Excellent suggestions for examples and/or areas of focus. I'll refer back
to these as I work through the docs.
Actually now I remember that it was your earlier email Stefano that
prompted me to write these docs. I started at the time, but lost the file,
and/or moved jobs, etc.
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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