Fast docking evaluation metrics: symmetry-corrected RMSD and PoseBusters filters
Project description
posecheck-fast
Fast docking evaluation metrics: symmetry-corrected RMSD and lightweight PoseBusters filters.
Installation
uv pip install posecheck-fast
Features
- Symmetry-corrected RMSD — accounts for molecular symmetry (benzene, carboxylates, etc.)
- Fast PoseBusters filters — 4 key checks in ~10ms instead of full 27-test suite (~1-2s)
Usage
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,
)
Related
- PoseBench — full benchmark suite
- PoseBusters — full 27-test validation
- spyrmsd — symmetry RMSD algorithms
License
MIT
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