Hi Phil,
The behavior you are seeing is by design. Here's the github issue where the
change was made; it includes some discussion of why it's there:
https://github.com/rdkit/rdkit/issues/553
A solution for you would be to temporarily remove the atom map numbers
before calling AssignStereochemistry:
In [12]: s_mapped = '[OH:1]CC([OH:4])CO'
In [13]: mol = Chem.MolFromSmiles(s_mapped)
In [14]: mol.GetAtomWithIdx(2).SetChiralTag(Chem.CHI_TETRAHEDRAL_CCW)
In [17]: mapnos = []
In [18]: for at in mol.GetAtoms():
...: mapnos.append(at.GetAtomMapNum())
...: at.SetAtomMapNum(0)
...:
In [19]: Chem.AssignStereochemistry(mol,force=True,cleanIt=True)
In [21]: for i,mapno in enumerate(mapnos):
...: if mapno:
...: mol.GetAtomWithIdx(i).SetAtomMapNum(mapno)
...:
In [22]: Chem.MolToSmiles(mol)
Out[22]: 'OCC(C[OH:1])[OH:4]'
Best,
-greg
On Mon, Apr 1, 2019 at 9:23 PM Phillip Yen via Rdkit-discuss <
[email protected]> wrote:
> Hello,
>
>
>
> I have a question stereocenters in symmetrical compounds.
>
> I’ve found that if I take a flat, mapped, symmetrical compound and
> artificially set the chiral tag of the center carbon to form a
> stereocenter, it won’t “correct itself” and remove the stereocenter when I
> run AssignStereochemistry:
>
>
>
> s_mapped = [OH:1][CH2:2][CH:3]([OH:4])[CH2:5][OH:6]
>
> mol = Chem.MolFromSmiles(s_mapped)
>
> mol.GetAtomWithIdx(2).SetChiralTag(Chem.CHI_TETRAHEDRAL_CCW)
>
> Chem.AssignStereochemistry(mol, cleanIt=True, force=True)
>
> print(Chem.MolToSmiles(mol))
>
>
>
> Output (still has the artifically introduced stereocenter):
>
> [OH:1][CH2:2][C@H:3]([OH:4])[CH2:5][OH:6]
>
>
>
> On the other hand, if I use an unmapped SMILES to create the mol and do
> the exact same steps, then AssignStereochemistry does successfully remove
> the artificially introduced stereocenter (which is what I want to happen
> with the mapped mol too).
>
>
>
> s_unmapped = 'OCC(O)CO'
>
> mol = Chem.MolFromSmiles(s_unmapped)
>
> mol.GetAtomWithIdx(2).SetChiralTag(Chem.CHI_TETRAHEDRAL_CCW)
>
> Chem.AssignStereochemistry(mol, cleanIt=True, force=True)
>
> print(Chem.MolToSmiles(mol))
>
> OCC(O)CO
>
>
>
> Is this normal rdkit behavior (to have this difference between using an
> unmapped vs mapped mol)? How can I get it so that the mapped mol doesn’t
> have that chiral tag anymore?
>
>
>
> Thanks for the help.
>
>
>
> Phil
> _______________________________________________
> Rdkit-discuss mailing list
> [email protected]
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>
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