Feature Requests item #2779223, was opened at 2009-04-23 00:41 Message generated for change (Settings changed) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=2779223&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: Functional Group Identification Initial Comment: 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 ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-04-23 16:02 Message: 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. ---------------------------------------------------------------------- Comment By: Mike Casey (mykc) Date: 2009-04-23 14:52 Message: 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. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-04-23 14:10 Message: OK, the file I made is at http://chemapps.stolaf.edu/jmol/docs/misc/groups.txt ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-04-23 13:47 Message: 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? ---------------------------------------------------------------------- Comment By: Mike Casey (mykc) Date: 2009-04-23 10:34 Message: 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. ---------------------------------------------------------------------- Comment By: Angel Herraez (aherraez) Date: 2009-04-23 02:53 Message: 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. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=2779223&group_id=23629 ------------------------------------------------------------------------------ Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
