Ligand Parameterisation

BATTER ships a lightweight parameterisation toolkit that converts staged ligand inputs into a content-addressed store of AMBER or OpenFF artefacts. The main entry point is batter.param.ligand.batch_ligand_process(), which produces GAFF/GAFF2 mol2/frcmod/lib bundles or OpenFF prmtop files that can be reused across simulations.

Typical usage

from batter.param.ligand import batch_ligand_process

hashes, metadata = batch_ligand_process(
    ligand_paths={
        "ligA": "ligands/adp.sdf",
        "ligB": "ligands/amp.mol2",
    },
    output_path="cache/ligands",
    ligand_ff="gaff2",
    charge_method="am1bcc",
)

print("Prepared hashes:", hashes)
print("Canonical SMILES:", metadata["ligands/adp.sdf"][1])

API Reference

Caching and validation

Ligand artifacts are content-addressed: input coordinates plus force-field/charge settings are hashed, so rerunning batch_ligand_process with the same inputs reuses cached mol2/frcmod/lib bundles instead of recomputing. Charge assignment errors and missing protonation states surface as exceptions; callers should surface those errors up the pipeline rather than silently skipping ligands. Validation also canonicalises SMILES so cache keys stay stable across input formats.

Output layout

By default, outputs land under the provided output_path in per-ligand folders that include the hash. Metadata (canonical SMILES, charge method, parameter files) is returned to the caller so builders can record it in SystemMeta and reuse the same parameter set across runs.