Add pLDDT analysis script for FoldX5 vs FoldX5.1 classification agree…#70
Open
angelikivliora wants to merge 2 commits into
Open
Add pLDDT analysis script for FoldX5 vs FoldX5.1 classification agree…#70angelikivliora wants to merge 2 commits into
angelikivliora wants to merge 2 commits into
Conversation
mtiberti
requested changes
May 19, 2026
Comment on lines
+80
to
+82
| except Exception as e: | ||
| print(f" could not process {protein_name}: {e}") | ||
| continue |
Contributor
There was a problem hiding this comment.
here it would make more sense to exit with error - otherwise you just skip over cases that might have problems
Comment on lines
+216
to
+219
| plot_plddt_distribution(df_mutations, args.output_dir) | ||
| plot_plddt_scatter(df_mutations, args.output_dir) | ||
| print("\n[3] per-protein summary...") | ||
| plot_per_protein_delta(df_mutations, args.output_dir) |
Contributor
There was a problem hiding this comment.
more of a note for the future:
if you're running 1 call per function, they usually don't need to be functions unless they have a more general use e.g. being imported
overusing function encapsulation can complicate things and makes the script more opaque
| # Matching is done by UniProt ID + protein name | ||
| # RMSD is computed only on overlapping residues between the two structures | ||
| # Run: python rmsd_matrix.py --foldx5_dir /path/to/folder --foldx51_dir /path/to/folder --output_dir ./rmsd_results | ||
| # Run: python rmsd_matrix.py -f /data/user/shared_projects/mavisp_ensemble_sim_length/foldx5.1_evaluation/foldx5_initial_structures -i /data/user/shared_projects/mavisp_ensemble_sim_length/foldx5.1_evaluation/data_collection_foldx5.1 -o ./rmsd_results |
Contributor
There was a problem hiding this comment.
this should be in a readme file, not in the code
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.
No description provided.