loss of stereochemistry after protonization

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

loss of stereochemistry after protonization

Sam Tonddast-Navaei
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
 

------------------------------------------------------------------------------

_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss