Tring to get importOldDatabase script working
Updated loadOld in KineticsLibraries so same keys used as load()

Commit 421d7472a83a46be6bfa69beef83ff387420ef1b changed the keys used in the entries dictionary
for loading new databases. This makes old database imports use the same keys, so that the change-detection
might work better.
Index KineticsLibraries with just their integer index, not "index:label" strings.

Following up on  421d7472a83a46be6bfa69beef83ff387420ef1b
which noticed some parts of the database have multiple entries the same index
(I think in reaction rules?) the entries were stored in a dictionary with 
keys "index:label". 

4f1a33e4fbefe12838cf039a652c39b008a35a7d tried to make the loadOld() method
do the same, but it causes problems with the duplicate removal methods.
As KineticsLibraries don't have this problem (they don't have indices or labels 
stored in the database) I am making the keys just equal to the index.
Saturate with H's when importing old Dictionaries from RMG-Java style database.

Addresses immediate problem in #180
Cope with weird text encodings when loading old database.

Aaron's name has umlauts and it wasn't saved in utf-8, so
was causing unicode errors. Rather than guess what encoding
(Latin? Windows?) we replace unknown characters. Sorry Aaron!
Say which file you're importing to make debugging easier.

This is to help the loadOldDatabase efforts
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 It has been superseded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
added molecular constraints to documentation

This regards RMG-Py issue #174. Also made sure
generatedSpeciesConstraints works properly.
Add new ketoenol family to list of unimolecular kinetic families.
Encode in UTF-8 otherwise we run into errors for unicode symbols.

If that fails, then encode in ascii and omit the symbols completely.
We run into too many errors otherwise.