PoseCheck Documentation

Warning: this documentation is WIP

PoseCheck is a python package for checking the quality of 3D molecules poses from molecular generative models.

Installation

Install from PyPI

git clone https://github.com/cch1999/posecheck.git
cd posecheck

pip install -e .
pip install -r requirements.txt
conda install -c mx reduce

Getting Started

We provide a simple top level API to easily interact with the whole of the benchmark. Just define the PoseCheck object once at the top of your existing testing code and test molecules by loading them in iteratively. You can also use all the testing functions manually as well (see Docs for more info).

from posecheck import PoseCheck

# Initialize the PoseCheck object
pc = PoseCheck()

# Load a protein from a PDB file (will run reduce in the background)
pc.load_protein_from_pdb("data/examples/1a2g.pdb")

# Load ligands from an SDF file
pc.load_ligands_from_sdf("data/examples/1a2g_ligand.sdf")
# Alternatively, load RDKit molecules directly
# pc.load_ligands_from_mols([rdmol])

# Check for clashes
clashes = pc.calculate_clashes()
print(f"Number of clashes in example molecule: {clashes[0]}")

# Check for strain
strain = pc.calculate_strain_energy()
print(f"Strain energy of example molecule: {strain[0]}")

# Check for interactions
interactions = pc.calculate_interactions()
print(f"Interactions of example molecule: {interactions}")

Citation

 @article{harris2023benchmarking,
title={Benchmarking Generated Poses: How Rational is Structure-based Drug Design with Generative Models?},
author={Harris, Charles and Didi, Kieran and Jamasb, Arian R and Joshi, Chaitanya K and Mathis, Simon V and Lio, Pietro and Blundell, Tom},
journal={arXiv preprint arXiv:2308.07413},
year={2023}
 }

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