":
logging.getLogger().setLevel(logging.WARNING)
from molecule import Molecule
compound_list = [
('D-Erythrulose',
'InChI=1S/C4H8O4/c5-1-3(7)4(8)2-6/h3,5-7H,1-2H2/t3-/m1/s1')
]
for name, inchi in compound_list:
print("Formula: %s\nCharge: %d" % GetFormulaAndCharge(inchi))
diss_table, major_ms = GetDissociationConstants(inchi)
m = Molecule.FromSmiles(major_ms)
print("Name: %s\nInChI: %s\npKas: %s" %
(name, m.ToInChI(), str(diss_table)))