8000 lonepair refinement by JohannesKarwou · Pull Request #1266 · ParmEd/ParmEd · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

lonepair refinement #1266

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
merged 3 commits into from
Mar 23, 2023
Merged

lonepair refinement #1266

merged 3 commits into from
Mar 23, 2023

Conversation

JohannesKarwou
Copy link
Contributor

When reading in CHARMM psf files, I experienced problems for certain psf files. I included one, generated by CHARMM-GUI, which does not work as expected (loading with load_psf works fine, but processing this file or saving it with save_psf produces errors):

step3_input.zip

I think the problem is, that _process_lonepair_section is only executed, if there is a MOLNT section, which is sometimes not the case (e.g. when using the openmm option in CHARMM-GUI, like for the example provided above)

tmp = psfsections['MOLNT'][1]
tag_molecules(self)
if len(tmp) == len(self.atoms):
    # We have a CHARMM PSF file; now do NUMLP/NUMLPH sections
    self._process_lonepair_section(psfsections["NUMLP NUMLPH"])

Is there a reason, why if len(tmp) == len(self.atoms): is used for deciding whether the _process_lonepair_section() function is executed or not?
If not, I suggest a check like this:

if len(psfsections["NUMLP NUMLPH"][1]) != 0:

swails
swails approved these changes Aug 31, 2022
View reviewed changes
Copy link
Contributor
@swails swails left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks!

This was referenced Feb 2, 2023
Closed
Closed
@swails swails enabled auto-merge (squash) March 23, 2023 14:45
@swails swails merged commit c897ebb into ParmEd:master Mar 23, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@swails swails swails approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@JohannesKarwou @swails
0