Typo: "...but for sure, you can run Cinfony and use the Java bindings
from __Jython__ very easily"
On 7 January 2013 16:55, Noel O'Boyle <baoille...@gmail.com> wrote:
> The jar file should be included with the distribution, and should have
> access to all of the stereo classes. In fact, Tim did some work
> ensuring that this was working just before the release.
>
> You don't need to use Cinfony, but for sure, you can run Cinfony and
> use the Java bindings from Python very easily:
>
> from cinfony impory pybel
> mol = pybel.readstring("smi", "C[C@](Br)(Cl)I").OBMol
> facade = pybel.ob.OBStereoFacade(mol)
> print facade.HasTetrahedralStereo(mol.GetAtom(1).GetId()) # False
> print facade.HasTetrahedralStereo(mol.GetAtom(2).GetId()) # True
>
> - Noel
>
> On 7 January 2013 16:32, Nick Vandewiele <nick.vandewi...@ugent.be> wrote:
>> Hi!
>>
>>
>>
>> I wanted to use some openbabel functionality in my java-based code, more
>> particularly the stereo-perception algorithm of Razinger, implemented in the
>> src/stereo/perception.cpp file.
>>
>> I am quite interested in this method because I believe it's the only
>> implementation of the Razinger algorithm that is around.
>>
>>
>>
>> So I looked at the java wrapper "openbabel.jar" on the home page, but I
>> couldn't find any classes related to stereochemistry in there. After reading
>> through the mailing list, I am aware that previously the code in the stereo
>> package was not ported yet.
>>
>> Could someone update me on the status of the java bindings for the stereo
>> functionality in OB?
>>
>>
>>
>> Does cinfony maybe provide wrappers for the stereochemistry part of
>> openbabel?
>>
>> Does anyone have creative ideas circumventing this problem?
>>
>>
>>
>> regards,
>>
>>
>>
>> Nick
>>
>>
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