def _nitrogen_protonate(self, nitrogens, previous):
"""
:param nitrogens: list of Nitrogens
:param previous:
:return:
"""
def reset():
for n in nitrogens:
self.rwmol.GetAtomWithIdx(n).SetNumExplicitHs(0)
reset()
p = Chem.DetectChemistryProblems(self.rwmol)
if len(p) == 0 or p[0].Message() != previous:
return True
for i in range(1, len(nitrogens)):
for c in itertools.combinations(nitrogens, i):
reset()
for n in c:
self.rwmol.GetAtomWithIdx(n).SetNumExplicitHs(1)
p = Chem.DetectChemistryProblems(self.rwmol)
if len(p) == 0 or p[0].Message() != previous:
return True
return False
self.log.debug(f'KekulizeException likely caused by nitrogen')
def _nitrogen_protonate(self, N, previous):
def reset():
for n in N:
self.mol.GetAtomWithIdx(n).SetNumExplicitHs(0)
reset()
p = Chem.DetectChemistryProblems(self.mol)
if len(p) == 0 or p[0].Message() != previous:
return True
for i in range(1, len(N)):
for c in itertools.combinations(N, i):
reset()
for n in c:
self.mol.GetAtomWithIdx(n).SetNumExplicitHs(1)
p = Chem.DetectChemistryProblems(self.mol)
if len(p) == 0 or p[0].Message() != previous:
return True
return False
log.debug(f'KekulizeException likely caused by nitrogen')
def fix_issues(self, _previous=None):
problems = Chem.DetectChemistryProblems(self.mol)
if self._iterations_done > 100:
log.error(f'Iterations maxed out!')
return None
elif self._subiterations_done > 5:
log.error(f'Unfixable')
return None
elif len(problems) == 0:
return None
else:
log.debug(
f'(Iteration: {self._iterations_done}) N problems {len(problems)}'
)
p = problems[0]
log.debug(
f'(Iteration: {self._iterations_done}) Issue {p.GetType()}: {p.Message()}'
)
if p.Message() == _previous:
self.triage_rings()
############################################################
if p.GetType() == 'KekulizeException':
if p.Message() != _previous:
N = self._get_nitrogens(p.GetAtomIndices())
if len(N) > 0 and self._nitrogen_protonate(N, p.Message()):
pass # been fixed.
else:
# triage rings should have altered any not ring atoms that are aromatic.
# self._get_ring_info()
# so it is likely a hetatom thing.
log.info(
f'Ring triages seems to have failed. Is it a valence thing?'
)
valence_issues = [
self._has_correct_valence(i)
for i in p.GetAtomIndices()
]
if not all(valence_issues):
for i in p.GetAtomIndices():
self.fix_valence(i)
else:
log.warning(
f'Attempting default valency (not max)')
self._valence_mode = 'default'
for i in p.GetAtomIndices():
self.fix_valence(i)
self._valence_mode = 'max'
else:
for i in p.GetAtomIndices():
self.downgrade_ring(self.mol.GetAtomWithIdx(i))
self.triage_rings()
############################################################
elif p.GetType(
) == 'AtomKekulizeException' and 'non-ring atom' in p.Message():
atom = self.mol.GetAtomWithIdx(p.GetAtomIdx())
atom.SetIsAromatic(False)
log.debug(f'Atom {p.GetAtomIdx()} set to non-aromatic.')
for bond in atom.GetBonds():
bond.SetBondType(Chem.BondType.SINGLE)
elif p.GetType(
) == 'AtomKekulizeException' and 'Aromatic bonds on non aromatic atom' in p.Message(
):
atom = self.mol.GetAtomWithIdx(p.GetAtomIdx())
log.debug(f'Atom {p.GetAtomIdx()} set to aromatic.')
atom.SetIsAromatic(True)
############################################################
elif p.GetType() == 'AtomValenceException':
i = p.GetAtomIdx()
self.fix_valence(i)
else:
log.error('???', p.GetType(), p.Message())
self._iterations_done += 1
if _previous != p.Message():
log.debug(f'{self._iterations_done} appears successful.')
self._subiterations_done = 0
else:
self._subiterations_done += 1
log.debug(f'{self._iterations_done} appears unsuccessful.')
return self.fix_issues(_previous=p.Message())
def fix_issues(self, _previous=None) -> None:
"""
This get run during instantiation. It is the third and final one run before sanitization.
Deals with a variety of problems.
It calls itself until no problems according to `Chem.DetectChemistryProblems` exits.
It is a bit shoddy and any oddity likely steps from here. TODO
:return: None
"""
self.modifications.append(self.mol) # may not have changed.
problems = Chem.DetectChemistryProblems(self.rwmol)
if self._iterations_done > 100:
self.log.error(f'Iterations maxed out!')
return None
elif self._subiterations_done > 5:
self.log.error(f'Unfixable')
return None
elif len(problems) == 0:
return None
else:
self.log.debug(
f'(Iteration: {self._iterations_done}) N problems {len(problems)}'
)
p = problems[0]
self.log.debug(
f'(Iteration: {self._iterations_done}) Issue {p.GetType()}: {p.Message()}'
)
if p.Message() == _previous:
self.triage_rings()
############################################################
if p.GetType() == 'KekulizeException':
if p.Message() != _previous:
N = self._get_nitrogens(p.GetAtomIndices())
if len(N) > 0 and self._nitrogen_protonate(N, p.Message()):
pass # been fixed.
else:
# triage rings should have altered any not ring atoms that are aromatic.
# self._get_ring_info()
# so it is likely a hetatom thing.
self.log.info(
f'Ring triages seems to have failed. Is it a valence thing?'
)
valence_issues = [
self._has_correct_valence(i)
for i in p.GetAtomIndices()
]
if not all(valence_issues):
for i in p.GetAtomIndices():
self.fix_valence(i)
else:
self.log.warning(
f'Attempting default valency (not max)')
self._valence_mode = 'default'
for i in p.GetAtomIndices():
self.fix_valence(i)
self._valence_mode = 'max'
else:
for i in p.GetAtomIndices():
self.downgrade_ring(self.rwmol.GetAtomWithIdx(i))
self.triage_rings()
############################################################
elif p.GetType(
) == 'AtomKekulizeException' and 'non-ring atom' in p.Message():
atom = self.rwmol.GetAtomWithIdx(p.GetAtomIdx())
atom.SetIsAromatic(False)
self.log.debug(f'Atom {p.GetAtomIdx()} set to non-aromatic.')
for bond in atom.GetBonds():
bond.SetBondType(Chem.BondType.SINGLE)
elif p.GetType(
) == 'AtomKekulizeException' and 'Aromatic bonds on non aromatic atom' in p.Message(
):
atom = self.rwmol.GetAtomWithIdx(p.GetAtomIdx())
self.log.debug(f'Atom {p.GetAtomIdx()} set to aromatic.')
atom.SetIsAromatic(True)
############################################################
elif p.GetType() == 'AtomValenceException':
i = p.GetAtomIdx()
self.fix_valence(i)
else:
self.log.error('???', p.GetType(), p.Message())
self._iterations_done += 1
if _previous != p.Message():
self.log.debug(f'{self._iterations_done} appears successful.')
self._subiterations_done = 0
else:
self._subiterations_done += 1
self.log.debug(
f'{self._iterations_done} appears unsuccessful.')
return self.fix_issues(_previous=p.Message())
