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Target Preprocessing

Pipeline from a UniProt organism ID to a filtered sweep_index.tsv for ../SweepScripts. Each step is a sbatch NN_run_*.sh wrapper; modify the conda environment name and pass flags to the underlying .py/.sh to override defaults.

  1. 01_run_fetch_uniprot_info.sh — fetch reviewed UniProt entries + annotations. → Data/UniProt/uniprot_reviewed_annotated.csv
  2. 02_run_fetch_afdb_pdbs_and_pae.sh — download AlphaFold PDBs + PAE matrices. → Data/AFDB_v6/{PDB,PAE}/
  3. 03_run_create_domains_from_pae.sh — call domains from PAE (via pae_to_domains/). → Data/AFDB_v6/CSV_Domains/*.domains.csv
  4. 04_run_segment_and_compute_domain_stats.sh — segment per-domain PDBs + compute stats (pLDDT, DSSP, Rg, contacts, membrane, AF-Bind). Needs a working DSSP binary. → Data/AFDB_v6/PDB_Domains/, Data/AFDB_v6/Statistics/domain_stats.csv
    • optional 04b_generate_idp_crops.py --design-root <path> — crop disordered (IDP) regions for BindCraft. → Data/AFDB_v6/{PDB_IDP_Crops,Settings_IDP}/, idp_crops_stats.csv, idp_bindcraft_jobs.txt
  5. 05_run_filter_domains_and_create_sweep_index.sh — filter by quality thresholds, write sweep index (add --idp for crops). → Data/Filtered/filtered_domain_stats.csv, sweep_index_batch{1..4}.tsv

Step 5's output feeds ../SweepScripts/01_create_sweep_dirs.sh.