> update the bug report and work on tracking down the wrong problem
That's how I sometimes do it too... ;)
Igor
On Wed, Feb 18, 2015 at 12:35 PM, Greg Landrum <greg.land...@gmail.com>
wrote:
> Yep, you guys are right.
> I diagnosed that too quickly.
> Thanks for pointing out the mistake.
>
> I'll update the bug report and work on tracking down the wrong problem
>
> -greg
>
>
> On Wed, Feb 18, 2015 at 4:58 PM, Markus Sitzmann <
> markus.sitzm...@gmail.com> wrote:
>
>> 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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