Hi Noel,
thanks for the quick reply. Actually, I was trying it through the library
directly (approximately
like below):
using namespace OpenBabel;
OBConversion conversion;
conversion.SetInFormat("INCHI");
OBMol molecule;
conversion.ReadString(&molecule, "InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,
(H,5,6)/t2-/m1/s1");
std::map<std::string, std::string> options;
options["gen2D"] = "";
molecule.DoTransformations(&options, &conversion);
FOR_BONDS_OF_MOL(obbond, molecule)
cout << obbond->IsWedgeOrHash() << endl;
... and the output indicated that no bond was a wedge or hash, as I would have
expected.
Alternatively, I put the above InChI string into a file and did the following:
obabel -i inchi /tmp/d-alanine.inchi -Otestout.mol
To the best of my understanding of the MOL format, the fourth column of the
bond block
should contain the stereo info if any. The output bond block reads:
1 2 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
3 5 2 0 0 0 0
3 6 1 0 0 0 0
so all zeros.
Again, I'm curious what I'm missing...
Best wishes,
Hendrik
On Thursday, June 08, 2017 20:30:09 you wrote:
> Hi there,
>
> The wiki is out of date. Stereo works fine. What was the specific command
> you used that you feel didn't work?
>
> Noel
>
> On 8 Jun 2017 8:08 p.m., "Hendrik Vennekate" <hvennek...@gmx.de> wrote:
>
> Hello OpenBabel list,
>
>
>
> a quick question regarding InChI support: on the corresponding wiki page it
> reads, "Experimental InChI read support was added in version 2.1, although
> this does not always support stereochemistry." Has this been improved
> meanwhile?
>
> In a little experiment with wikidata's InChI string for D-alanine
> (1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1), I could not seem
> to successfully reproduce the stereochemistry.
>
>
>
> Any support is greatly appreciated.
>
>
>
> Kind regards,
>
>
>
> Hendrik
>
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