Reading a Gromacs topology fails with insertion code or negative number #1222
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
swails
reviewed
Feb 15, 2022
parmed/gromacs/gromacstop.py
Outdated
| type=words[1], charge=charge, mass=mass) | ||
| # check for insertion code | ||
| if words[2].isnumeric(): | ||
| try: |
Contributor
There was a problem hiding this comment.
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()):
Contributor
|
Thanks! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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.