🧬 superdarks: Code files : 1-query_code/library

• 📄 3rd_party_requirements.txt – Download
• 📄 compGeometry.py – Download
• 📄 convexHull3D_2_0.py – Download
• 📄 convexHull4D_2_22.py – Download
• 📄 determinants.py – Download
• 📄 goFo.py – Download
• 📄 pHinderSurface.py – Download
• 📄 pdbFile.py – Download
• 📄 pdbFile_cif.py – Download
• 📄 ssco.py – Download

📜 Scripts in this folder

These are the shared computational-geometry / PDB-I/O modules imported by the stage-1 query scripts. They are the Isom-Lab library core and are also used (copied) by other stages and projects.

• compGeometry.py — Core computational-geometry primitives: tolerance estimation (geom_tol), Vertex / Vertex4D types, Edge / Triangle simplex classes, plane coefficients (planeCoefficients3D / 4D), general-position tests (gp2D / 3D / 4D), distance and centroid helpers.
• determinants.py — Explicit inline 2×2 / 3×3 / 4×4 determinants (no matrix-library dependency), tuned for tight orientation-test loops.
• convexHull3D_2_0.py — Incremental 3D convex-hull builder plus a triangulation2D helper that extracts and labels Delaunay edges for downstream network construction.
• convexHull4D_2_22.py — Incremental 4D convex-hull builder that uses the horizon-ridge trick, Simplex1..3 classes, and general-position jostling — the basis for reduced Delaunay-like representations of aligned structures.
• pdbFile.py — Hand-rolled PDB parser: PDBfile (atom / hetatm dicts, chain selection from -chains. filenames, gzip-aware I/O), PseudoAtom, and the residue-class constants (NONPOLAR / POLAR / IONIZABLE / ALL_SIDECHAINS / ACTIVE).
• pdbFile_cif.py — Sibling of pdbFile.py for mmCIF input: streams _atom_site.* records into the same PseudoAtom / residue data model.
• pHinderSurface.py — pHinder surface reducer: builds ionizable / polar / apolar surface networks from a PDB using convexHull4D_2_22 + goFo, with gzip output and perf_counter timers.
• goFo.py — Recursive “go-forward” walk through a triangulation or network: forbids revisits, carries level / edge bookkeeping, and supports PSA filtering and edge-skip lists — the graph-traversal primitive reused across pHinder and superdarks.
• ssco.py — Secondary-Structure Constrained-Object extractor: grab_ssco pulls helical and sheet CA residues from a PDB (via PseudoAtom + 4D circumspheres) and optionally writes _helix, _sheet, or combined PDBs.
• 3rd_party_requirements.txt — External dependencies required by the stage-1 scripts: bjobs, bsub (LSF), and numpy.

⚠️ Disclaimer

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