SPACE2

5-30 minutesPaperCodeProduction Ready

Cluster antibodies by structural similarity and accurately group those bind the same epitope

Readiness

Readiness: Production Ready
Smoke: passed_real_slurm_runner
Artifacts: verified
Production: production_pass_space2_agglomerative_clustering
Storage: <5GB
Strategy: shared python312_slim.sif + palm_py312_site + SPACE2 source + staged numba/llvmlite target
Next: Production Ready for scoped SPACE2 structural antibody clustering on IMGT-numbered PDBs. Optional hardening: expose uploaded PDB batch handling and CDR/framework selection controls.

SOP agent cloned upstream SPACE2 revision 1c98bd1feb2bf3eb54200453bc6eceafc589fe30 to /media/nik/seagate_nik/bio_server/repos/space2; repo about 15M and no large model/database requirement found. Shared python312_slim.sif is bare and missing numpy/pandas/scipy/sklearn/numba/joblib. Seagate-hosted venv failed because filesystem rejected lib64 symlink; pip --target to /media/nik/seagate_nik/bio_server/tools/space2/python was started but interrupted before validation. Synthetic IMGT-numbered benchmark script was being created but no direct or Slurm benchmark completed. 2026-07-09T01:11+08:00 SOP production validation: promoted from Production Blocked to Production Ready. Staged numba 0.61.2 and llvmlite 0.44.0 into /media/nik/seagate_nik/bio_server/tools/space2/python, while ordering PYTHONPATH so shared palm_py312_site supplies compatible numpy 1.26.4, pandas, scipy, scikit-learn, and joblib. Validated upstream oxpig/SPACE2 source revision 1c98bd1 through Ubuntu runner API job 37565a77c1a7 / Slurm job 579. Benchmark generated four synthetic IMGT-numbered H/L antibody C-alpha PDBs, ran SPACE2.agglomerative_clustering with cutoff 1.25, and produced 4 cluster assignments across 2 RMSD structural clusters. Run completed in 9.644 s. Artifacts verified: summary.json, results.csv, space2_clusters.csv, space2_records.json, ab_01.pdb, ab_02.pdb, ab_03.pdb, ab_04.pdb, run_space2.py, space2_stdout.txt, space2_stderr.txt, slurm.out, slurm.err.