Legolas

secondsPaperCodeProduction Ready

Predict protein chemical shifts from PDB structures

Readiness

Readiness: Production Ready
Smoke: passed_real_slurm_runner
Artifacts: verified
Production: production_ready_real_runner_configured
Storage: <5
Strategy: shared python312_slim.sif + staged Python dependency sites
Next: Production Ready. Optional hardening: expose additional atom type/output controls and add uploaded trajectory/topology validation.

Legolas source staged from roitberg-group/legolas rev 9485a137a94981523a2dd9c68fc280700413f245; submodule internal-legolas-aev at 86dea01bc2a7387ec1ea171760a02da9e3ff1182. MIT license. Size ~92-109 MB, no large external database observed beyond bundled test/model assets. Existing runtimes lack torchani and mdtraj; upstream cpu_env.yaml not installed. No Slurm smoke yet. 2026-07-05 SOP triage: Legolas source and submodule are staged, with no large database observed, but current runtimes lack torchani and mdtraj and upstream cpu_env.yaml is not installed. No direct Slurm smoke or runner exists. Reclassified from Smoke Pending to Production Blocked until the CPU env/container is built. 2026-07-08T23:41+08:00 SOP production validation: promoted from Production Blocked to Production Ready. Reused shared python312_slim.sif with /media/nik/seagate_nik/bio_server/envs/palm_py312_site, /media/nik/seagate_nik/bio_server/envs/cluster_pdbs_mdtraj_py312_site, and staged internal LEGOLAS torchani source. Validated roitberg-group/legolas source revision 9485a137a94981523a2dd9c68fc280700413f245 through Ubuntu runner API job 541d31ca064c / Slurm job 576 on bundled A001_1KF3A.pdbH with atom types H,C,N. Run completed in 3.082 s and produced 370 finite chemical-shift predictions (C=124, H=122, N=124; min -3.0580482482910156, max 180.4242401123047, mean 101.68281978916478). Artifacts verified: summary.json, results.csv, legolas_predictions.csv, legolas_predictions.parquet, legolas_chemical_shifts.pdb, legolas_stdout.txt, legolas_stderr.txt, A001_1KF3A.pdbH, slurm.out, slurm.err.