model comparison
Cleaning up all the unnecessary files!
Pruning documentation is added!
Merge pull request #288 from KEHANG/official-doc

Pruning documetation added
correct initialization of props attribute to object attribute

by defaulting to None rather than {}, the props attribute becomes a
object attribute rather than a (shared) class attribute.
unit test showing the behavior of props dicts in Species

the props attribute should always be a local object attribute,
never shared among other instances.
Rename a couple of unit tests

The first line of the test docstring ends up in the unit test nose log,
so it's good to be succinct.
Merge branch 'pr/293' to fix Species.props dictionary.

Closes #292 and #293
Small change to input doc for rmg familes

Just made it a little clearer that the 'default' option is just a
string, while multiple Families are designated as a list of strings
Tweak the chemkin docstrings and documentation.

Written by: Enoch Dames <enoch.dames@gmail.com>
Rebased by: Richard West <r.west@neu.edu>
Make CanTherm alert user if reacting species is not lowest E conformer

For large molecules, it's not always easy to know that the species you
use during a reaction is at it's lowest energy conformation. However,
the scan calculations that are used for inclusion of hindered rotors can
be used to alert a user if this is potentially the case, since most/all
users utilize the geometry from one of their reacting species to
initiate a scan calculation.

This commit now incorporated suggestions by @nickvandewiele
Merged and rebased by Richard West <r.west@neu.edu>
Added a CanTherm example for methoxy decomposition to H + CH2O.

Commit by: Enoch Dames <enoch.dames@gmail.com>
Signed-off-by: Richard West <r.west@neu.edu>
Added a bunch of CanTherm unit tests.

Written by: Enoch Dames <enoch.dames@gmail.com>
Rebased by: Richard West <r.west@neu.edu>
Help CanTherm unit tests find the input file.

If you're running it from a different root directory, eg. via nosetests
or `make test`, this helps it find the input file.
(Not sure where we should put input files like this, but this works for now.)
Merge branch 'pr/287' to get Enoch's CanTherm fixes, examples, and tests.

This closes #287.

1) It now alerts the user if they are not using the lowest energy conformer
   (based on the hindered rotor scans).
2) There is an example for methoxy decomposition.
3) There are some unit tests.
Moved files under rmgpy/cantherm/test to rmgpy/cantherm/files directory so they aren't categorized as unittests.
Changed toleranceKeepInEdge, which was initially a flux, into a ratio of edge rate against characteristic rate!

A unitless tolerance makes more sense than flux.
Minor import fix in makeProfileGraph funciton.

Fixes problem of gprof2dot getting imported as a module rather than a class.
Reduced the unnecessary calls to calculateSymmetryNumber when calculating radical thermo.

calculateSymmetryNumber for saturated structure was called too frequently
when calculating entropy of radical.
Add decrement lone pair atomtypes for 'C' and 'Cs' atomtypes.

For reactions with carbene or carbon atom.