Substructure highlighting

Using Marvin 5.1.2 I perform substructure highlighting to a MViewPane using the following methods:





mviewPane.setAtomSetColor() // Pick the colour


mviewPane.setAtomSetSeq() // Select the hit atoms





This works well, but I have already coloured my atoms to represent activity. I was hoping to vary the thickness of this hit using mviewPane.setWireThickness(), but now see this applies to the whole molecule.





Is there a way to alter the wirethickness for a subset of atoms? Or is there another way to highlight the query without using colour?





Many thanks


Craig

Dear Craig,





Do you mean changing the bond thickness? Are you using JChemSearch to get the hit atoms?


In that case you can get the result of the search in highlighted/colored form with the help of the HitDisplayTool class:


http://www.chemaxon.com/forum/viewpost17024.html





Best Regards,


Erika.

Hi Erika,





Thanks for your response. Yes I do mean changing the bond thickness. The link you mention is what I based my code on, using MolSearch. I've attached images of my current output (purple highlighted benzene) and what I'm aiming for (only alter thickness of benzene).





This is the only way I can think of that shows the hit and keeps my colour coded atoms present.





I looked at HitDisplayTool and HitColoringAndAlignmentOptions but don't see which method would alter bond thickness?





Many thanks


Craig

Hi Craig,





Altering bond thickness in MViewPane is possible with MDocument. HitDisplayTool is for coloring only. I created an example to demonstrate how to alter bond thicknes in MViewPane.





Best regards,


Erika

Hi Erika,





That looks perfects!





Thanks


Craig