Hi all,
I'm running some code (Python 3.7, OB 3.1) that checks the chirality, so I
thought about putting to put to work the know-how that Noel put together[1,2].
After some testing, I boiled down my experience to the following code:
============================
from openbabel import openbabel as ob
mol_parser = ob.OBConversion()
mol_parser.SetInAndOutFormats('smi','smi')
# check 1
mol = ob.OBMol()
mol_parser.ReadString(mol, 'Br[C@H](F)C')
ob.PerceiveStereo(mol)
print("is chiral:", mol.GetAtom(2).IsChiral())
# check 2
mol = ob.OBMol()
mol_parser.ReadString(mol, 'BrC(F)C')
ob.PerceiveStereo(mol)
print("is chiral:", mol.GetAtom(2).IsChiral())
============================
From my understanding of Noel's docs, I was expecting that the PerceiveStereo()
method would get the same result for both molecules, therefore IsChiral() would
be true in the two cases. Although, only the first is true, the second is not:
$ python3 test_chiral.py
is chiral: True
is chiral: False
According to the documentation IsChiral() checks "Is this atom chiral?", and is based on
OBStereoFacade.HasTetrahedralStereo(), which checks "if atom with id is a tetrahedral
center".
So, is atom 2 chiral in both cases? To me that's clearly true, and it is
independent from the fact that its configuration is defined or not.
Is this correct, or am I missing something?
Thanks!
S
[1] https://baoilleach.blogspot.com/2020/02/
[2] https://open-babel.readthedocs.io/en/latest/Stereochemistry/stereo.html
--
Stefano Forli, PhD
Assistant Professor
Dept. of Integrative Structural
and Computational Biology, MB-112A
Scripps Research
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: +1 (858)784-2055
email: fo...@scripps.edu
http://www.scripps.edu/faculty/forli/
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