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import os
import sys
import glob
def pdbs_to_pdbqts(pdb_dir, pdbqt_dir, dataset):
for file in glob.glob(os.path.join(pdb_dir, '*.pdb')):
name = os.path.splitext(os.path.basename(file))[0]
outfile = os.path.join(pdbqt_dir, name + '.pdbqt')
pdb_to_pdbqt(file, outfile, dataset)
print('Wrote converted file to {}'.format(outfile))
def pdb_to_pdbqt(pdb_file, pdbqt_file, dataset):
if os.path.exists(pdbqt_file):
return pdbqt_file
if dataset == 'crossdocked':
os.system('prepare_receptor4.py -r {} -o {}'.format(pdb_file, pdbqt_file))
elif dataset == 'bindingmoad':
os.system('prepare_receptor4.py -r {} -o {} -A checkhydrogens -e'.format(pdb_file, pdbqt_file))
else:
raise NotImplementedError
return pdbqt_file
if __name__ == '__main__':
pdbs_to_pdbqts(sys.argv[1], sys.argv[2], sys.argv[3])
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