Re: [Open Babel] Protonation issues in 2.3.2 version

[David H. <li...@co...>]

both these molecules perform as expected in the latest code on github.

https://github.com/openbabel/openbabel

-David

On Thu, Mar 19, 2015 at 9:42 AM, ggbs <lui...@gm...> wrote:

> 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>
>
>
>
>
>
> --
> View this message in context:
> http://forums.openbabel.org/Protonation-issues-in-2-3-2-version-tp4658239.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
>
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