substructure highlighting in Marvin

Hello,


I know that Marvin can highlight certain atoms and bonds in its display applet. Can it highlight an entire substructure, if I knew that this substructure existed in a compound that is being displayed. I have the smiles code for the compound and the smarts code for the substructure that is contained in the compound.


Thanks!

And on a related subject. If I highlight part of a Marvin structure, is there a way for JavaScript to obtain an MRV file that includes the information that part of the molecule has been highlighted? Currently, if we want users to mark part of a molecule, we ask them to map atoms. But it would be better to have them just highlight the atoms or bonds of interest.





I note that there is a SelectionMolecule object in the JChem API.

renjutj wrote:

Can it highlight an entire substructure, if I knew that this substructure existed in a compound that is being displayed. I have the smiles code for the compound and the smarts code for the substructure that is contained in the compound.

This is not possible directly in Marvin applets, but you can use JChem for this purpose. See this example, that uses JChem, Marvin applets and JSP(Java Server Pages):


http://www.chemaxon.com/jchem/examples/sss/index.jsp width="90%" cellspacing="0" cellpadding="3" border="0" align="center"> bobgr wrote: And on a related subject. If I highlight part of a Marvin structure, is there a way for JavaScript to obtain an MRV file that includes the information that part of the molecule has been highlighted? Currently, if we want users to mark part of a molecule, we ask them to map atoms. But it would be better to have them just highlight the atoms or bonds of interest. There is an easier way: you can use methods isAtomSelected(int) and getAtomCount() or getSelectedMol(String) of the JMSketch applet.





I hope this helps.





Szabolcs