The first question to check is whether we are reading the stereo correctly:
obabel -iinchi -:"InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1"
-osmi
C[C@H](C(=O)O)N
This SMILES does indeed represent D-Alanine.
The problem is that you have generated a 0D mol file:
e.g. obabel -iinchi
-:"InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1" -omol
...where the tetrahedral stereo is stored on the atom rather than on the bonds.
In other words, gen2D didn't work for you (all the atoms have 0
coordinates I'm guessing). I'm not familiar with DoTransformations,
but it should work fine via OBOp.FindType("gen2D") or so.
- Noel
On 8 June 2017 at 21:37, Hendrik Vennekate <hvennek...@gmx.de> wrote:
> 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 The wiki is out of date.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
>
>>
>
>> ------------------------------------------------------------
>
>> ------------------
>
>> Check out the vibrant tech community on one of the world's most
>
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>> _______________________________________________
>
>> OpenBabel-discuss mailing list
>
>> OpenBabel-discuss@lists.sourceforge.net
>
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
