test.py

from datasets.process_mols import (
    generate_conformer,
    read_molecule,
)
from rdkit.Chem import AddHs
import os
from p_tqdm import p_map

# Get list of ligand file paths
ligand_dir = 'screening_data/2rgp/screening_ligand'
ligand_files = [os.path.join(ligand_dir, f) for f in os.listdir(ligand_dir)]

def process_ligand(ligand_description):
    """Processes a ligand: reads, removes conformers, adds hydrogens, and generates conformers."""
    mol = read_molecule(ligand_description, remove_hs=False, sanitize=True)
    mol.RemoveAllConformers()
    mol = AddHs(mol)
    status = generate_conformer(mol)
    return ligand_description if not status else None

# Run in parallel
failed_ligands = list(filter(None, p_map(process_ligand, ligand_files)))

print(f"Failed ligands: {failed_ligands}")