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import dask.dataframe as dd
import pandas as pd
import sys
import os
import numpy as np
from Bio.PDB import PDBList
from Bio import SeqIO
import warnings
def get_sequence(pdb_id):
try:
pdbfile = PDBList().retrieve_pdb_file(pdb_id.upper(),file_format='pdb',pdir='/tmp')
seq = str(next(SeqIO.parse(pdbfile, "pdb-seqres")).seq)
os.unlink(pdbfile)
return seq
except Exception as e:
print(e)
pass
if __name__ == '__main__':
import glob
filenames = glob.glob(sys.argv[3])
seqs = []
smiles = []
active = []
targets = pd.read_csv(sys.argv[1],sep=' ',keep_default_na=False)
for fn in filenames:
df = pd.read_csv(fn,header=None,sep=' ')
actives = df[0].unique()
decoys = df[1].unique()
smiles += actives.tolist()+decoys.tolist()
active += [True]*len(actives) + [False]*len(decoys)
split = os.path.basename(fn).split('-')
target = split[2].upper()
if len(split) > 5:
target += '-'+split[3].upper()
print(target)
seq = get_sequence(targets[targets.name.str.upper()==target].pdb.values[0])
seqs += [seq]*(len(actives)+len(decoys))
ddf = dd.from_pandas(pd.DataFrame({'seq': seqs, 'smiles': smiles, 'active': active}),npartitions=1)
ddf = ddf.repartition(partition_size='1M')
ddf.to_parquet(sys.argv[2])
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