The incantation is print
facade.GetTetrahedralStereo(idx-1).GetConfig().specified
I imagine that Tim intended that IsSpecified() calls this, but this
was never done.
- Noel
On 20 November 2014 20:37, Stefano Forli <fo...@scripps.edu> wrote:
> Hi,
>
> I'm trying to find a robust method to identify if chirality is specified or
> not in a
> molecule, i.e.:
>
> OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O (yes)
> OCC1OC(O)C(O)C(O)C1O (no)
>
> I've tried OBAtom.HasChiralitySpecified() (even if deprecated) and
> OBTetrahedralStereo.IsSpecified(), but none of them seems to give the
> information I'm
> looking for:
> ====================
> 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()
> =======================
> Basically, for both molecules, the two methods return always False and True
> (atom's and
> facade's methods, respectively).
>
> Any help would be very much appreciated.
>
>
> S
>
>
> --
> Stefano Forli, PhD
>
> Staff Scientist
> Molecular Graphics Laboratory
> Dept. of Integrative Structural
> and Computational Biology, MB-112F
> 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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