pdbbind.py

from mpi4py import MPI
from mpi4py.futures import MPICommExecutor

import warnings
from Bio.PDB import PDBParser, PPBuilder, CaPPBuilder
from Bio.PDB.NeighborSearch import NeighborSearch
from Bio.PDB.Selection import unfold_entities

import numpy as np
import dask.array as da

from rdkit import Chem

import os
import re
import sys

# all punctuation
punctuation_regex  = r"""(\(|\)|\.|=|#|-|\+|\\|\/|:|~|@|\?|>>?|\*|\$|\%[0-9]{2}|[0-9])"""

# tokenization regex (Schwaller)
molecule_regex = r"""(\[[^\]]+]|Br?|Cl?|N|O|S|P|F|I|b|c|n|o|s|p|\(|\)|\.|=|#|-|\+|\\|\/|:|~|@|\?|>>?|\*|\$|\%[0-9]{2}|[0-9])"""

max_seq = 2046 # = 2048 - 2 (accounting for [CLS] and [SEP])
max_smiles = 510 # = 512 - 2
chunk_size = '1G'

def parse_complex(fn):
    try:
        name = os.path.basename(fn)

        # parse protein sequence and coordinates
        parser = PDBParser()
        with warnings.catch_warnings():
            warnings.simplefilter("ignore")
            structure = parser.get_structure('protein',fn+'/'+name+'_protein.pdb')

        ppb = CaPPBuilder()
        seq = []
        xyz_receptor = []
        for pp in ppb.build_peptides(structure):
            seq.append(str(pp.get_sequence()))
            xyz_receptor += [tuple(a.get_vector()) for a in pp.get_ca_list()]
        seq = ''.join(seq)

        # parse ligand, convert to SMILES and map atoms
        suppl = Chem.SDMolSupplier(fn+'/'+name+'_ligand.sdf')
        mol = next(suppl)
        smi = Chem.MolToSmiles(mol)

        # position of atoms in SMILES (not counting punctuation)
        atom_order = [int(s) for s in list(filter(None,re.sub(r'[\[\]]','',mol.GetProp("_smilesAtomOutputOrder")).split(',')))]

        # tokenize the SMILES
        tokens = list(filter(None, re.split(molecule_regex, smi)))

        # remove punctuation
        masked_tokens = [re.sub(punctuation_regex,'',s) for s in tokens]

        k = 0
        token_pos = []
        for i,token in enumerate(masked_tokens):
            if token != '':
                token_pos.append(tuple(mol.GetConformer().GetAtomPosition(atom_order[k])))
                k += 1
            else:
                token_pos.append((np.nan, np.nan, np.nan))

        return name, seq, smi, xyz_receptor, token_pos

    except Exception as e:
        print(e)
        return None


if __name__ == '__main__':
    import glob

    filenames = glob.glob('data/pdbbind/v2020-other-PL/*')
    filenames.extend(glob.glob('data/pdbbind/refined-set/*'))
    filenames = sorted(filenames)
    comm = MPI.COMM_WORLD
    with MPICommExecutor(comm, root=0) as executor:
        if executor is not None:
            result = executor.map(parse_complex, filenames)
            result = list(result)
            names = [r[0] for r in result if r is not None]
            seqs = [r[1] for r in result if r is not None]
            all_smiles = [r[2] for r in result if r is not None]
            all_xyz_receptor = [r[3] for r in result if r is not None]
            all_xyz_ligand = [r[4] for r in result if r is not None]

            import pandas as pd
            df = pd.DataFrame({'name': names, 'seq': seqs, 'smiles': all_smiles, 'receptor_xyz': all_xyz_receptor, 'ligand_xyz': all_xyz_ligand})
            df.to_parquet('data/pdbbind.parquet')