Protein Properties

secondsPaperCodeProduction Ready

Calculate properties on input sequence/structure

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: production_ready_chemfeatx_runner_validated
Storage: <5
Strategy: validated shared python312_slim.sif + MSMS/DSSP structural descriptor runtime
Next: Production Ready; monitor user PDB edge cases and larger multi-chain structures.

SOP main-thread triage cloned upstream SFBBGroup/AbSet revision dd09fd402e25aad392e6da68662bfb5a6955f1c1 at /media/nik/seagate_nik/bio_server/tools/protein-properties/source. AbSet ChemFeatX is a PDB molecular-descriptor workflow, not the current sequence-only proxy runner. Slurm job 385 attempted ChemFeatX molecular_descriptors_calculator.py on bundled 1a2y_1.pdb using existing Python target sites; it failed because Bio.PDB ResidueDepth requires msms and /bin/sh reported msms not found. Upstream also documents DSSP and MGLtools prerequisites. Current web protein-properties runner remains a simple proxy calculator and is not sufficient for Production Ready. 2026-07-09T14:28:56+08:00 SOP blocked recheck: live backend still lacks msms, mkdssp/dssp, reduce, and probe on PATH. ChemFeatX molecular_descriptors_calculator.py requires Biopython ResidueDepth/MSMS for mean_dpx and mkdssp for secondary structure/phi/psi; disabling those would be an incomplete proxy rather than SOP production validation. No promotion; keep Production Blocked until MSMS/DSSP/MGLtools-compatible structural descriptor runtime is packaged and benchmarked. 2026-07-10T17:36:52+08:00 SOP production validation: promoted from Production Blocked to Production Ready. Staged MSMS 2.6.1 from the Bioconda linux-64 package at /media/nik/seagate_nik/bio_server/tools/protein-properties/msms_bioconda, reused /home/nik/bio_server_venvs/alphacutter_runtime DSSP wrappers, and ran upstream SFBBGroup/AbSet ChemFeatX molecular_descriptors_calculator.py through shared python312_slim.sif with palm_py312_site dependencies. Direct validation at /media/nik/seagate_nik/bio_server/artifacts/protein-properties/direct_20260710_172719 produced output/1a2y_1.csv with 352 residue rows. Added real runner adapter and validated via Ubuntu runner API remote job 89ff4f2c7f10 / Slurm job 689 in 8.82 s. Verified artifacts include summary.json, results.csv, protein_properties.csv, protein_properties_summary.json, stdout/stderr, slurm.out, slurm.err, and job.log. Metrics: residue_count 352, chain_count 3, chains C,H,L, mean_sasa 45.590795, mean_rasa 30.868994, mean_residue_depth 2.631233.