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Fix nitrogen symmetry #1064

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merged 2 commits into from
Jun 27, 2017
Merged

Fix nitrogen symmetry #1064

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c500e2a
improve error checking for symmetry estimation with resonance hybrids
goldmanm Jun 26, 2017
044f0d8
remove special case for atom symmetry
goldmanm Jun 26, 2017
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8 changes: 3 additions & 5 deletions rmgpy/molecule/symmetry.py
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Original file line number Diff line number Diff line change
Expand Up @@ -99,6 +99,9 @@ def calculateAtomSymmetryNumber(molecule, atom):
elif double == 2:
# Two double bonds
if count == [2]: symmetryNumber *= 2
# for nitrogen resonance hybrids
elif single == 0:
if count == [2]: symmetryNumber *=2
elif atom.radicalElectrons == 1:
if single == 3:
# Three single bonds
Expand All @@ -111,11 +114,6 @@ def calculateAtomSymmetryNumber(molecule, atom):
if count == [2]:
symmetryNumber *= 2

if atom.isNitrogen():
for groupN in groups:
if groupN.toSMILES() == "[N+](=O)[O-]":
symmetryNumber *= 2

return symmetryNumber

################################################################################
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9 changes: 8 additions & 1 deletion rmgpy/species.py
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Expand Up @@ -403,7 +403,14 @@ def getSymmetryNumber(self):
if self.symmetryNumber < 1:
cython.declare(resonanceHybrid = Molecule, maxSymmetryNum = cython.short)
resonanceHybrid = self.getResonanceHybrid()
self.symmetryNumber = resonanceHybrid.getSymmetryNumber()
try:
self.symmetryNumber = resonanceHybrid.getSymmetryNumber()
except KeyError:
logging.error('Wrong bond order generated by resonance hybrid.')
logging.error('Resonance Hybrid: {}'.format(resonanceHybrid.toAdjacencyList()))
for index, mol in enumerate(self.molecule):
logging.error("Resonance Structure {}: {}".format(index,mol.toAdjacencyList()))
raise
return self.symmetryNumber

def getResonanceHybrid(self):
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