CADD_Docking_Toolkit

End-to-end, config-driven workflows (RDKit, Open Babel, Vina, PLIP, PyMOL/ChimeraX) with reproducible seeds and clean outputs.

Quickstart

1. Install Python deps: pip install -r requirements.txt
2. Install external tools and ensure they’re on PATH: vina, obabel, (optional) plip, pymol, chimerax.
3. Put your inputs under data/ (e.g., data/ligands/*.sdf, data/receptors/apo_receptor.pdbqt).
4. Edit configs/example.yml to set grid and paths.

How to run

1. Setup git clone https://github.com//cadd-docking-toolkit.git cd cadd-docking-toolkit pip install -r requirements.txt ** Ensure external tools are on PATH: vina, obabel (optional: plip, pymol, chimerax)

2. Put data in place data/ ├─ receptors/ # e.g., apo_receptor.pdbqt └─ ligands/ # e.g., *.sdf / *.pdb / *.mol2

3. Edit config configs/example.yml receptor_pdbqt: "data/receptors/apo_receptor.pdbqt" ligand_dir: "data/ligands" prepared_ligand_dir: "outputs/prepared_ligands" output_dir: "outputs/docking" grid: { center: [17.933, -9.862, 12.530], size: [116, 68, 66] } vina: { energy_range: 4, num_modes: 10, exhaustiveness: 12, seed: 2122021504 }

4. Run docking python -m src.scripts.dock_batch -c configs/example.yml --ligand_ext sdf

Other tools

Validate/fix SDFs: python validate_fix_sdf.py --in_dir data/ligands --out_dir outputs/fixed_sdf --clear_logs

Convert PDB→SDF: python -m src.scripts.convert_pdb_to_sdf --in_dir data/ligands_pdb --out_dir data/ligands_sdf

Export first-pose complexes: python -m src.scripts.export_first_pose_complexes --receptor data/receptors/apo_receptor.pdbqt
--docking_dir outputs/docking --out_dir outputs/complexes

PLIP XML → plot: python -m src.scripts.parse_visualize_interactions --xml outputs/plip/report.xml --out_dir outputs/analysis