omic/propka
1
0
Fork 0
Code Issues Pull Requests Actions 1 Packages Projects Releases Wiki Activity

Missing N or O in AMD Group: Keep going

Browse Source 
Print a warning but don't fail if the N or O atoms are missing in an
amide group. This is consistent with how other groups handle missing
atoms.

Closes https://github.com/jensengroup/propka/issues/17
This commit is contained in:
Thomas Holder
2020-12-07 09:26:53 +01:00
parent 3937cb1467
commit f028562026
1 changed files with 4 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
propka/group.py
View File

@@ -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')