gtcf-oncology-verification-rj 0.1.2

Computational verification pipeline for GTCF-Onc

GTCF-Onc Computational Verification

Computational verification pipeline for the two oncology witness theorems in "Geometry–Topology Coequal Framework in Oncology (GTCF-Onc): Locating Structural-Blindness and Topological-Sensitivity Gaps in Cancer Structural Biology" (Rajesh Kumar, independent researcher).

This repository implements Section 7 ("Required Computational Verification") of that paper: it computes the geometric functor G and topological functor T for the two witness pairs and tests whether they exhibit Structural Blindness (Theorem 1) and Topological Sensitivity (Theorem 2).

Theorem	Witness pair	Claim
1 — Structural Blindness	KRAS GDP-bound (4OBE) vs KRAS GTP-γS-bound (5VQ6)	G differs (switch I/II rearrangement); T predicted equal
2 — Topological Sensitivity	Telomeric G-quadruplex antiparallel basket (143D) vs parallel propeller (1KF1)	G equal (coarse compactness); T differs (loop connectivity)

Status of this repository, honestly stated

This repo was built inside a sandboxed agent environment whose network egress is restricted to a small allow-list of code-hosting domains (github.com, pypi.org, npmjs.com, etc.) and does not include files.rcsb.org. That was verified directly: a request to files.rcsb.org from that sandbox returns HTTP 403 Forbidden.

As a result:

• The full pipeline code is complete, tested, and correct — see tests/test_pipeline.py (7/7 passing) and the two smoke-test runs described in RESULTS.md.
• One real, partial fragment of PDB entry 4OBE (header, full sequence, full secondary-structure records for both chains, and chain-A backbone atoms for residues 1–32) was retrieved through a web-fetch tool and is committed at data/4OBE/4OBE_partial.pdb. It is real crystallographic data, not synthetic — but it is one nucleotide state only, and it stops mid-structure (before switch II), so it cannot by itself establish or refute Theorem 1.
• No coordinate data for 5VQ6, 143D, or 1KF1 was retrievable in that sandboxed session.
• Theorem 1 and Theorem 2 therefore remain conditional, exactly as stated in the paper — this repository does not claim otherwise.

How to complete the verification (takes ~1 minute with normal internet)

pip install -r requirements.txt
python src/fetch_structures.py      # downloads 4OBE, 5VQ6, 143D, 1KF1 from RCSB
python src/verify_theorem1.py       # full real-data run once files are present
python src/verify_theorem2.py       # full real-data run once files are present

Each verify_theorem*.py script auto-detects whether the full structure files are present under data/<PDB_ID>/<PDB_ID>.pdb. If they are, it runs the real Section 7 computation (Kabsch RMSD + Vietoris–Rips persistence diagrams + bottleneck distance) and prints ESTABLISHED / NOT SUPPORTED for that theorem. If they are not, it falls back to reporting what can honestly be said from the partial real data plus a clearly-labeled synthetic smoke test that only demonstrates the code is working correctly — never presented as evidence for the paper's claims.

Repository layout

data/                   PDB coordinate files (only 4OBE_partial.pdb is committed;
                        run fetch_structures.py to populate the rest)
src/
  pdb_utils.py          minimal PDB ATOM-record parser
  geometry.py           G functor: Kabsch RMSD, radius of gyration, diameter, bend angle
  topology.py           T functor: Vietoris-Rips persistence diagrams, bottleneck distance
  fetch_structures.py   downloads the four witness structures from RCSB PDB
  verify_theorem1.py    Structural Blindness verification (KRAS)
  verify_theorem2.py    Topological Sensitivity verification (G-quadruplex)
tests/
  test_pipeline.py      unit tests against synthetic ground truth (no network needed)
RESULTS.md              exact output of every script run so far, with dates
requirements.txt
LICENSE

Citation

If you use this code, please cite the paper it accompanies:

Kumar, R. Geometry–Topology Coequal Framework in Oncology (GTCF-Onc): Locating Structural-Blindness and Topological-Sensitivity Gaps in Cancer Structural Biology. Preprint, 2026.

License

MIT (see LICENSE). PDB data retrieved via fetch_structures.py is subject to RCSB PDB's own data usage policies.