Dear all,
Using pybel, I would like to generate a smarts with explicit H before
doing a substructure search.
Actually, I'm seeking analogs of a reference molecule - let's say HO-CH2-NH2.
I want to keep the HO-CH2 part (the "scaffold").
I delete the NH2 and generate the smarts for HO-CH2 (and I hope that
OpenBabel doesn't add spontaneously the "missing" hydrogen).
The smarts generated is "OC" if I guess well.
Then, I look for analogs matching the smarts - e.g. HO-CH2-CH3.
With my current code,it is matching CH3-O-CH3 too. Sure, it's correct...
But I want only analogs with the HO-CH2 scaffold. Is it possible to
generate the corresponding smarts with explicit hydrogens, i.e.
[H]OC([H])[H] or [OX2H1][CX4H2] ?
My current code is:
mol.OBMol.AddHydrogens() # adding H doesn't change anything
for num in smarts.findall(mol): # smarts is [H]N[H]
atomToDel.append(mol.atoms[num-1])
for atom in atomToDel:
mol.OBMol.DeleteAtom(atom.OBAtom)
scaffoldSmiles = mol.write("can")
scaffoldSmarts = pybel.Smarts(scaffoldSmiles)
print len(scaffoldSmarts.findall(molAnalog))
Thanks,
Regards,
Pascal
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