bio.py

import openbabel as ob
import pybel

ASPIRIN = "CC(=O)OC1=CC=CC=C1C(=O)O"
SALICIL = "C1=CC=C(C(=C1)C(=O)O)O"
smiles = [ASPIRIN, SALICIL]


mols = [pybel.readstring("smi", x) for x in smiles]
for mol in mols:
    mol.OBMol.AddHydrogens()

fps = [x.calcfp() for x in mols]
print fps[0].bits, fps[1].bits
print fps[0] | fps[1]

bio2.py

from rdkit import Chem
from rdkit.Chem import AllChem, Draw, Descriptors

BENZENE = "C1=CCC=CC=C1"
METH = "CC(CC1=CC=CC=C1)NC"

m = Chem.MolFromSmiles(BENZENE)

# add hydrogen
m_hydrogenized = Chem.AddHs(m)

Draw.MolToFile(m_hydrogenized, 'cdk2_mol1.o.png')


for desc in Descriptors._descList:
    desc_name = desc[0]
    desc_value = desc[1](m_hydrogenized)
    print(str(desc_value) + "\t" + desc_name)


# http://www.qsar4u.com/files/rdkit_tutorial/rdkit.html