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
> >>
> >>
> >>
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> >>
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> >>
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> >>
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> >>
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