From: E.L. W. <eg...@sc...> - 2003-10-20 10:05:31
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On Monday 20 October 2003 10:58, Christoph Steinbeck wrote: > >>So one wants to be able to wander around within the > >>part (molecule) and find those points which are > >>connected by the fewest chemical bonds -- i.e. those > >>points where chemists may be able to execute specific > >>reactions to join two or more large, tightly interconnected > >>molecules via a small number of bonds and simple > >>chemical reactions. ... > >> > >>So if Jmol were to add a "seek low interconnectivity" > >>function it might provide chemists with the bridge > >>between looking at something pretty and something they > >>can actually manufacture. > > > > Jmol is designed as a molecular visualization tool. > > > > So, the problem of finding a 'highly connected subgraph' is beyond the > > scope Jmol's charter. Not sure what the problem is. You move around a big blob of atoms towards a second blob, and then you want to move it to that position where the first bonds are created? Created is undefined... this could be based on normal covalent radii, or it could include reaction knowledge/prediction with some AI rules... the first is implemented, the latter not... > > However, this may be an interesting problem in the context of CDK, the > > Chemistry Development Kit. It is many of the same players as Jmol. I have > > cc'd the CDK developers on this message. > > Agreed. > If you want something like this (which should be 10-20 lines of CDK > code) then you would write a small wrapper application, place Jmol in > the center, add you little "seek low interconnectivity" panel wherever > you like and interact with the display via the scripting API in order to > visualize the "low interconnectivity" part of your molecule. I still don't get the idea of "seek low interconnectivity"... but in general, the plugin mechanism would be best suited for this... > Or, even *better*, use the new Jmol plug-in API in order to implement > this. This API will be (or already is?) making it possible to place code > for additional UI elements and functionality into a loadable plug-in. > Egon will certainly be able to comment on this. A second window is opened for this right now... so no nice docking yet... (patches welcome ;) The plugin mechanism is rather new and therefore fluid at this moment... so please send in comments on the mechanism... The plugin API is defined in org.openscience.cdk.applications.plugin.something... very limited at this moment, but should basically also include: - runScript() which takes a RasMol/Chime script Anyone interesting in setting up a script for 2D ? > This has been made especially for those application cases, that would > otherwise be beyond the scope of the central program. And the nice thing > is that you can in principle use the same plug-in for our 2D application > JChemPaint, which then would also allow you to modify your program. Egon -- eg...@sc... PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 |