code: public List<List<PharmacophoreAtom>> getMatchingPharmacophoreAtoms() {
          if (pharmacophoreMolecule == null || mappings == null) return null;
          return getPCoreAtoms(mappings);
      }
docs: Get the matching pharmacophore groups.
  
  The method should be called after performing the match, otherwise the return value is null.
  The method returns a List of List's. Each List represents the pharmacophore groups in the
  target molecule that matched the query. Each pharmacophore group contains the indices of the
  atoms (in the target molecule) that correspond to the group.
  
  @return a List of a List of pharmacophore groups in the target molecule that match the query
  @see org.openscience.cdk.pharmacophore.PharmacophoreAtom