| 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') | |