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> 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>> 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>
> >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel
> >
> >
> >
> > _______________________________________________
> > OpenBabel-Devel mailing list
> > 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
> http://www.scripps.edu/~forli/
>
>
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