added support for graphs not starting at 0

added support for graphs not starting at 0

It has always been implicitly assumed that graph->start==0.
This assumption would only fail for a topology starting with
single atom molecules followed by multi-atom molecules.
Furthermore, for mk_graph at_start could only be 0, a check
has been added for this, and at_end was not stored.

In t_graph start is now replaced by at_start and end by at_end,
where at_end is end+1, now the first atom not part of the graph.

Change-Id: I0d4c09c90cbba1a7f4a1d84cf1f90a7643c17cd8