🧬 superdarks: Code files : 3-post_query_informatics/library

• 📄 3rd_party_requirements.txt – Download
• 📄 compGeometry.py – Download
• 📄 determinants.py – Download
• 📄 pdbFile.py – Download

📜 Scripts in this folder

This is the stage-3 copy of the Isom-Lab computational-geometry / PDB core — the same modules that ship under 1-query_code/library/, bundled again here so stage-3 scripts (Clustal-Omega traceback mapping, BLASTP → network, go-forward traversal) can import them without referring across stages.

• compGeometry.py — Core computational-geometry primitives: geom_tol, Vertex / Vertex4D, Edge / Triangle simplex classes, plane coefficients, general-position tests, distance and centroid helpers.
• determinants.py — Explicit inline 2×2 / 3×3 / 4×4 determinants (no matrix-library dependency) used inside the convex-hull and orientation-test loops.
• pdbFile.py — Hand-rolled PDB parser: PDBfile, PseudoAtom, residue-class constants (NONPOLAR / POLAR / IONIZABLE / ALL_SIDECHAINS / ACTIVE), gzip-aware I/O.
• 3rd_party_requirements.txt — External dependencies required by the stage-3 scripts: Bio (Biopython), mmseqs, numpy, tqdm.

⚠️ Disclaimer

This is research-grade code provided for academic and exploratory purposes only. It is not intended for professional or clinical deployment.