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from mpi4py import MPI
from mpi4py.futures import MPICommExecutor
from Bio.PDB import PDBParser, PDBIO, Select, PPBuilder
import warnings
import tempfile
import os
import sys
from rdkit import Chem
import pandas as pd
def is_het(residue):
res = residue.id[0]
return res != " " and res != "W"
class ResidueSelect(Select):
def __init__(self, het):
self.het = het
def accept_residue(self, residue):
""" Recognition of heteroatoms - Remove water molecules """
return (self.het and is_het(residue) or not self.het and not is_het(residue))
def get_complex(fn):
try:
parser = PDBParser()
io = PDBIO()
structure = parser.get_structure('complex',fn)
io.set_structure(structure)
with tempfile.NamedTemporaryFile(mode='w',delete=False) as f:
name_receptor = f.name
with tempfile.NamedTemporaryFile(mode='w',delete=False) as f:
name_ligand = f.name
io.save(name_receptor,ResidueSelect(het=False))
io.save(name_ligand,ResidueSelect(het=True))
parser = PDBParser()
receptor = parser.get_structure('protein',name_receptor)
ppb = PPBuilder()
seq = []
for pp in ppb.build_peptides(structure):
seq.append(str(pp.get_sequence()))
seq = ''.join(seq)
mol = Chem.MolFromPDBFile(name_ligand)
smiles = Chem.MolToSmiles(mol)
os.unlink(name_ligand)
os.unlink(name_receptor)
return seq, smiles
except Exception as e:
print(e)
pass
if __name__ == '__main__':
import glob
filenames = glob.glob(sys.argv[2])
comm = MPI.COMM_WORLD
with MPICommExecutor(comm, root=0) as executor:
if executor is not None:
result = executor.map(get_complex, filenames)
names = []
all_seq = []
all_smiles = []
for n,r in zip(filenames,result):
try:
all_seq.append(r[0])
all_smiles.append(r[1])
names.append(os.path.basename(n))
except:
pass
df = pd.DataFrame({'name': names, 'seq': all_seq, 'smiles': all_smiles})
df.to_parquet(sys.argv[1])
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