Deleting one molecule template from another

I've been trying to use the MarvinBeans Java code to perform a simple operation on two molecules, where the smaller molecule is removed from the larger one, and the remaining fragments are output as a Molecule graph. (Basically, deleting the common parts of both, and showing the difference).

I currently do this by recording the bond indexes for the smaller molecule, and then performing running Molecule.removeBond for each on the larger molecule, cleaning up the remaining fragments by looking for any atom only connected to hydrogens. The problem I have is that sometimes the fragment left fits that bill and is cleaned away.

Does anyone know of a cleaner method for doing this that will prove more reliable?

Hi James, 

If I understand you use the bond indexes of the smaller molecule to remove bonds from the bigger (target) molecule. I don't see why this should remove the same molecule part in both molecule as the order of bonds can be changed easily.

I think you should use MolSearch.

You can find sample codes that you can use in this topic. 

Best regards, 

Peter

Thanks, I'll take a look, but that seems to solve it.