protected List < Map < IAtom , IAtom > > getOverLaps ( IAtomContainer source , IAtomContainer target , boolean removeHydrogen ) throws CDKException { mappings = new ArrayList < Map < IAtom , IAtom > > ( ) ; connectedBondOrder = new TreeMap < Integer , Double > ( ) ; this . source = source ; this . target = target ; if ( source . getAtomCount ( ) == 1 || ( source . getAtomCount ( ) > 0 && source . getBondCount ( ) == 0 ) ) { setSourceSingleAtomMap ( removeHydrogen ) ; } if ( target . getAtomCount ( ) == 1 || ( target . getAtomCount ( ) > 0 && target . getBondCount ( ) == 0 ) ) { setTargetSingleAtomMap ( removeHydrogen ) ; } postFilter ( ) ; return mappings ; }
Returns single mapping solutions .