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