remember the discussion around March about being able to download chemistry
from the internet with a syntax like:
(or whatever other index) ?
Back then, I implemented it for Jmol 10 preseries in the scripting language,
but it had to be commented out because it would conflict with the applet
I've now finally had time to finish a genuine CDK plugin that does the job,
see attached screenshot. I'm going to add it as default plugin for both
JChemPaint and Jmol 10, it works with both, and thus will be part of the next
release. (Miguel, since it's a plugin, it won't conflict with the applet
PS. sorry for the crossposts...
PhD on Molecular Representation in Chemometrics
Radboud University, Nijmegen
From: Egon Willighagen <e.willighagen@sc...> - 2005-03-20 19:42:49
On Sunday 20 March 2005 15:25, Peter Murray-Rust wrote:
> At 19:38 19/03/2005, Egon Willighagen wrote:
> >remember the discussion around March about being able to download
> > chemistry from the internet with a syntax like:
> >(or whatever other index) ?
> This looks very good.
> It raises questions with addressing and discovery. An ID is just that - an
> ISBN doesn't tell you which bookshop to buy it from and a CAS number
> doesn't tell you where to look (or indeed whether the site is allowed to
> hold the CAS numbers). the PDB can almost be expected to be an address, as
> perhaps could be NCI, PubChem, or at present WWM and NMRShiftDB.
> Can you indicate how the system identifies the resource?
The <any> points to 'any' known super database to the plugin. There are a few
of these available:
Each of these super databases point to actual database, e.g. the NCI database,
ChemFinder, NIST, ChemExper and the NMRShiftDB. Or actually, an XML file that
details how information from those databases can be accessed using regular
URLs. For example, see:
Principally, it will be possible to explicitely point to one super.xml, for
example by using:
This is not available from the plugin in Jmol yet, but will be released as
part of the next plugin version.
PhD student on Molecular Representation in Chemometrics
Radboud University Nijmegen