Ok, I just checked in a set of changes to address the problems with InChI
generation and InChI ->mol conversion for 3-coordinate atoms.
There are some notes and pointers to the code changes here:
https://github.com/rdkit/rdkit/issues/437
Please note the final comment there: JP's original example now gives a
correct InChI, and it looks like that InChI is correctly converted into a
SMILES, but the resulting SMILES is not properly canonicalized. Grrrrrrrr.
I will continue to look at that.
In the meantime, I would be extremely grateful if someone else could take a
look at the testing code I added:
https://github.com/rdkit/rdkit/blob/ca0c4956765952e8c0556885c6ac8e62bac197e1/External/INCHI-API/test.cpp#L256
and let me know if they see any problems with the expected InChIs I'm using.
Best,
-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
> >>>
> >>>
> >>>
> ------------------------------------------------------------------------------
> >>> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> >>> from Actuate! Instantly Supercharge Your Business Reports and
> Dashboards
> >>> with Interactivity, Sharing, Native Excel Exports, App Integration &
> more
> >>> Get technology previously reserved for billion-dollar corporations,
> FREE
> >>>
> >>>
> http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg.clktrk
> >>> _______________________________________________
> >>> Rdkit-discuss mailing list
> >>> Rdkit-discuss@lists.sourceforge.net
> >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> >>>
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> >> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> >> with Interactivity, Sharing, Native Excel Exports, App Integration &
> more
> >> Get technology previously reserved for billion-dollar corporations, FREE
> >>
> >>
> http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg.clktrk
> >> _______________________________________________
> >> Rdkit-discuss mailing list
> >> Rdkit-discuss@lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> >>
> >
> >
> >
> ------------------------------------------------------------------------------
> > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> > from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> > with Interactivity, Sharing, Native Excel Exports, App Integration & more
> > Get technology previously reserved for billion-dollar corporations, FREE
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg.clktrk
> > _______________________________________________
> > Rdkit-discuss mailing list
> > Rdkit-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> >
>
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg.clktrk
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
