Contact MS

secondsPaperCodeProduction Ready

Contact molecular surface area for protein-protein interfaces

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: production_pass_py_contact_ms
Storage: <5
Strategy: shared python312_slim.sif + contact_ms_py312_site and py_contact_ms source overlay
Next: Production Ready. Optional hardening: expose multi-chain selection and richer PDB upload validation in the UI.

No obvious large model/database dependency identified; validate upstream docs before install. 2026-07-05 SOP batch recheck: backend inventory found no staged Contact-MS runner/artifacts. Upstream py_contact_ms is CPU Python/BioPython and documents no GPU requirement; GPU flag corrected to no. Kept Smoke Pending. 2026-07-05 18:35 +08:00 backend re-audit: no staged Contact-MS runner/artifacts or Slurm/API artifacts found; CPU Python/BioPython path remains likely. Kept Smoke Pending. 2026-07-06 implementation pass: cloned py_contact_ms source revision 724c2a66d886cd92e5dba44868bc76e91b2a2a7c under /media/nik/seagate_nik/bio_server/tools/contact-ms/source after upstream pyproject.toml packaging failed validation, staged numpy/scipy/BioPython in /media/nik/seagate_nik/bio_server/envs/contact_ms_py312_site, and ran direct Slurm job 448 at /media/nik/seagate_nik/bio_server/runs/contact-ms/smoke_20260706_041500 using shared python312_slim.sif. The A/B chain benchmark on sc_example.pdb produced finite Contact-MS 264.239362 A^2 with summary.json, results.csv, per_atom_contact_surface.csv, PDB copy, job.log, slurm.out, and slurm.err. 2026-07-08T20:05:05+08:00: Production Ready promotion: backend runner API job dda53e60a183 / Slurm job 560 completed cleanly using shared python312_slim.sif plus contact_ms_py312_site and py_contact_ms source rev 724c2a66d886cd92e5dba44868bc76e91b2a2a7c. Produced zero-byte slurm.out/slurm.err, results.csv, per_atom_contact_surface.csv, and finite Contact-MS 264.23936236405154 A^2 on the A/B chain benchmark.