docs/scripts.md

📁 scripts/

Python and R utilities for scoring, clustering, and model selection.

Main scripts

• runSCC.py – calculate SCC scores for all models
• runRPF.py – run RPF scoring (slow, I/O heavy)
• getRPF.py – extract RPF scores into rpf.sc
• getpLDDT.py – extract pLDDT from AFsample/AF outputs into pLDDT.sc
• getScores.py – combine scores into scores.all
• dmPCAClustering.R – PCA + clustering of distance matrices
• selectModels.py – select conformers based on scores
• groupModels.py – group selected models into ensembles

Input conventions

• ESmodels/ – all PDB models
  • supports relaxed*.pdb or relaxed*_new.pdb
• RPF/ – input/output for RPF runs
• RCI.csv – edited RCI output with columns: Number, RCI, Residue

Then follow the commands from the Quick Start to generate:

• scc.sc – SCC scores
• rpf.sc – RPF scores
• pLDDT.sc – pLDDT scores
• scores.all – combined scoring table