This method is called automatically by automodel after the default
restraints are generated. By default, it does nothing. However, you can
redefine it to add
additional user-defined restraints to those calculated by automodel.
Symmetry restraints, excluded atom pairs, and rigid body definitions can
also be set up in this routine.
The routine is passed aln, which is the alignment between the templates
and the target sequence.
See section 2.2.11 for an example.