DiffDock-L

Basics

• Entry point: python -m inference; supply one flag per line.
• Common flags: --protein_path, --ligand_description (SMILES), --ligand (SDF/MOL2), --protein_ligand_csv (batch), --out_dir.
• Write --out_dir somewhere under /outputs so poses and scores are captured.

Quick SMILES docking

--protein_path=/inputs/protein.pdb
--ligand_description=CC(=O)Oc1ccccc1C(=O)O
--complex_name=aspirin_demo
--out_dir=/outputs/aspirin_run

Dock a prepared ligand file

--protein_path=/inputs/target.pdb
--ligand=/inputs/ligand.sdf
--out_dir=/outputs/sdf_run

Batch from CSV

CSV columns: complex_name,protein_path,ligand_description (paths relative to /inputs).

--protein_ligand_csv=/inputs/pairs.csv
--out_dir=/outputs/batch_run

Submit

Launch via New Job -> DiffDock-L; the form pre-fills the SMILES example.