#156 Functional Group Identification

closed
nobody
None
5
2009-07-08
2009-04-23
Anonymous
No

I'd looooooooveee to see a molecular modelling program with this simple feature,everyone overlooks it even commercial packages.Plus it's so ridiculously simple.Org Chemistry is all about f(x) groups,a particle in a box utility would be nice for carotenes etc but that's CDK.
I'd love to see the day when cdk can hold its own,the databasing ability like chemfolder is missing too,but that's cdk. Jmol is great but please add functional group identification in the next release

Discussion

  • Angel Herraez

    Angel Herraez - 2009-04-23

    Please, sign your posts.
    If it's so simple, why do you think it is not in any programs? Maybe it's not so simple! Or go and do it yourself!
    You should investigate Jmol syntax for atom expressions; the "connected" keyword allows to select functional groups, and there are examples already there.

     
  • Mike Casey

    Mike Casey - 2009-04-23

    Jmol allows highly specific selection of groups of atoms using atom expressions, and this can be used to identify functional groups. I modified a script file written by Bob Hanson for this purpose, and it can be seen in action at: http://www.ucd.ie/chem/molvis/drugs.html. Mike Casey.

     
  • Bob Hanson

    Bob Hanson - 2009-04-23

    Dear anon,

    You are sooooooooooooooo lucky. As Mike points out, you can very easily write scripts that identify functional groups. This is nothing that needs to be added to Jmol. It's just a matter of getting the script and working with it yourself. Mike, where is that .spt file?

     
  • Mike Casey

    Mike Casey - 2009-04-23

    Hi Bob, long time, no see. You're doing a brilliant job with Jmol. I'm a newbie (that's obvious from my website), but I'm trying to tap the tremendous potential of Jmol. Sorry, I forgot to provide a link to the script. It's at http://www.ucd.ie/chem/molvis/groups.txt Please note that it is intended for use with molecule files in which double triple and aromatic bond types are already specified (e.g. some *.mol and *.gpr files), and won't function correctly with many other formats. Cheers, Mike.

     
  • Bob Hanson

    Bob Hanson - 2009-04-23

    One more comment here -- If you are interested in identifying functional groups, and the files you are using do not include multiple bonds, check out the connect AROMATIC option and then "calculate aromatic". This is as far as I can tell a unique feature of Jmol -- the capability of determining hybridization from structure and pretty much nailing where double bonds should go. This isn't necessarily important for the identification of functional groups, which can be done with simple connection counting, but it does vastly improve the capability of Jmol to display simple structures in "expected" ways.

     
  • Bob Hanson

    Bob Hanson - 2009-07-08
    • status: open --> closed
     

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