Hello,
I am trying to adjust the protonization based on the PH for a given
molecule and I am using pybel and openbabel for python. I am using the
following code:
>>> mol = pybel.readstring('smi', 'C1=CC=C(C=C1)C[C@H](C(=O)[O-])[NH3+]')
> >>> len(mol.atoms)
> 16
> >>> mol.OBMol.AddHydrogens(True, True, 7.4)
> True
> >>> len(mol.atoms)
> 15
>>> mol.write('smi').rstrip()
> 'c1ccc(cc1)C[C@H](C(=O)[O-])[NH3+]'
> >>> mol.write('inchi').rstrip()
> ==============================
> *** Open Babel Warning in InChI code
> #0 :Proton(s) added/removed
>
> 'InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)/t8-/m1/s1'
> >>> mol.write('inchikey').rstrip()
> ==============================
> *** Open Babel Warning in InChI code
> #0 :Proton(s) added/removed
> 'COLNVLDHVKWLRT-MRVPVSSYSA-N'
It seems that there are two issues after the conversion is successfully
done.
1. When I output the SMILES, it is not affected, however the inchi and
inchikey are changed
>>> mol.write('smi').rstrip()
> 'c1ccc(cc1)C[C@H](C(=O)[O-])[NH3+]'
> >>> mol.write('inchikey').rstrip()
> ==============================
> *** Open Babel Warning in InChI code
> #0 :Wrong 0D stereo descriptor(s): #1; Proton(s) added/removed; Omitted
> undefined stereo
> 'COLNVLDHVKWLRT-UHFFFAOYSA-N'
> >>> mol.write('inchi').rstrip()
> ==============================
> *** Open Babel Warning in InChI code
> #0 :Wrong 0D stereo descriptor(s): #1; Proton(s) added/removed; Omitted
> undefined stereo
> 'InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)'
2. The original stereochemistry information of the molecule is lost now.
I was wondering if someone can help me to figure out why the SMILES is not
updated after the PH-correction and why the stereochemistry is lost?
Thanks,
Sam
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