How RgroupDecomposition API handle rgroups in fused ring?

Hi, I know the RgroupDecompostion can handle fused ring if R is inside a fused ring. I can see this clearly from RGroupDecomposition in JchemForExcel's function. When I try to do similar decomposition using Java RgroupDecomposition i cannot get the fused ring system decomposed at all. I have attached my query molecule and the molecule with fused ring that failed decomposition. 

I suspect there might be a setting or parameter i did not set. I am using vanilla setting to initialize the RgroupDecomposition, and Decomposition object, following is how i did it. Can you let me know how i can make it handle the fused ring 

I am using JChem 16.11.14.0 library

Thanks

Dong

//init rgd

RGroupDecomposition rgd = new RGroupDecomposition();

rgd.getSearchOptions().setRLigandEqualityCheck(false);

rgd.getSearchOptions().setBridgingRAllowed(false);

rgd.setAttachmentType(chemaxon.sss.search.RGroupDecomposition.ATTACHMENT_RLABEL);

 

public static Molecule[] decomposition(Molecule query, Molecule target){

Decomposition d = null;

st.standardize(query);

rgd.setQuery(query);

st.standardize(target);

rgd.setTarget(target);

try{

d=rgd.findFirstDecomposition();

}catch(SearchException e) {

return null;

}

if(d!=null){

    return d.getLigands();

}

return null;

}

Hi Dong,

You should set the BridgingRAllowed option to true in order to allow R4 and R5 to represent a fused ring together. That is called "R-group bridging", because the additional atoms and bonds seem to form a bridge between two atoms of the ring in the query structure.

So you should replace
  rgd.getSearchOptions().setBridgingRAllowed(false);
with
  rgd.getSearchOptions().setBridgingRAllowed(true);
in the code.

Regards,
Péter