Geometry operations

[3dot141592]

Description

Introduces new geometric functions:

• extract_points_from_cif: extracts the atom coordinates for a given residue range
• build_convex_hull: builds a 3D convex hull mesh
• meshes_intersect: checks whether two triangle meshes intersect
• meshes_distance: calculates the minimum Euclidean distance between two triangle meshes

Changes

Added new librarys trimesh 4.11.5 and python-fc 0.7.0.11.
Added geometry_operations.py.

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

[github-actions]

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
backend/protzilla/data_analysis
geometry_operations.py					1-182
Project Total

This report was generated by python-coverage-comment-action

[jorisfu]

Looks generally good as a starting point for the upcoming stuff, wouldn't merge yet though as we have not finally decided on how we do the 3D stuff

[jorisfu]

Suggested change

	:return: array of n points und x, y, z coordinates. (n, 3)
	:return: array of n points and x, y, z coordinates. (n, 3)