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#158 Retrosynthesis


Hey great Job,just wondering whether or not retron/synthon identification was possible with jmol.How far does jmol go with respect to inorganic/organometallics,what elements can I model in jmol? Can anyone suggest a good particle in a box program besides hyperchem for my students?
I have started modifying jmol to do it for polyenes,got as far as the 1d box being half the number of double bonds,how would I go about integrating a box parallel to the polyene and associated energy levels? I am using the graphic that links atoms as the boundaries of the box,still working on integrating the calculator.
I'll create an account and post when I'm through.


  • Bob Hanson

    Bob Hanson - 2009-04-25

    dear anon,

    Sounds like a nifty application you are working on. Please be aware of the lesser GNU license -- that any modification you make to Jmol must become publicly available. The typical way this is done is to start a branch and do all the modications there, using Eclipse to update it. This is very generally useful, because then when you get stuck you can refer to that branch, and other programmers can test and provide advice.

    I assume you are working with Jmol 11.7 in this? It would not be advisable starting with 11.6, which is now many subversions behind 11.7.

    In answer to your questions:

    retron/synthon -- you can use the functionality of Jmol to develop this. I don't think anything particular would be necessary for any changes to Jmol itself. It's all valence/connection based, and that is all easily determined using methods already in place.

    elements/modeling -- they are all there; the only aspect Jmol "models" is that it does incorporate the Universal Force Field, which was specifically designed by the Goddard group to encompass organometallic and inorganic compounds.

    Actually, rereading what you have there, I would highly recommend not modifying Jmol. The web-based interface is so extensive, why not just consider this a web page development project? It would be far more accessible, you would have a much greater audience, and it wouldn't require any Java programming.

    Not trying to be insensitive here, but surely simple 1d particle-in-a-box applets are out there. No? It's sort of a classic example system. I know the temptation to "do it yourself" but, for example, see -- why involve Jmol?

    Bob Hanson

  • Bob Hanson

    Bob Hanson - 2009-08-12
    • status: open --> closed

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