public List < List < Integer > > getMatchingAtoms ( ) { List < List < Integer >> matched = new ArrayList < List < Integer > > ( mappings . size ( ) ) ; for ( int [ ] mapping : mappings ) matched . ( Ints . asList ( mapping ) ) ; return matched ; }
Get the atoms in the target molecule that match the query pattern . Since there may be multiple matches the return value is a List of List objects . Each List object contains the indices of the atoms in the target molecule that match the query pattern