Reading a Gromacs topology fails with insertion code or negative number #1222
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swails
reviewed
Feb 15, 2022
parmed/gromacs/gromacstop.py
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| @@ -491,10 +491,10 @@ def _parse_atoms(self, line, params): | |||
| atom = Atom(atomic_number=atomic_number, name=words[4], | |||
| type=words[1], charge=charge, mass=mass) | |||
| # check for insertion code | |||
| if words[2].isnumeric(): | |||
| try: | |||
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It looks like the problem is that a leading - leads to isnumeric() returning False. What about we change line 494 to this instead:
if words[2].isnumeric() or (words[2].startswith('-') and words[2][1:].isnumeric()):There was a problem hiding this comment.
Done via a8d0e3f
|
Thanks! |
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Hi Jason. I found a bug in my previous PR. Although rare, negative residues numbers fail with this setup. So I replaced the conditional with a
try-exceptclause. According to the tests I did, it should work correctly in all cases.