I mistakenly replied only to Richard.
---------- Forwarded message ----------
From: Greg Landrum <[email protected]>
Date: Fri, Feb 7, 2014 at 4:11 AM
Subject: Re: [Rdkit-discuss] Cartridge fingerprint customisation & IPython
integration
To: Rich Lewis <[email protected]>
Dear Richard,
On Thu, Feb 6, 2014 at 3:09 PM, Rich Lewis <[email protected]> wrote:
>
> I'm new here, so to introduce myself, I'm currently a 1st year PhD student
> under Andreas Bender at the Unilever Centre for Molecular Informatics in
> Cambridge.
>
Welcome!
> I've got an install of the rdkit head on Mac OS X Mavericks using Eddie
> Cao's homebrew formula (thanks!), and a functioning install of the
> PostgreSQL cartridge.
>
>
I was wondering if there is a way to change the default lengths for the
> fingerprints in the cartridge, short of changing the MORGAN_FP_SIZE
> constant in adaptor.cpp and recompiling? I have been using 2048 bit Morgan
> for a project, and would rather keep using them than 512 bit, but would
> prefer to retain an unmodified install.
>
There's not currently any way to do this other than editing the constant
and recompiling. It's a nice idea though.
I need to investigate a bit more, but I believe that I can add
configuration variables that control the fingerprint sizes. These can then
be set at the database level using the "alter database" SQL command.
Here's the feature request: https://github.com/rdkit/rdkit/issues/216
Also, as I am using the IPython notebook, I wanted to see if anyone was
> looking into deeper use of the rich display system, for example using
> JavaScript to render pannable 3D, like OpenBabel has (
> https://github.com/openbabel/openbabel/pull/30).
>
I hadn't seen that. The 3D functionality is something that it would be very
nice to have available in the notebook, and I think it's only fair to
borrow some ipython ideas back from OpenBabel. ;-)
Looking through the code, it seems they've borrowed some files from the
three.js examples to get the scenes set up and then the rendering itself is
being done using three.js itself. Three.js and its examples are MIT
licensed, so incorporating bits of them into the RDKit would not be a
problem.
I'll create an entry for this in the issue tracker; I'm not sure if/when I
will manage to find the time to get around to it, but pull requests are
always welcome if anyone else wants to take a look:
https://github.com/rdkit/rdkit/issues/215
> Thanks to everyone who has worked on the RDKit, it's a remarkable piece of
> open source software!
>
Thanks!
-greg
------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
