def compare(self, inchi, u_indices=None, p_indices=None):
u_layer = U_LAYER_PREFIX + U_LAYER_SEPARATOR.join(map(
str, u_indices)) if u_indices else None
p_layer = P_LAYER_PREFIX + P_LAYER_SEPARATOR.join(map(
str, p_indices)) if p_indices else None
aug_inchi = compose_aug_inchi(inchi, u_layer, p_layer)
mol = from_augmented_inchi(Molecule(), aug_inchi)
ConsistencyChecker.check_multiplicity(mol.get_radical_count(),
mol.multiplicity)
for at in mol.atoms:
ConsistencyChecker.check_partial_charge(at)
spc = Species(molecule=[mol])
spc.generate_resonance_structures()
ignore_prefix = r"(InChI=1+)(S*)/"
aug_inchi_expected = re.split(ignore_prefix, aug_inchi)[-1]
aug_inchi_computed = re.split(ignore_prefix,
spc.get_augmented_inchi())[-1]
self.assertEquals(aug_inchi_expected, aug_inchi_computed)
return mol
def _check_molecule(mol, aug_inchi):
"""
Check if the molecular structure is correct.
Checks whether the multiplicity contained in the augmented inchi,
corresponds to the number of unpaired electrons + 1 found in the molecule.
Checks whether the valence of each atom is compatible with the bond order,
number of unpaired electrons, lone pairs and charge.
"""
cython.declare(inchi=str, at=Atom)
ConsistencyChecker.check_multiplicity(mol.get_radical_count(),
mol.multiplicity)
_, u_indices, _ = decompose_aug_inchi(str(aug_inchi))
assert (mol.get_radical_count() == len(u_indices))
for at in mol.atoms:
ConsistencyChecker.check_partial_charge(at)