Dear all,
Thanks for your answers!
I have no objection to Chris' code modification proposal.
With Craig's suggestion and Noel's blog (so useful for code
inspiration (plagiarism...) - at least for me :), I got this working
with pybel:
conv = ob.OBConversion()
conv.SetInAndOutFormats("smi", "can")
conv.SetOptions("h", conv.OUTOPTIONS)
for mol in pybel.readfile("smi", "file.smi"):
mol.OBMol.AddHydrogens()
smiles = conv.WriteString(mol.OBMol)
print smiles
Output is e.g.;
[CH3][CH2]N([CH3])C(=O)N([CH3])c1[cH][cH][cH][cH][cH]1 mol1
[NH2]C(=O)N([CH3])c1[cH][cH][cH][cH]c1[OH] mol2
I'll try to place this in my program and see the behaviour with the
atom deletions.
I keep Andrew's proposal in mind anyway :)
Regards,
Pascal
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