Fix issue #288 #289
Merged
Fix issue #288 #289
Conversation
This file contains 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
lohedges
temporarily deployed
to
biosimspace-build
GitHub Actions
Inactive
lohedges
temporarily deployed
to
biosimspace-build
GitHub Actions
Inactive
lohedges
had a problem deploying
to
biosimspace-build
GitHub Actions
Failure
lohedges
had a problem deploying
to
biosimspace-build
GitHub Actions
Failure
lohedges
temporarily deployed
to
biosimspace-build
GitHub Actions
Inactive
chryswoods
approved these changes
May 15, 2024
lohedges
added a commit
that referenced
this pull request
May 16, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
This PR closes #288 by checking both the element and ambertype properties when detecting dummy atoms. This avoids a round-trip self-consistency issue when creating
somd1input from perturbable molecules created viasire.morph.create_from_pertfile, where the element property will have been replaced with the value of the end state with the largest number of protons, i.e. dummies may no longer haveElement("Xx").This PR supersedes #287.
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]Suggested reviewers:
@chryswoods