🧬 superdarks: Code files : 1-query_code

• 📁 library/
• 📄 1-superDark-jobParser.py – Download
• 📄 1-superDark.py – Download
• 📄 2-collectResults.py – Download
• 📄 3-alignResults-jobParser.py – Download
• 📄 3-alignResults.py – Download
• 📄 4-parseHits-jobParser.py – Download
• 📄 4-parseHits.py – Download

📜 Scripts in this folder

• 1-superDark.py — Per-node TM-align runner: aligns the query PDB against a shard of AlphaFold Database predictions on one compute node (driven by getopt flags from the job parser).
• 1-superDark-jobParser.py — LSF bsub wrapper that distributes 1-superDark.py across up to 1,000 Triton / Pegasus / BU-SCC nodes, tracks per-node jobs, and supports resubmission of failed shards.
• 2-collectResults.py — Consolidates per-node result objects into a single hit listing, applying configurable min_tm_score and min_residues thresholds from its CONFIG block.
• 3-alignResults.py — Re-aligns top-ranked hits to the query to produce aligned PDBs suitable for figure generation.
• 3-alignResults-jobParser.py — LSF bsub wrapper for 3-alignResults.py that fans the re-alignment step out across cluster nodes.
• 4-parseHits.py — Parses rank--coverage-tm--UNIPROT-…-full.pdb filenames into a structured hit listing (rank, coverage, TM-score, UniProt ID).
• 4-parseHits-jobParser.py — LSF bsub wrapper for 4-parseHits.py.

⚠️ Disclaimer

This is research-grade code provided for academic and exploratory purposes only. It is not intended for professional or clinical deployment.