Protonation State

secondsPaperCodeProduction Ready

Dominant protonation state at a given pH

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: production_pass_dimorphite_dl
Storage: <5
Strategy: shared python312_slim.sif + protonation_state_dimorphite_py312_site Dimorphite-DL/RDKit CPU layer
Next: Production Ready. Optional hardening: expose SDF upload and pH-range controls 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 protonation-state runner/Dimorphite artifacts. Dimorphite-DL can use existing RDKit-capable chemistry runtime or small overlay; no heavy SIF needed. Kept Smoke Pending. 2026-07-05 18:29 +08:00 backend re-audit: no staged Dimorphite artifacts/runner or object-store API/Slurm evidence found. Kept Smoke Pending. 2026-07-06 implementation pass: installed Dimorphite-DL 2.0.2 with RDKit 2025.09.6 at /media/nik/seagate_nik/bio_server/envs/protonation_state_dimorphite_py312_site and ran direct Slurm job 442 at /media/nik/seagate_nik/bio_server/runs/protonation-state/smoke_20260706_031000. Aspirin and imidazole pH 7.4 smoke returned 3 parseable protonation variants with summary.json, results.csv, job.log, slurm.out, and slurm.err. 2026-07-08T12:05:56+08:00: Production Ready promotion: backend runner API job 418d485bb833 / Slurm job 543 completed cleanly using shared python312_slim.sif plus protonation_state_dimorphite_py312_site. Dimorphite-DL 2.0.2 at pH 7.4 produced 3 parseable protonation variants for aspirin and imidazole with zero-byte slurm.out/slurm.err and results.csv.