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
Limit the search for electronic states to atoms involved in reaction

- limit search on labeled atoms
- this is currently RMG-specific to track electronic states as attribute
of single atoms, we have to consider moving on to tracking it as a
species
property
Remove importOldDatabase.py script which is now in RMG-database project.

This version hasn't been updated since May 2011. It has been superseded
by various scripts in the RMG-database project.
added installation dependencies

I noticed I had to install both freetype2 and libpng-dev before
matplotlib could be installed (on a 64 bit machine running linux)
expanded documentation

Added a couple things to output and running sections
added rate rule caveat to documentation

...it might be wise to double check existing rules to ensure there are
not too many instances of this