Fix: CIF parser wasn't respecting parseCAOnly - #1156
Merged
Merged
Conversation
sbittrich
self-requested a review
September 15, 2026 06:01
sbittrich
approved these changes
Sep 15, 2026
sbittrich
left a comment
Member
There was a problem hiding this comment.
LGTM, thanks.
Would consider moving the fixed logic though.
Comment on lines
+322
to
+323
| // keep only C-alpha atoms; requiring element C excludes calcium ions, whose atom name is also CA | ||
| if (!(labelAtomId.get(atomIndex).equals(StructureTools.CA_ATOM_NAME) && "C".equals(typeSymbol.get(atomIndex)))) { |
Member
There was a problem hiding this comment.
Suggested change
| // keep only C-alpha atoms; requiring element C excludes calcium ions, whose atom name is also CA | |
| if (!(labelAtomId.get(atomIndex).equals(StructureTools.CA_ATOM_NAME) && "C".equals(typeSymbol.get(atomIndex)))) { | |
| for (int atomIndex = 0; atomIndex < atomSite.getRowCount(); atomIndex++) { | |
| if (params.isParseCAOnly()) { | |
| // keep only C-alpha atoms; requiring element C excludes calcium ions, whose atom name is also CA | |
| if (!(labelAtomId.get(atomIndex).equals(StructureTools.CA_ATOM_NAME) && "C".equals(typeSymbol.get(atomIndex)))) { | |
| continue; | |
| } | |
| } | |
| boolean startOfNewChain = false; |
There may be another bug here. Because the check happens this late, lots of empty groups and chains are created.
How about moving it all the way up and making it the first action in the loop?
Contributor
Author
There was a problem hiding this comment.
Indeed, good point. The empty chain/groups are actually another bug by itself. Should be fixed in 0b8427a
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
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.
Including a new unit test for it.