Hi Greg,
I believe it's an RDKitMol -> InChI issue rather than InChI -> RDKitMol.
The correct InChI (below) is different from that in the iPython listing.
InChI=1S/C24H27N3O3/c28-22(25-15-14-17-6-2-1-3-7-17)19-12-10-18(11-13-19)16-27-23(29)20-8-4-5-9-21(20)26-24(27)30/h1-9,18-19H,10-16H2,(H,25,28)(H,26,30)/t18-,19-
J
Regards,
John W May
john.wilkinson...@gmail.com
On 18 February 2015 at 04:57, Greg Landrum <greg.land...@gmail.com> wrote:
> 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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>
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