JP,
Looks like that's a bug in the way ring stereochemistry is handled while
translating the InChI back into an molecule.
It's reproducible with a small example:
In [1]: from rdkit import Chem
In [2]: mol1 = Chem.MolFromSmiles("C[C@H]1CC[C@H](O)CC1")
In [3]: Chem.MolToSmiles(mol1,True)
Out[3]: 'C[C@H]1CC[C@H](O)CC1'
In [4]: inchi = Chem.MolToInchi(mol1)
In [5]: mol2 = Chem.MolFromInchi(inchi)
In [6]: Chem.MolToSmiles(mol2,True)
Out[6]: 'C[C@H]1CC[C@@H](O)CC1'
Conversion of InChI to molecules is something that's not in general
guaranteed to work perfectly, but I will go ahead and create a bug report.
-greg
On Tue, Feb 17, 2015 at 2:50 PM, JP <jeanpaul.ebe...@inhibox.com> wrote:
> Hi there,
>
> I have a question for the 3D enabled of you (I wish the world looked like
> GTA2 !)
>
> I am seeing a case of an RDKit mol -> Inchi -> RDKit mol, that I think is
> changing the stereochemistry of the molecule. I have 12 example-pairs
> where this happens (but all very structurally similar). I don't care much
> that the last rdkit molecule is a different tautomer than the starting one
> - but if this is the case the stereochemistry should still be conserved, no?
>
> I did an ipython notebook (most useful tool of the decade after RDKit?)
> gist here:
>
>
> http://nbviewer.ipython.org/urls/gist.githubusercontent.com/anonymous/7c158926a0f3bf9a4978/raw/d91cc808ac91eccc8bf0e45d9eacd2af382e5105/gistfile1.txt
>
> I appreciate if anyone could shed some light. I'd just like to understand.
>
> Thank you for your time!
>
> -
> JP
>
>
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