Another Python options question.
I can use the protonation option on the CLI:
echo "C1=C(NC=N1)C[C@@H](C(=O)O)N" | obabel -i smi -o mol -p 3
But I can't figure it out with the Python API:
import openbabel
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("smi", "mol")
mol = openbabel.OBMol()
obConversion.AddOption("p", obConversion.GENOPTIONS, "3.0")
obConversion.ReadString(mol, "C1=C(NC=N1)C[C@@H](C(=O)O)N")
output = obConversion.WriteString(mol)
print output
Output is generated but it's not protonated. Same if using OUTOPTIONS
instead of GENOPTIONS.
Is the use of the options in Python documented anywhere?
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