Fixed H_Abstraction reaction template to use X_H_or_Xrad_H.

This is apparently not correctly imported from the RMG-Java database. If
you use X_H instead of X_H_or_Xrad_H, you will find that RMG-Py crashes
when it is only able to match R: + R'H -> R.H + R'. in the forward
direction.
Change Y_1centerbirad group to allow CO in H_abstraction.

In RMG-Py (at least), CO is strictly distinct from Cd, so we need to
specify CO here in order to allow for H abstraction reactions that convert
HCO to CO.
Redefined Substitution_O to allow for biradical substitution.

The previous definition had an issue with reactions of the form

R-O-R' + R": -> R-O-R". + R'.

which could only be matched in the forward direction (causing an error
message to appear in the log). I've changed the definition to allow for
R-O-R". to also match the appropriate top-level node (now called
O-RR_or_RRrad). This should stop the error message, but I suspect the rate
estimates will be pretty terrible (which could be okay as long as they
aren't sensitive, but who knows).
Changed Y_1centerbirad group to triplet in Substitution_O.

On a practical basis this simply prevents CH2(S) and other singlet carbenes
from participating in Substitution_O reactions (similar to how singlet
carbenes do not participate in H_abstraction reactions).
Removed experimental Enol_keto_tautomerization kinetics family.

This is a family I had been experimenting with as a possible explanation for
some model discrepancy. It never got to the point to be promoted to a full-
fledged reaction family, so it does not belong on the master branch.
Merge remote-tracking branch 'official/master'
Fixes to group Intra_R_Add_Endocyclic definitions
Added missing rate rules for several families.

The rate rules were missing because they came from rules that shared an
index with a later rule in the same family. This was caused mainly by the
sulfur rules, many of which overlap with non-sulfur rules. In the long
term we should give each rule a unique index, but this works for now.
Fixes to group Intra_R_Add_Endocyclic
Merge remote-tracking branch 'fariba/master'
Fix to OCOO rule in HO2_Elimination_from_PeroxyRadical.

For some reason this rule was not properly imported from the RMG-Java
database before.
Changed definition of OJ in Substitution_O to allow adjacent biradical.

This avoids an error where the Substitution_O family could only identify
a reaction in one direction (this family is its own reverse, so you
should be able to identify it in both directions).
Imported polycyclic thermo groups from RMG-Java.
Merge branch 'master' of github.com:GreenGroup/RMG-database
Adding subtree 'R5-SD-DD' in 'R5-SD' group to fix degeneracy calculation error, RMG-Py issue#69!
Add Cdd atom type to *3 in Intra-R-Add-Endocyclic reaction family.

Some of these have been added already in recent commits.
Now, we went through systematically and added them all.
Removed a node we recently added.
Added some comments to the longDesc fields.
Added parseAndRunCommandLineArguments() to kineticsGroups.py.

This simply wraps the code that parses the command-line arguments.
Updated version of kinetics group additivity values generator.

The kineticsGroups.py script is now again able to generate group
additivity values for the reaction families. Much of the code for this
was moved to KineticsGroups.generateGroupAdditivityValues() in the
RMG-Py codebase. A few other functions -- notably generate() and
createDataSet() -- needed some updating to reflect recent changes in
the KineticsFamily and related classes.
Removed several H_Abstraction NIST entries with forbidden molecules.

All of these reactions involved the forbidden Carbene_D group (forbidden
in all families, not just H_Abstraction). Leaving these present causes
an UndeterminableKineticsError when trying to evaluate the kinetics group
additivity values.
Updated version of kinetics group additivity evaluator.

This is again restored to working order, including the ability to interact
with the generated plot by clicking on points to see which reaction they
correspond to.