Hello,
If interested in clustering in python I can recommend, as usual, sklearn:
http://scikit-learn.org/stable/modules/clustering.html
It's pretty much all you should need. Have fun!
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2015-02-23 11:43 GMT+01:00 Anthony Bradley <anthony.brad...@worc.ox.ac.uk>:
> Hi Anthony,
>
>
>
> On Sun, Feb 22, 2015 at 11:03 AM, Anthony Bradley <
> anthony.brad...@worc.ox.ac.uk> wrote:
>
> Hi all,
>
> I am currently working with RDKit from the Java API (well jython actually).
>
> As has been discussed most of the documentation for this is found by
> trawling:
>
> Code/JavaWrappers/gmwrapper/src-test/org/RDKit/
> and
> Code/JavaWrappers/gmwrapper/src/org/RDKit/
>
> However I'm trying to perform a simple clustering. I can build my distance
> matrix - but I can't see where the actual clustering algorithms live.
>
> It may well be my grepping skills are not what they should be!
>
>
>
> No need to have any concerns about your skills with grep, the clustering
> functionality is not exposed via the SWIG wrappers. As currently configured
> the code isn't available as a library, it's really only useable from
> python. It's a medium-sized amount of work to convert this to a library, so
> it's doable, but I'm not sure it's worth it.
>
>
>
> That seems fair enough and there are definitely other options out there.
> It was more of method consistency thing – so I could be using the same code
> from the python / jython side.
>
>
>
> I've been assuming that there are high(er) quality replacements available
> for most of the RDKit "machine learning" functionality. Since it's somewhat
> removed from the "cheminformatics" focus, I haven't really put any time
> into that code in the past few years. Does this sound wrong to anyone? Any
> arguments that the clustering code is worth investing some time in?
>
>
>
> Unless anybody else is interested – I can see why it would be low
> priority!
>
>
>
> -greg
>
>
>
> Thanks a lot for responding so quickly and effectively!
>
>
>
> Best,
>
>
>
> Anthony
>
>
>
>
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
>
> http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg.clktrk
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg.clktrk
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
