Hi Anthony,
On Sun, Feb 22, 2015 at 11:03 AM, Anthony Bradley
<anthony.brad...@worc.ox.ac.uk<mailto: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
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