Align README and usage guide with numbering and parsing behavior - #222
Merged
Merged
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
The README and usage guide present IMGT domain ranges without qualifying the numbering scheme, and their Python examples use permissive PDB parsing that can silently discard duplicate atoms.
Clarify that each domain retains its selected scheme’s residue numbers and receives an offset of 0, 1000, 2000, and so on, with the listed ranges explicitly identified as IMGT examples. Update both Python examples to use
PDBParser(PERMISSIVE=False, QUIET=True), matching the CLI’s rejection of malformed duplicate atom records.Validation
12e8_H.pdbfixture; renumbering succeeded and preserved atom counts.PDBConstructionException.mkdocs build --strictpassed.git diff --checkpassed.