public static List < CDKRMap > getIsomorphAtomsMap ( IAtomContainer sourceGraph , IAtomContainer targetGraph , boolean shouldMatchBonds ) throws CDKException { if ( sourceGraph instanceof IQueryAtomContainer ) { throw new CDKException ( "The first IAtomContainer must not be an IQueryAtomContainer" ) ; } List < CDKRMap > list = checkSingleAtomCases ( sourceGraph , targetGraph ) ; if ( list == null ) { return makeAtomsMapOfBondsMap ( CDKMCS . getIsomorphMap ( sourceGraph , targetGraph , shouldMatchBonds ) , sourceGraph , targetGraph ) ; } else if ( list . isEmpty ( ) ) { return null ; } else { return list ; } }
Returns the first isomorph atom mapping found for targetGraph in sourceGraph .