def main():
parser = argparse.ArgumentParser(description='Generate chemical \
fingerprints from smiles strings')
parser.add_argument('-S',
'--smiles',
action='store',
nargs=1,
dest='smiles',
help='List of smiles strings to convert to chemical \
chemical fingerprint - should be in a column named \
"smiles" (.csv format)')
parser.add_argument('-f',
'--fingerprint',
action='store',
nargs='*',
dest='fingerprints',
help='Desired fingerprint type \
(avalon, ecfp, fcfp, or maccs)')
parser.add_argument('-n',
'--name',
action='store',
nargs=1,
dest='name',
help='Name of fingerprint csv file \
to write')
parser.add_argument('-i',
'--input_directory',
action='store',
nargs=1,
dest='input',
default=['./'],
help='Directory where input files are stored')
parser.add_argument('-o',
'--output_directory',
action='store',
nargs=1,
dest='output',
default=['./'],
help='Directory where output files should be written')
args = vars(parser.parse_args())
for fptype in args['fingerprints']:
data = pd.read_csv(args['input'][0] + args['smiles'][0],
usecols=['smiles'])
ofile = args['output'][0] + args['name'][0]
time_start = time.time()
with open(ofile, 'w') as csv_file:
writer = csv.writer(csv_file, delimiter=',', lineterminator='\n')
for smiles in data.smiles.unique():
mol = MolFromSmiles(smiles)
try:
if fptype == 'avalon':
fp = GetAvalonFP(mol, nBits=2048)
elif fptype == 'ecfp':
fp = GetMorganFingerprintAsBitVect(mol, radius=2)
elif fptype == 'fcfp':
fp = GetMorganFingerprintAsBitVect(mol,
radius=2,
useFeatures=True)
elif fptype == 'maccs':
fp = MACCSkeys.GenMACCSKeys(mol)
fp_bitstr = list(fp.ToBitString())
fp_bitstr.insert(0, smiles)
writer.writerow(fp_bitstr)
except:
writer.writerow((smiles, "NA"))
print('Issue with conversion to ' + fptype +
' fingerprint: ' + str(smiles))
print('Done writing ' + fptype + ' fingerprints! Time elapsed: \
{} seconds'.format(time.time() - time_start))
def convert_to_avalon(SMILES):
mol = MS(SMILES)
desc_val = GetAvalonFP(mol)
desc_val_float_list = list(
np.asarray(list(desc_val.ToBitString()), dtype=float))
return desc_val_float_list