jglaser/binding_affinity

1from mpi4py import MPI2from mpi4py.futures import MPICommExecutor3 4from openbabel import pybel5from Bio import SeqIO6 7import os8def parse_complex(fn):9    try:10        name = os.path.basename(fn).split('.')[0]11        print(name)12        seq = str(next(SeqIO.parse(fn, "pdb-seqres")).seq)13        return name, seq14    except:15        return None16 17 18if __name__ == '__main__':19    import glob20 21    filenames = glob.glob('binding_moad/BindingMOAD_2020/*.bio1')22    comm = MPI.COMM_WORLD23    with MPICommExecutor(comm, root=0) as executor:24        if executor is not None:25            result = executor.map(parse_complex, filenames)26            result = list(result)27            names = [r[0] for r in result if r is not None]28            seqs = [r[1] for r in result if r is not None]29 30            import pandas as pd31            df = pd.DataFrame({'name': names, 'seq': seqs})32            df.to_parquet('data/moad_complex.parquet')33