code: public void setMatchingAtoms(int[] atomIndices) {
          this.matchingAtoms = new int[atomIndices.length];
          System.arraycopy(atomIndices, 0, this.matchingAtoms, 0, atomIndices.length);
          Arrays.sort(matchingAtoms);
      }
docs: Set the atoms of a target molecule that correspond to this group.
  
  This method is generally only useful in the context of pharmacophore matching
  
  @param atomIndices The indicies of the atoms in a molecule that match
  the pattern for this group.
  @see #getMatchingAtoms()
  @see org.openscience.cdk.pharmacophore.PharmacophoreMatcher