RFpeptides

5-30 minutesPaperCodeProduction Ready

Design macrocyclic proteins

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: production_ready_shared_rfdiffusion_sif_cpu_macrocycle_slurm_verified
Storage: 5-20GB installed
Strategy: Production adapter reuses the shared RFdiffusion SIF and checkpoint cache with CPU fallback on this RTX 5050 host; macrocyclic peptide smoke uses the bundled 7zkr_GABARAP example.
Next: Optional optimization: rebuild RFdiffusion/RFpeptides SIF with PyTorch/CUDA supporting RTX 5050 sm_120 for GPU acceleration. Functional CPU Slurm/API macrocycle path is production-ready for small jobs.

generative structure/design model weights likely >5GB 2026-07-16T20:35:00+08:00 SOP Need >5GB next-10 audit: remains Need >5GB. Registry maps to rfpeptides-smoke and implementation generates fixed peptide/proxy scores; RF/RFdiffusion peptide runtime and checkpoints are not staged. 2026-07-18T19:02:14+08:00 SOP Need >5GB active install batch: Audit confirmed RFpeptides is an RFdiffusion macrocyclic peptide workflow with public BSD RFdiffusion source/checkpoints. Mandatory RFdiffusion checkpoints are about 3.15GiB before CUDA runtime and downstream workflow assets; current runner remains proxy smoke. 2026-07-18T20:49:48+08:00 SOP targeted make-ready/reclassify batch: Kept in active Need >5GB. It remains public/stageable, but requires RFdiffusion source/checkpoints and peptide workflow assets before a real macrocyclic peptide benchmark can replace the proxy smoke. 2026-07-18T21:37:01+08:00 SOP Need >5GB batch source-staging: Official RFdiffusion repo cloned to backend /media/nik/seagate_nik/bio_server/repos/rfdiffusion at 86507b6 (29MB). Agent audit confirmed macrocyclic RFdiffusion workflow/checkpoints are public; required RFdiffusion checkpoints total about 3.38GB before CUDA/DGL runtime. No checkpoint cache/SIF/benchmark yet. 2026-07-18T22:34:12+08:00 SOP Need >5GB continuation batch: No new runtime build completed in this continuation. RFdiffusion source remains staged; next production step remains checkpoint download plus shared RFdiffusion CUDA/DGL SIF and macrocyclic peptide benchmark. 2026-07-19T22:38:00+08:00 SOP Need >5GB active install batch: RFdiffusion source remains staged at /media/nik/seagate_nik/bio_server/repos/rfdiffusion commit 86507b6. The active backend asset script will cache the seven public RFdiffusion checkpoints under /media/nik/seagate_nik/bio_server/cache/rfdiffusion/models after RFantibody weights complete. No RFdiffusion CUDA/DGL/SE3 SIF or macrocyclic peptide Slurm benchmark yet. 2026-07-19T23:00:00+08:00 SOP Need >5GB active install continuation: RFpeptides remains queued behind the same RF asset script. Classic RFdiffusion checkpoint cache /media/nik/seagate_nik/bio_server/cache/rfdiffusion/models was still empty because RFantibody weights were not finished. Shared RFdiffusion/RFpeptides SIF plan confirmed: classic RFdiffusion SIF plus shared checkpoint directory, separate command template for macrocyclic peptide benchmark. 2026-07-20T22:45:00+08:00 SOP Need >5GB continuation: shared classic RFdiffusion checkpoint cache is now populated under /media/nik/seagate_nik/bio_server/cache/rfdiffusion/models with seven 462MB checkpoints (3.2GB total). Reclaimed disk by cleaning Singularity and micromamba package caches, raising free space from 19GB to 37GB. Started shared RFdiffusion SIF pull from docker://rosettacommons/rfdiffusion:latest into /media/nik/seagate_nik/bio_server/containers/rfdiffusion/rfdiffusion.sif; process still running, cache observed at 2.3GB, no SIF or benchmark yet. 2026-07-25T19:12:00+08:00 SOP Need >5GB batch: promoted to Production Ready using shared RFdiffusion SIF/cache. Direct CPU macrocycle benchmark passed with input /app/RFdiffusion/examples/input_pdbs/7zkr_GABARAP.pdb, contigmap.contigs=[12-12 A3-117/0], cyclic=True, diffuser.T=15, final_step=14. Deployed real rfpeptides adapter to /home/nik/bio_mega_runner and verified API/Slurm job ae3e9ae5fb64 / Slurm 830 COMPLETED. Artifacts verified: rfpeptides_macrocycle_0.pdb 34,036 bytes, rfpeptides_macrocycle_0.trb 15,164 bytes, residue_count=127, summary.json, results.csv, empty slurm.err. GPU path remains an optional future rebuild because the current RFdiffusion SIF PyTorch CUDA stack lacks RTX 5050 sm_120 kernels.