I agree with John, the InChI for mol1 and mol2 should be
http://cactus.nci.nih.gov/chemical/structure/O=C(NCCc1ccccc1)[C@H]1CC[C@H](Cn2c(O)nc3ccccc3c2=O)CC1/stdinchi
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-
So the + at the end should be a -
Markus
On Wed, Feb 18, 2015 at 2:53 PM, John M <john.wilkinson...@gmail.com> wrote:
> 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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