Remove output files generated by example in rmgpy/cantherm/files
Update species representation documentation (adjlist update for O2)

A student pointed this out to me (since using this will of course cause
RMG to fail), just updating it now before I forget.
Remove unused CoreEdgeReactionModel.loadSeedMechanism() method.

I think this stopped being used four years ago in commit 3599f34b550ef7a53ad7081d62b93aa41c44e057
Author: Josh Allen <jwallen@mit.edu>
Date:   Thu Aug 5 15:32:43 2010 -0400
and is now thoroughly broken. Removing it to reduce confusion.
Add .gitignore to prevent output in rmgpy/cantherm/files being tracked.

These will only appear if you manually run cantherm on the input file,
as I don't think (currently) this is done as part of a unit test 
(though I don't see why it couldn't be in the future).
Refactor the pruning algorithm a little bit.

This should be a bit faster, and a bit clearer.
Faster because we have fewer lookups of self.edge.species[index]
and because we can stop iterating as soon as we reach a small enough edge.

Now that this has been debugged, I'm not sure we need the logging statement
on line 1101, because the same info is logged about 15 lines further down...
Add description to the methoxy example README (and rename README.txt)
Revert "Minor import fix in makeProfileGraph funciton."

This reverts commit ae84b9b3979329fb7e9745e844af1a0bcf1d6b44.

It was changed the other way in c881a72a8e442c6fb2672837c84100b325b069d5.
I suggest checking gprof2dot is not in your $RMGpy/external/ folder,
and that you have a recent version (eg. via `pip install --upgrade gprof2dot`)
Attempt to clarify #290 re. Symmetry corrections in HBI radical GA estimates.

I changed a method name, added an assertion, and added some text to the docstring.
Just trying to clarify what is currently being done, without changing anything.

My remaining concern is with how this interacts with QMThermo, where the "stable" 
(saturated parent) molecule is estimated via PM6 or something. This current 
implementation assumes that the the entropy has not been corrected for symmetry
(because that is what it now does for group additive thermo).
Small CanTherm bug fix with a couple updates to documenation

CanTherm was crashing for cases when users specified TS frequencies in
the input file. I also updated part of the documentation for input
files. I think the kinetics function example was for Measure, and if
used with RMG-Py, would cause cantherm to crash. Added more doc relevant
to new T-parameter functionality implemented by Shamel, and a
Troubleshooting/FAQ section with one entry.
mimic the main() method instead of deprecated Main() class of gprof2dot

see
https://code.google.com/p/jrfonseca/source/detail?r=bf25a2abb09bf2cb821832d76900f0dd8326eb8a&repo=gprof2dot

for more info on this change of gprof2dot.

The main method is copied, except the optparser part that reads from
sys.arg. The output of optparser is replaced by an empty Options class
populated with hard-coded options.

Only gprof2dot imports to a limit number of classes, attributes were made.
pip install specific commit of gprof2dot

The use of gprof2dot in RMG-py is tailored to the version of gprof2dot
contained in this commit.

To prevent people with older versions of gprof2dot to run into problems,
we checkout this commit specifically.
Tweaks gprof2dot implementation.

1. Change the wording in the warning when the import fails. 
   (To suggest a different version).
2. Prevent a ton of PostScript warnings when running dot on MacOS X
   (calling a font by the wrong name).
3. Remove an out of date comment
Update URL to Oasa library in requirements.txt
Remove Oasa library from requirements.txt

This is no longer needed.
Point travis to my own RDKit fork, temporarily.

The only change on my fork is the URLs of the InChI API.
This is to test it works, then I'll send a PR upstream to rdkit,
and we can switch back to tracking the official fork.
Revert "Point travis to my own RDKit fork, temporarily."

This reverts commit 99e9090e48fb9517decd08fc0dbb9a68bb417308.
RDKit have now merged my pull request to them, so their
fork has the needed fix.
Cantherm fix, doc update, more bondE corrections

Cantherm was crashing if the input file did not have a model chemistry
with a bond energy correction dictionary. Creation of an initial empty
dictionary fixes this. Also added B3LYP bond energy corrections  from
the same table and source as the CBS-QB3 corrections. Made some small
updates to the doc.
Condense code for adding a wildcard set of unpairedElectrons, lonePairs, or charges.
Raise an error if there is a duplicate group in a kinetics family.
make orbitals global in adjlist and correct some of them.

The maximum number of valence orbitals is defined per period of the
periodic table. Each orbital can contain a maximum of 2 electrons.
We assume that period 2 and 3 have a maximum of 8 valence electrons so
this leads to a maximum of 4 valence orbitals.