Fast docking evaluation metrics: symmetry-corrected RMSD and lightweight PoseBusters filters.
uv pip install posecheck-fast- Symmetry-corrected RMSD — accounts for molecular symmetry (benzene, carboxylates, etc.)
- Fast PoseBusters filters — 4 distance/clash checks optimized for throughput (auto-uses CUDA if available)
Designed for throughput: ~0.03–0.12 ms/pose on the fast filter set (CPU/GPU depending on batch size).
from posecheck_fast import compute_all_isomorphisms, get_symmetry_rmsd_with_isomorphisms
# Symmetry-corrected RMSD
isomorphisms = compute_all_isomorphisms(rdkit_mol)
rmsd = get_symmetry_rmsd_with_isomorphisms(true_coords, pred_coords, isomorphisms)from posecheck_fast import check_intermolecular_distance
# Fast filters: not_too_far_away, no_clashes, no_volume_clash, no_internal_clash
results = check_intermolecular_distance(
mol_orig=rdkit_mol,
pos_pred=pred_positions, # (n_samples, n_atoms, 3)
pos_cond=protein_positions, # (n_protein_atoms, 3)
atom_names_pred=lig_atoms,
atom_names_cond=prot_atoms,
)- PoseBench — full benchmark suite
- PoseBusters — full 27-test validation
- spyrmsd — symmetry RMSD algorithms
MIT