setcolors in toBinFormat

I need to convert smiles to jpeg with selected atoms colored.


I made some changes to the example code SimpleConverter.java.


I assign Set number 0 to all atoms, then Set 1 to selected atoms.


But when I use the (new) setcolors options in toBinFormat, e.g.


"jpeg:w200,setcolors", the output file is still colored by atom type,


the same as if I'd used "jpeg:w200". Do I need to define the


colors of my Sets? How do I do that?





Thanks,


TJ

Try this code. It works for me.

Code:

String selectedindexes = "0,1,2"; StringTokenizer selection = new StringTokenizer(selectedindexes,","); while(selection.hasMoreTokens()) {     String s = selection.nextToken();     try{         int index = Integer.parseInt(s);         MolAtom a = mol.getAtom(index);         a.setSetSeq(1);     } catch(Exception e) {         System.err.println("invalide index:"+s);      } } // colors selected atoms byte[] data = mol.toBinFormat("jpeg:w200,mono,setcolors");

Thanks, Tamas. I must have been working too late last night.


I added the code to setSetSeq AFTER the toBinFormat.


It's all working fine now.





TJ