bioclipse/bioclipse.cheminformatics — pull request #27 by egonw (2013-04-05 23:35:48+00:00)
Title: Added script codes to highlight part of the structure in the active editor.

I am using this for cheat sheets I am developing right now, with combined script to go like:

mol = cdk.fromSMILES("O=C(O)C(N)CCCCN");
jcp.setModel(mol); // reusing an existing editor here... not very robust :(
jcp.selectAtoms("1, 2, 3");

This particular example highlights the acid group of an amino acid.