Added CanTherm class to rmgpy.cantherm.main module.

The CanTherm class represents an instance of a CanTherm job, used to
compute properties of species and reactions. Wrapping this functionality
in a class enables us to more easily generate jobs programmatically as
well as using input files. Methods for parsing the command-line arguments,
initializing the logging system, and running the job are provided.
Updated cantherm.py script to use CanTherm class.

This remains the route to running individual CanTherm calculations using
standalone input files. Most of the functionality has been moved out of
this execution script and into the rmgpy.cantherm submodule.
Updated GaussianLog class to read in conformer information.

The updated GaussianLog class works with the new rmgpy.statmech classes.
Some functionality that has been duplicated elsewhere (e.g. the fitting
of the cosine or Fourier potentials to a hindered rotor scan) has been
deleted.
Added StatMechJob class to rmgpy.cantherm.statmech module.

A StatMechJob is used to generate the statistical mechanical degrees of
freedom for a molecular configuration. This job is often a prerequisite
of other jobs, e.g. for computing thermodynamic or kinetic parameters.

In a StatMechJob, a secondary input file is read containing the
information about the molecular conformer, including: atom and bond
counts; geometry, energy, and frequency log files; symmetry number and
optical isomers; and hindered rotor parameters. You can easily store
energies for multiple model chemistries in one such file.

This module replaces the rmgpy.cantherm.states module, which has now been
removed.
Added ThermoJob class to rmgpy.cantherm.thermo module.

A ThermoJob is used to generate a thermodynamics model for a species
by evaluting its statistical mechanical degrees of freedom. Either a
Wilhoit or NASA model can be fit; as usual, the NASA is fit from the
Wilhoit fit. A plot comparing the fitted thermo model to the thermo
values evaluated from the statistical mechanical modes is also generated
if matplotlib is installed.
Added KineticsJob class to rmgpy.cantherm.kinetics module.

A KineticsJob is used to generate and fit a kinetics model for the
(high-pressure limit) kinetics of a reaction, including tunneling
corrections. A plot comparing the fitted Arrhenius model to the directly
computed k(T) values is generated if matplotlib is installed.
Added PressureDependenceJob class to rmgpy.cantherm.pdep module.

The PressureDependenceJob class provides functionality for computing the
pressure-dependent rate coefficients k(T,P) for a unimolecular reaction
network and fitting them to a kinetics model. Plots of the computed
k(T,P) values and the fitted kinetics models are produced if matplotlib
is installed. A depiction of the network is produced if Cairo and its
Python wrapper are installed.

This is largely a merger of MEASURE into CanTherm.
Updated loadInputFile() in rmgpy.cantherm.input module.

The updated version of the loadInputFile() function loads the CanTherm
input files for the statistical mechanics, thermodynamics, kinetics, and
pressure dependence jobs. Some functionality that was duplicated in other
files (e.g. the projecting out of the hindered rotors from the force
constant matrix) has been removed from this module.
Added prettify() function to rmgpy.cantherm.output module.

This function takes repr() output for a Python object and "prettifies" it
by spreading it onto multiple lines with appropriate indentation. This
function is used in each job to generate the output file. The
implementation involves walking the Python abstract syntax tree for a
given snippet of code, which is easily done using the ast module.

This may be useful outside of CanTherm as well, but as CanTherm is the
only thing using it at the moment, I am placing it inside the cantherm
subpackage for now.
Import content of submodules when importing rmgpy.cantherm subpackage.

This is the recommended way of referring to these classes.
Added CanTherm example input files for several species.

Ethane (C2H6) is probably the most "complete" example, as it includes a
hindered rotor. H, C2H4, and C2H5 will be used in an example of a
reaction.
Added CanTherm example input files for a simple reaction.

This also uses the species H, C2H4, and C2H5 added previously.
Added CanTherm example input files for a few pressure dependent networks.

Both a single-well and a multi-well network are provided as examples.
Merge branch 'cantherm'
Make all Arrhenius and ArrheniusEP parameters into quantity objects.

This is so we can store uncertainty parameters with all of the parameters.
We can still enforce that these values are dimensionless.
Added highPlimit attribute to PDepKineticsModel class.

This attribute provides a place to store the high-P kinetics that
corresponding to a pressure-dependent reaction, if applicable. This
information can then be preserved e.g. in Chemkin output.
Add small extrapolation allowance in ThermoData.

This is ostensibly so that we can extrapolation from 300 K to 298 K
without needing to give a value for Cp0. A better approach would be to
actually provide the Cp0 (and CpInf), since they are easy to determine
from a chemgraph.
Add calculateCp0() and calculateCpInf() to Species and Molecule classes.

These make it easy to determine Cp0 and CpInf for a given species that
has molecular structure data.
Re-added ArrheniusEP.toArrhenius() method.

This is used to convert an ArrheniusEP object to an Arrhenius object for
a given enthalpy of reaction by evaluating the Evans-Polanyi relation.
Remove thirdBody attribute from template, library, depository reactions.

This attribute was previously removed from the Reaction class because it
was only ever set to True when a ThirdBody kinetics was in use, which
made it redundant.