openbabel/openbabel — pull request #106 by dkoes (2014-11-18 14:25:01+00:00)
Title: 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.