code: public boolean hasContactToAtom(Point3d[] iAtoms, Point3d[] jAtoms, Point3d query, double cutoff) {
  		for( int i : iIndices ) {
  			double distance = iAtoms[i].distance(query);
  			if( distance<cutoff)
  				return true;
  		}
  		if (jAtoms!=null) {
  			for( int i : jIndices ) {
  				double distance = jAtoms[i].distance(query);
  				if( distance<cutoff)
  					return true;
  			}
  		}
  		return false;
  	}
docs: Tests whether any atom in this cell has a contact with the specified query atom
  @param iAtoms the first set of atoms to which the iIndices correspond
  @param jAtoms the second set of atoms to which the jIndices correspond, or null
  @param query test point
  @param cutoff
  @return