public static List < List < CDKRMap > > getSubgraphAtomsMaps ( IAtomContainer sourceGraph , IAtomContainer targetGraph , boolean shouldMatchBonds ) throws CDKException { List < CDKRMap > list = checkSingleAtomCases ( sourceGraph , targetGraph ) ; if ( list == null ) { return makeAtomsMapsOfBondsMaps ( CDKMCS . getSubgraphMaps ( sourceGraph , targetGraph , shouldMatchBonds ) , sourceGraph , targetGraph ) ; } else { List < List < CDKRMap >> atomsMap = new ArrayList < List < CDKRMap > > ( ) ; atomsMap . add ( list ) ; return atomsMap ; } }
Returns all subgraph atom mappings found for targetGraph in sourceGraph . This is an ArrayList of ArrayLists of CDKRMap objects .