Re: [OpenBabel-scripting] Graph Kernels

[S J. S. <swa...@gm...>]

Priyashree,

Openbabel is more of a molecule parsing program then a graph kernel
program. Your best bet might be to use it just for SDF parsing, then
write the DFS code (pretty simple) yourself, and the tanimoto/minmax
yourself too.

S Joshua Swamidass

On 8/8/06, Noel O'Boyle <no...@ca...> wrote:
> Hello Priyashree,
>
> I am copying this email to the openbabel-scripting mailing list so that
> other developers can help with this question.
>
> On Mon, 2006-08-07 at 15:08 -0700, pri...@ya... wrote:
> > I need to use pyopenbabel to obtain the outcome (i.e. similarity
> > measures) of tanimoto kernel, Minmax and Hybrid kernel on a SDF file
> > which contains a large number of molecules. Are these kernels already
> > implemented in this software or do I need to code them. Also in order
> > to implement the above kernels I will need to perform DFS on the
> > molecules, is this functionality provided in pyopenbabel. Also it
> > would be great if you could guide me to the installation process as i
> > am new to pyopenbabel.
> First of all, I am fairly sure that these methods are not present in
> OpenBabel. However, I know that Joerg Wegner has done a lot of work with
> graph kernels, and these features may be available in JOELIB2 (a Java
> cheminformatics library similar to OpenBabel). I have copied him into
> this reply.
>
> If you decide to code these yourself, either in C++ or Python, we would
> encourage you to donate your code to OpenBabel so that it will be
> available to others. We can discuss this further if you are interested.
>
> Regarding DFS specifically, I believe it is present but I am not sure
> where. I'm sure that Geoff can comment on this.
>
> Regarding installation, we should have an install page on the web site.
> At the moment we don't have one, but I will write one as soon as
> possible. What operating system do you use? If you are using Windows, I
> am afraid you will not be able to use Python to access OpenBabel, you
> can only use C++.
>
> Best regards,
>   Noel
>
>
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