Fix a performance problem with parsing PDB files that have overlapping
fragments in them.  Since the fragments overlap, ConnectTheDots adds a
ton of bonds, most of which then need to be deleted (really shouldn't add any
considering there are connect records..).  The problem is that each
call to DeleteBond triggered a re-perception since it calls EndModify.

The fix is just to wrap the whole code in Being/EndModify.
The reduces the time to parse the PDB file from minutes/hours to less than a second.
Merge pull request #106 from dkoes/upstream

Fix a performance problem with parsing PDB files that have overlapping