I just filed a bug report on about a possible bug [1] in the IsEster() function
in OBBond.
What I found is that IsEster() is true if there's a free carboxy group (i.e.,
no ester present).
The bug report page has "eaten" the code formatting of the Python test, so I'm
posting it here too, just in case.
============
import pybel
ob = pybel.ob
smi = [ 'OC(=O)', 'CC(O)=O', 'O=C(O)c1ccccc1']
for s in smi:
mol = pybel.readstring('smi',s).OBMol
for b in ob.OBMolBondIter(mol):
if b.IsEster():
print "FOUND ESTER BOND"
==============
By reading the online documentation, the function description seems to hint at
an insufficient criterion, since the condition checked ("Is the bond an ester
link (i.e., between a carbonyl C and an O)?") doesn't account for the portion
that's establishing the bond (i.e., if it's not an alcohol, it's not an ester).
[1] https://sourceforge.net/p/openbabel/bugs/970/
--
Stefano Forli, PhD
Assistant Professor of Integrative
Structural and Computational Biology,
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: [email protected]
http://www.scripps.edu/~forli/
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