GV

GeezerVison

The World Wide Web, restored to 800 pixels of glory.

Home|About|Gaming cabinet|Archives|How it works|Starter sites

On this site

  • Sign in
  • ActionsCI/CD and automation
  • CodespacesCloud development environments
  • All Features
  • Documentation
  • Training
  • Certifications
  • Build with Copilot
  • Customize Copilot
  • Integrations
  • Trending repos
  • GitHub Sponsors
  • Developer articles
  • Enterprises

This view

  • Original page
  • New address

GeezerVison is showing github.com — Quaternary symmetry calculation edge-case by josemduarte · Pull Request #1120 · biojava/biojava

Conversation

@josemduarte

@josemduarte josemduarte commented Dec 8, 2025

Copy link
Copy Markdown
Contributor

When computing symmetry with structural clustering for 9y9z an IllegalArgumentException was occurring in QuatSymmetrySubunits. Also added some logging improvements.

Sorry, something went wrong.

Uh oh!

There was an error while loading. Please reload this page.
All reactions
@josemduarte
Bugfix: edge-case with no equiv residues in alignment wasn't dealt wi…
423cd86 
…th and led to IllegalArgumentException.

Also: improved logging
@josemduarte
josemduarte requested a review from lafita December 8, 2025 23:29
josemduarte
josemduarte commented Dec 8, 2025
View reviewed changes
Comment thread biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
if (thisAligned.isEmpty() && otherAligned.isEmpty()) {
logger.warn("No equivalent aligned atoms found between SubunitClusters {} via structure alignment. Will not merge the second one into the first.", pairName);
return false;
}

@josemduarte josemduarte Dec 8, 2025

Copy link
Copy Markdown
Contributor Author

There was a problem hiding this comment.

Choose a reason for hiding this comment

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

This is the fix. The rest are formatting and logging improvements.

Sorry, something went wrong.

Uh oh!

There was an error while loading. Please reload this page.
All reactions
@josemduarte
josemduarte merged commit 8edaed7 into master Dec 10, 2025
9 of 10 checks passed

Uh oh!

There was an error while loading. Please reload this page.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@lafita lafita Awaiting requested review from lafita

Uh oh!

There was an error while loading. Please reload this page.

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

Uh oh!

There was an error while loading. Please reload this page.

1 participant

@josemduarte
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.
You are visitor 01402503 — GeezerVison does not store the pages you look up.
Best viewed with Netscape Navigator 4.7 or Internet Explorer 6 at 800×600. No cookies required.