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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