Hi Stefano,
When you call GetConfig() you are setting the winding yourself. I see now
that this wasn't clear. By default, you are saying "give me the atoms in
clockwise order looking from atom x". In other words, you will never need
to check the winding of a config - you will always know it - it'll be
whatever you set when you called GetConfig().
While you can use the first example on the page to iterate through
OBStereoData and check for cases of ob.OBStereo.TrigonalBipyramidal if you
want, there's no code in the library to perceive these from 3D structures,
so they will never exist. The only thing we do have right now beyond tetra
and cistrans is square planar from SMILES ("Cl[Pt@SP1](F)(I)Br"), and even
that is not perceived.
Regards,
- Noel
On Tue, 11 Feb 2020 at 16:20, Stefano Forli <fo...@scripps.edu> wrote:
> Hi Noel,
> indeed, that was my initial attempt to figure out how to deal with
> stereogenic centers,
> and I still didn't have a decent understanding of Id vs Idx.
> Incidentally, this is particularly clear in your documentation.
>
> I have one suggestion.
> In the section about the inversion of stereochemistry, it would be helpful
> if the example
> would show how to read the current winding.
> For example, would this work?
>
> --
> if config.winding == ob.OBStereo.Clockwise:
> print("Clockwise winding")
> elif config.winding==ob.OBStereo.AntiClockwise:
> print("Anti-clockwise winding")
> else: # elif config.winding==ob.OBStereoUnknownWinding: ?
> print("Undefined winding winding")
> --
>
> Also, I know the support for non-tetrahedral chirality is not complete,
> but I'm wondering
> if there a way to use the OBStereo.Type with the facade to infer if it is
> recognized or not.
>
> Thanks!
>
> S
>
> On 2020-02-09 12:36, Noel O'Boyle wrote:
> > Just a note on the code above. Many years ago Tim replaced the
> stereochemistry handling,
> > and I helped a bit. But vestiges of the original handling were left
> lying around to avoid
> > breaking the API. I guess we thought we'd remove them sooner than we
> did, as looking back
> > it makes no sense to have them lying around confusing everyone.
> >
> > Anyway, now with version 3.0, mol.FindChiralCenters() and
> atom.HasChiralitySpecified()
> > have both been removed. atom.IsChiral() I kept (though I thought about
> removing it also)
> > but changed the code so that it's now a convenience function that just
> calls the functions
> > in the modern API.
> >
> > And just to note that you should avoid subtracting 1 from the Idx to get
> the Id. Right now
> > it works, but we don't guarantee that relationship, and it certainly
> won't be true if you
> > delete atoms. Better to get the atom and then call GetId().
> >
> > - Noel
> >
> > On Thu, 6 Feb 2020 at 06:58, Stefano Forli <fo...@scripps.edu <mailto:
> fo...@scripps.edu>>
> > wrote:
> >
> > Noel,
> > this is great! I've been following the stereochemistry issue for a
> while in the mailing
> > list and you addressed pretty much all the key aspects.
> >
> > One thing that seems to be missing is the discussion on how to
> invert chirality. In the
> > past I've tried writing code to enumerate all possible enantiomers
> of molecules with
> > unspecified chiral centers or to explicitly invert the defined ones.
> >
> > An issue found while digging into that was that
> OBAtom.HasChiralitySpecified(), and
> > facade.GetTetrahedralStereo(idx).IsSpecified() were giving
> conflicting results.
> >
> > It's been a while since I tested it, but the code was this:
> > ====================
> > import pybel
> > ob = pybel.ob
> > mols = [ 'OCC1OC(O)C(O)C(O)C1O',
> > 'OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O']
> > for smi in mols:
> > print "\nMOL->", smi
> > m = pybel.readstring('smi', smi).OBMol
> > m.FindChiralCenters()
> > facade = ob.OBStereoFacade(m)
> > for a in ob.OBMolAtomIter(m):
> > if a.IsChiral():
> > idx = a.GetIdx()
> > print "ATOM", a.GetIdx(), a.IsChiral(),
> > a.HasChiralitySpecified(),
> > print
> facade.GetTetrahedralStereo(idx-1).IsSpecified()
> > =======================
> >
> > It would be interesting to test it with the latest development code
> and see if there are
> > still issues.
> >
> > Thas
> >
> > On 2020-02-05 14:51, Geoffrey Hutchison wrote:
> > > Yes, Naruki and I were running into confusion when using these
> classes for the
> > distance
> > > geometry implementation.
> > >
> > > The key challenge is that we'd want to save the expected stereo
> configuration
> > around atoms
> > > and bonds - and then when generating 3D coordinates, test to see
> if the generated
> > > configurations match the expected ones.
> > >
> > > I think we can probably go through the code and examine, but if
> you have
> > suggestions on
> > > how to save the expected configs for future comparison, that
> would be great.
> > >
> > > -Geoff
> > >
> > >
> > >> On Feb 5, 2020, at 4:30 PM, Noel O'Boyle <baoille...@gmail.com
> > <mailto:baoille...@gmail.com>
> > >> <mailto:baoille...@gmail.com <mailto:baoille...@gmail.com>>>
> wrote:
> > >>
> > >> Hi there,
> > >>
> > >> I've been very slowly pulling together some docs on using the
> API for stereo. I
> > remember
> > >> someone on the list a few months back discussing difficulties
> with this part of the
> > >> library - if anyone has any particular examples they'd like me
> to discuss, this
> > would be
> > >> a good time to mention them.
> > >>
> > >> Progress so far:
> > >>
> https://github.com/baoilleach/documentation/blob/stereo/Stereochemistry/stereo.rst
> > >>
> > >> Regards,
> > >> - Noel
> > >> _______________________________________________
> > >> OpenBabel-Devel mailing list
> > >> OpenBabel-Devel@lists.sourceforge.net
> > <mailto:OpenBabel-Devel@lists.sourceforge.net>
> > <mailto:OpenBabel-Devel@lists.sourceforge.net
> > <mailto:OpenBabel-Devel@lists.sourceforge.net>>
> > >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
> > >
> > >
> > >
> > > _______________________________________________
> > > OpenBabel-Devel mailing list
> > > OpenBabel-Devel@lists.sourceforge.net <mailto:
> OpenBabel-Devel@lists.sourceforge.net>
> > > https://lists.sourceforge.net/lists/listinfo/openbabel-devel
> > >
> >
> > --
> >
> > Stefano Forli, PhD
> >
> > Assistant Professor
> > Center for Computational Structural Biology
> >
> > Dept. of Integrative Structural
> > and Computational Biology, MB-112A
> > The Scripps Research Institute
> > 10550 North Torrey Pines Road
> > La Jolla, CA 92037-1000, USA.
> >
> > tel: +1 (858)784-2055
> > fax: +1 (858)784-2860
> > email: fo...@scripps.edu <mailto:fo...@scripps.edu>
> > http://www.scripps.edu/~forli/
> >
>
> --
>
> Stefano Forli, PhD
>
> Assistant Professor
> Center for Computational Structural Biology
>
> Dept. of Integrative Structural
> and Computational Biology, MB-112A
> The Scripps Research Institute
> 10550 North Torrey Pines Road
> La Jolla, CA 92037-1000, USA.
>
> tel: +1 (858)784-2055
> fax: +1 (858)784-2860
> email: fo...@scripps.edu
> http://www.scripps.edu/~forli/
>
>
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