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Merge pull request #114 from jensengroup/issue-17

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Missing N or O in AMD Group: Keep going
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Nathan Baker
2020-12-13 10:45:27 -08:00
committed by GitHub
parent 82879cdda5 f028562026
commit 2f10ecdd1f
1 changed files with 4 additions and 0 deletions
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propka/group.py
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@@ -740,6 +740,10 @@ class AMDGroup(Group):
# Identify the oxygen and nitrogen amide atoms # Identify the oxygen and nitrogen amide atoms
the_oxygen = self.atom.get_bonded_elements('O') the_oxygen = self.atom.get_bonded_elements('O')
the_nitrogen = self.atom.get_bonded_elements('N') the_nitrogen = self.atom.get_bonded_elements('N')
if not (the_oxygen and the_nitrogen):
_LOGGER.warning(f"Missing N or O atom: {self}")
self.set_center([self.atom])
return
# add protons to the nitrogen # add protons to the nitrogen
PROTONATOR.protonate_atom(the_nitrogen[0]) PROTONATOR.protonate_atom(the_nitrogen[0])
the_hydrogens = the_nitrogen[0].get_bonded_elements('H') the_hydrogens = the_nitrogen[0].get_bonded_elements('H')