On Sunday 15 June 2003 11:48, Peter Murray-Rust wrote: > If there are a lot of molecules you don't want separate windows!
Yes, that's true... > I partially tackled this problem in JUMBO4 as follows: > - read in many CML files (limit was ca 1500 before the memory ran out). > - translate all to DOM and store in a Hashtable > - create a Swing ComboBox listing the names of all molecules > - allow the user to step through these (or scroll and select). Each > selection *replaced* the current display in Jmol. > > I think you want to consider (if not implement) all the following: > > (a) a JUMBO-like display of "compound card" containing a JCP window (2D) > and Jmol 3D for the molecule. In JUMBO this worked reasonably well but > occasionally Swing gave problems. I'm not proud and if you want to include > the approach in Jmol feel free. (Actually I think there is a potential role > for a "ChemEdit" - rather like JEdit which encompasses several of the > opensource tools) > > (b) a <list> or <molecule>s which are directly superimposable (i.e. all in > same reference frame.). There are many reasons for doing this - > pharmacophores, supramolecules, etc. An extension is to go to a service to > generate the superimposition matrices > > (c) a *small* number of separate windows (?2) for human comparison of > molecules Yes, indeed... > (d) a <list> of unrelated molecules which should be shown sequentially on > user command. This is what I currently need - we have files of 500 > unrelated molecules in a single file and want to eyeball them. The ability > to select by name (a la JUMBO) would be extremely useful > > (e)a list of related molecules (animation-like) - Jmol already does this, > but it could be useful to have display of individual titles > > >The problem: > > > >at this moment the Jmol Readers take a DisplayControl only, and no > > reference to Jmol itself... it can thus not call a specific Jmol > > method... But, it could use the approach used in the NewwinAction... > > > >However, problem 2: > > > >the Reader cannot open up a second window just like that... that would > > break it for use in the applet... which cannot open up a second window... > > In the applet it is particularly useful to be able to step through > molecules. At present we generate 500 HTML pages, each with an applet and > display them on demand. It would be useful to have one applet. I suppose > there is a javascript workaround so we can poke in the CML to a single > applet? If so, it would be useful even though I don't like Javascript for > portability reasons The JavaScript on the Jmol website includes an example for reading files... And that code is quite portable... I believe the only platform/browser combo it does not work on is IE on Mac... Egon ------------------------------------------------------- This SF.NET email is sponsored by: eBay Great deals on office technology -- on eBay now! Click here: http://adfarm.mediaplex.com/ad/ck/711-11697-6916-5 _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
