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from mpi4py import MPI
from mpi4py.futures import MPICommExecutor
from openbabel import pybel
from Bio import SeqIO
import os
def parse_complex(fn):
try:
name = os.path.basename(fn)
seq = str(next(SeqIO.parse(fn+'/'+name+'_protein.pdb', "pdb-seqres")).seq)
mol = next(pybel.readfile('sdf',fn+'/'+name+'_ligand.sdf'))
smi = mol.write('can').split('\t')[0]
return name, seq, smi
except:
return None
if __name__ == '__main__':
import glob
filenames = glob.glob('pdbbind/data/v2019-other-PL/*')
filenames.extend(glob.glob('pdbbind/data/refined-set/*'))
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]
import pandas as pd
df = pd.DataFrame({'name': names, 'seq': seqs, 'smiles': all_smiles})
df.to_parquet('data/pdbbind_complex.parquet')
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