Atom/bond set highlighting behavior

When I use Marvin Atom/Bond Sets to highlight a substructure, it seems that unmatched bonds directly connected to matched atoms are also highlighted. Worse, if such a bond is a wedged one, the whole bond gets highlighted. The example below shows the result of SSS highlighting after mapping the ring structure onto cholestane. You can see that the wedged bonds that are not part of the substructure are also highlighted in magenta. Is there a way to change this behavior?

Dear ningyu18!

Could you please tell us what did you use to highlight the molecule ? 

I could reproduce the same scenario in sketch; If the selected molecule has an atom which has got a wedge bond outside of the selection, and we paint the selection to some colour, the wedge bond will be painted aswell.

If you highlight from api, painting bonds where one of the atom is in the selection and the other atom is outside, is a possible workaround. Could this solution work for you?

Best regards,

Tamas Fazekas-Vigh

Thanks for your quick response! I can try your walkaround and see if it meets our needs. Could you post a snippet for painting a molecule using MolPrinter?

Hi,

I am not a programmer, but you can find some bond coloring example here: http://www.chemaxon.com/marvin/examples/applets/view/colorsets.html and the API documentation about the related parameters: http://www.chemaxon.com/marvin/help/developer/viewman.html#parameters.atomSetColor

I hope, it helps.

Efi