Dear Users,
I repropose a problem I already mentioned some time ago.
I am using openbabel to protonate molecules from sdf file.
Using obabel version 2.3.2, several molecules cannot be protonated.
Using the python binders pybel/openbabel, I noticed that the the problem is
related to the output of the structure as a new sdf file.
I.e.
1: load molecule
cpd = pybel.readfile("sdf", moli).next()
2: protonation
cpd.OBMol.AddHydrogens(False, pHcorr, pH)
3: save output
pybel.Outputfile("sdf",fname,overwrite=True)
The problem is never related to the step 1 or 2 (even changing the
protonation options) but at step 3, the code gets stuck.
The same problem happens when running openbabel from terminal
i.e.
obabel -isdf am0000000003.sdf -osdf -p 7.4
or obabel -isdf am0000000003.sdf -osdf -p
The issue takes place ONLY with some compounds and it is reproducible among
them (in attachment you can find an example), even if I couldn't find a
regular pattern. Associated to this problem, an analogue problem takes place
when 3d coordinates generation is performed for the same molecules ("obabel
--gen3D" or "obgen" or through python bindings).
The same compounds are correctly protonated using older versions of
openbabel (both 2.3.0 and 2.3.1, install from rpm packages available within
debian, ubuntu and centos). The version that gives problem is the 2.3.2,
both when compiled from source (without no apparent errors) and from the
precompiled version (ubuntu 14.04) on different systems.
I was wondering if anyone experienced similar problems with 2.3.2 version
and what are the major warnings in downgrading to 2.3.1 version (that seems
to not show this issue).
In attachment you can find two compounds showing this very problem.
Thank you in advance,
Luigi
am0000000003.sdf
<http://forums.openbabel.org/file/n4658239/am0000000003.sdf>
CHEMBL194749.sdf
<http://forums.openbabel.org/file/n4658239/CHEMBL194749.sdf>
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