peptidomimetics/scripts/pcomole.sh

#!/usr/bin/env bash
set -euo pipefail
ROOT="$(cd "$(dirname "$0")/../.." && pwd)"
cd "$ROOT/peptidomimetics"
python -u pcomole.py \
  --pcomol_config "$ROOT/configs/config_selfies.yaml" \
  --bindevaluator_config "$ROOT/peptidomimetics/bindevaluator_config.yaml" \
  --ckpt "$ROOT/peptidomimetics/ckpt/SELFIES_EditFlows.ckpt" \
  --num_steps 20 \
  --num_candidates 50 \
  --num_rollouts 20 \
  --objective_weights 4 2 4 0.2 4 2 1 \
  --input 'CC[C@H](C)[C@H]1C(=O)NCC(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@H](C(=O)NCC(=O)N[C@@H](CSSC[C@@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N1)CCCNC(=N)N)CC(=O)O)CC(C)C)CCCCN)CC(C)C)CC2=CC=CC=C2)NC(=O)CNC(=O)[C@H](CCCCN)NC(=O)[C@H](CO)NC(=O)[C@H](CC(C)C)NC(=O)CN)C(=O)O)CC(C)C)CO)CCSC)CO' \
  --target 'RNLTLAVVLPEHNLSYAWAWPRVGPAVALAVEALGRALPVDLRFVSSELEGACSEYLAPLSAVDLKLYHDPDLLLGPGCVYPAASVARFASHWRLPLLTAGAVASGFSAKNDHYRTLVRTGPSAPKLGEFVVTLHGHFNWTARAALLYLDARTDDRPHYFTIEGVFEALQGSNLSVQHQVYAREPGGPEQATHFIRANGRIVYICGPLEMLHEILLQAQRENLTNGDYVFFYLDVFGESLRAGPTRATGRPWQDNRTREQAQALREAFQTVLVITYREPPNPEYQEFQNRLLIRAREDFGVELGPSLMNLIAGCFYDGILLYAEVLNETIQEGGTREDGLRIVEKMQGRRYHGVTGLVVMDKNNDRETDFVLWAMGDLDSGDFQPAAHYSGAEKQIWWTGRPIPWVKGAPPSDNPPCAFDLDDPSCDKTPLSTLAI' \
  --motifs '50-87,100-113,143-165' \
  --specificity \
  --output_file "$ROOT/outputs/peptidomimetic_pcomole.csv"