Thanks Otis. I thought I'd give this path a try just to see what happened. I extracted the structure ABELEZ from the CSDB and saved it as a .mol2 file. Fired up the Jmol application and opened that mol file and the structure comes up nicely. But there is no option to export this structure as SMILES.
All of this really needs to work as a standalone unit rather than as a web page anyway but, just seeing what happens with a complex molecule is of interest. The problem seems to be that if things have to go through a 2D stage then a fair amount of work needs to done by the user in order to see the multiple stereocenters because of the overlap of various parts of the molecule. I can read the ABELEZ.mol2 file into marvinsketch and then do all this there but it isn't nearly as clean and straightforward as I'd like to see. Bob, is it possible to make use of that module Gilleain mentioned from the CDK inside Jmol to apply the C-I-P rules and maybe come back with an array of atom names and configurations? Rich On Jul 29, 2011, at 6:46 PM, Otis Rothenberger wrote: > Rich, > > The answer to your question is NIH Resolver. The following illustrates > the process using SMILES: > > http://cactus.nci.nih.gov/chemical/structure/C[C@@H](CC)Cl/image > > Resolver will also accept molfile input, but there are query string > length limitations. Since Jmol can convert a molfile to SMILES, Jmol can > mediate the above translation. If you want to see this in action, go to: > > http://chemagic.com/web_molecules/script_page_large.aspx > > Click "The Molecular Editor" Then "Image." The "NIH 2D Capture" link > will illustrate the Jmol mediated translation. > > Otis > > Otis Rothenberger > chemagic.com > > > On 7/28/2011 6:30 PM, Richard Ball wrote: >> I know that assigning R and S to 3D molecules is too complex a task for Jmol >> but I wondered what programs are available for doing this. The .mol file >> format has the ability to describe both 3D coordinates as well as bonding so >> is there a program that can read a structure in that format and assign the >> stereocenters? >> >> Platon will do some but it isn't a general solution since the bonding isn't >> explicit and the assignment rules are not fully implemented (IOW it makes >> mistakes). >> >> I have the luxury of having access to non-commercial proprietary software to >> do this but is there something more generally available, either free or not >> too costly, I could recommend to others? >> >> Rich >> >> ------------------------------------------------------------------------------ >> Got Input? Slashdot Needs You. >> Take our quick survey online. Come on, we don't ask for help often. >> Plus, you'll get a chance to win $100 to spend on ThinkGeek. >> http://p.sf.net/sfu/slashdot-survey >> _______________________________________________ >> Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > ------------------------------------------------------------------------------ > Got Input? Slashdot Needs You. > Take our quick survey online. Come on, we don't ask for help often. > Plus, you'll get a chance to win $100 to spend on ThinkGeek. > http://p.sf.net/sfu/slashdot-survey > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
