Quick and dirty fix for #177 for Mopac parsing.

MOPAC has changed its output slightly.
This is a quick fix, but still not terribly robust.
Part of me feels we shouldn't be keeping a separate fork of cclib.
Fix PDep Pruning bug introduced in e712697

Commit e712697f18c01e0d6ab419c37bc5248e1e3d3e8b changed the way we store PDep networks
so they are in a dictionary (keyed by entrance source) instead of a long list. This
greatly sped things up. However, it meant you have to iterate over two loops instead of one.
In modifying the code, some parts were not indented so were not included in the inner loop.
Hopefully this is not the only reason things sped up!! (although it must have helped!)

I noticed this while looking at the code around issue #176, which was just an off-by-one 
problem indexing an array from 1 instead of 0. The off-by-one thing doesn't actually hurt things
much because we don't use the array for anything anyway! (I'll remove it in the next commit)
Store PDep networks in List *and* Dictionary.

This means we can use the list when we want them to be in the same order,
and use the dictionary when we want to look them up (quickly) by source.

Perhaps an "ordered dictionary" class would be better, rather than us having 
to maintain two things (it'd be easy to not delete from or add to one of these 
stores at some point, especially when pruning)….

This addresses #176
Merge branch 'GreenGroup/master'
change loop length over PdepNetworks in search for maximum leak rates

- numPdepNetworks = self.networkCount was the number of PdepNetworks
ever created in that model

- len(self.networkList) is the number of actually existing PdepNetworks
at any time

fixes #176