Hi Noel,
that did the trick, indeed.
Is that worth opening a bug report?
Thanks a lot,
S
On 11/20/2014 01:37 PM, Noel O'Boyle wrote:
> 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/
>>
>> ------------------------------------------------------------------------------
>> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
>> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
>> with Interactivity, Sharing, Native Excel Exports, App Integration & more
>> Get technology previously reserved for billion-dollar corporations, FREE
>> http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
--
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/
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
