ptm sphere

[3dot141592]

Description

fixes #405
Adds trimesh spheres for PTMs and amino acids and displays them in the validation step if they intersect.
The user can also specify the number of neighboring amino acids around the PTM that should be ignored when calculating intersections.

Changes

• Added a PTM validation step that detects intersections between PTMs and amino acids.
• Added trimesh spheres for PTMs and intersecting amino acids to the structure visualization.
• Added an input for ignoring neighboring amino acids during intersection calculations.
• Added a table listing the detected intersections.
• Only intersecting amino acid spheres are displayed. PTM spheres are always shown, while amino acid spheres are only rendered when they intersect with a PTM sphere.
• Neighbor filtering is chain-specific. Only neighboring residues within the specified sequence distance and on the same chain are ignored.

Testing

1. Import a protein structure containing PTMs.
2. Add and run the PTM Validation step.
3. Verify that detected intersections are listed in the output table.
4. Verify that the PTMs and intersecting amino acids are displayed as spheres in the structure visualization.
5. Change the number of ignored PTM residue neighbors and verify that the results update accordingly.

• Maybe check code for stupidity :)

How is a sphere calculated?

A sphere is calculated for each PTM and amino acid. Its center is the mean position of all corresponding atom coordinates. Its radius is the maximum distance from this center to any atom, extended by that atom's van der Waals radius.

Two spheres are considered intersecting when the distance between their centers is smaller than the sum of their radii.

PR checklist

Development

• If necessary, I have updated the documentation (README, docstrings, etc.)
• If necessary, I have created / updated tests.

Mergeability

• main-branch has been merged into local branch to resolve conflicts
• The tests and linter have passed AFTER local merge
• The backend code has been formatted with black
• The frontend code has been formatted with pnpm format and checked with pnpm lint

Code review

• I have self-reviewed my code.
• At least one other developer reviewed and approved the changes

[NeleRiediger]

Testing worked great and the code looks good to me too. Although I can't really verify, whether all the logic is completely correct.

[tE3m]

Everything works from what I can see, good work there! I didn't check the frontend code too closely as I'm out of my depth there. Since the PR is rather large, I didn't focus on the geometrical/trimesh operations but rather on the pandas/df operations.
See my comments about the column titles, I'm a big proponent of using the constants but you don't have to if you think it's better this way. I was just a bit confused by the wording throughout the code, I feel like amino_acid should in most cases be replaced by something like unmodified, since PTMs are just modifications on amino acids, they're not really different concepts.
Also check out the merge conflicts, since those currently block merging this addition

[github-actions]

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
backend/main
views_helper.py					239-252
backend/protzilla/data_analysis
amino_acid_spheres.py					28-60, 72-102, 111-135, 143-194
crosslinking_validation.py					83
geometry_operations.py					25-29, 48-94, 107-117, 121, 128, 139-144, 156-168, 184, 186, 190, 212-224, 242-246, 258-263
ptm_analysis.py					106-142
backend/protzilla/methods
data_analysis.py					2514
backend/protzilla/utilities
ptm_helper.py					67, 69, 78-90
Project Total

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