I haven't looked at the specifics, but sounds like a good idea.
I plan to rewrite some of the stereo API in the near future, and will
keep your suggestion in mind. Ideally, it would be nice to have the
possibility of retaining the exact input stereo without reperception
or reassigning bond wedges or hashes. This would make reading SMILES
strings (for example) much faster.
- Noel
On 11 June 2017 at 11:41, Hendrik Vennekate <hendrik.vennek...@posteo.de> wrote:
> Ok, to sum up, OBDepictPrivate::SetWedgeAndHash(OBMol*) is the function I
> want to use, which essentially amounts to copying it into my application.
> This function seems to be "dead code" (in the sense that it is not
> referenced anywhere) -- but still very useful for my scenario to have. Why
> not make it a public function somewhere in stereo/stereo.h?
>
>
>
> Best,
>
>
>
> Hendrik
>
>
>
> On Saturday, June 10, 2017 21:14:08 Hendrik Vennekate wrote:
>
>> Hi Noel,
>
>>
>
>> thanks again for the quick reply and my apologies for my newb-ish mistakes
>
>> in this field (on an unrelated note: inspecting the code, I realized that
>
>> if anything I should have checked IsWedge() and IsHash() separately). So,
>
>> IsChiral() is indeed true for the one relevant atom.
>
>>
>
>> My goal in this, however, would have been to arrive at an OBMol with hash
>
>> and/or wedge bonds. It seems there is some way to accomplish that using
>
>> what is around in stereo/perception.cpp, but documentation seems to be
>
>> rather scarce. I'm guessing I'll have to eventually mimic what
>
>> OBDepict::DrawMolecule() does (or TetStereoToWedgeHash() called therein).
>
>>
>
>> I'll keep exploring, but thanks again for clearing up that
>> stereo-chemistry
>
>> _is_ indeed processed.
>
>>
>
>> Best,
>
>>
>
>> Hendrik
>
>>
>
>> On Friday, June 09, 2017 13:12:31 Noel O'Boyle wrote:
>
>> > 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
>
>
>
> --
>
> Postanschrift:
>
> Ahornstraße 12d
>
> 85774 Unterföhring
>
> Telefon: (0176) 2298 7524
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