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.
Fixed a few entries in the NIST H_Abstraction database.

The problem is not one of transcription, as the NIST website matched the
original values. Now that we can evaluate the kinetics group additivity
(and rate rule) methods again, these will be easier to spot.
Adjusted A factor in H_Abstraction rule #75.

The previous A-factor was orders of magnitude larger than other A-factors
from the Saeys rules. We attempted to use the Saeys group values to
estimate the correct value, and got a number far closer to 3e12 than
3e18. This is also much more consistent with an estimate from Tsang.
Fixed n value in H_Abstraction NIST entry #1134.

In that reference, the main table gives an n of 5.1, while the discussion
on p. 21 gives a value of 2.5. The latter is the same as the n value for
the analogous reaction to form t-butyl (instead of isobutyl) radical.
The latter is also closer to the preexisting rate rule for this reaction.
Removed Java support from kineticsGroups.py script.

The "Java" databases had been deleted, and since we now have a rate rule
algorithm implementation in RMG-Py, I've updated the kineticsGroups.py to
use that algorithm instead. You can control whether the plots use the
rate rules or group additivity method using the --rules flag.
Use reaction.kinetics instead of entry.data when evaluating kinetics.

The former is filled in by getForwardReactionForFamilyEntry(), and is
always in the forward direction of the reaction family. The latter might
be in the reverse direction, since that is something we allow in the
training and test sets.
Minor bugfix to convertKineticsToPerSiteBasis().

Now uses value_si instead of value(s), in keeping with the ScalarQuantity
and ArrayQuantity objects.
Some prettifying of the graphs produced when evaluating kinetics.

In an effort to produce publication-quality plots.
Can now control plotting of exact or estimate kinetics during evaluation.

The --exact and --estimate command-line arguments control whether only
exact or only estimated rates are plotted. You should use one, the other,
or neither of these arguments. The file name of the saved plots now
contains this information as well.
Fixed entry #47 in NIST R_Recombination depository.

Seems to have been incorrectly transcribed by the NIST folks; I got these
values from the original paper.
Removed some non-high-P kinetics from the R_Recombination NIST depository.

The source paper (2004LI/KAZ7671-7680:12) gave the kinetics for this
reaction at several pressures, and the NIST folks transcribed each of
these as separate entries instead of as a single PDepArrhenius entry.
I've kept only the one for the high-pressure limit.
Fixed a few other values in the R_Recombination NIST depository.

Again, these seem to be transcription errors when input into the NIST
kinetics database. Updated values come from the original sources.
Honor temperature range when plotting evaluated kinetics.

It's not a fair evaluation if the k(T) from the literature is outside the
valid temperature range. This does reduce the number of plotted points
somewhat, as many experimental measurements are only valid over a small
temperature range.
Fixed sign errors in H_Abstraction NIST entries #600 and #601.

Based on the source paper, I can see where someone would get confused as
to the sign of the Ea values.
Updated entries #458 and #459 in R_Addition_MultipleBond NIST depository.

Someone had used the k(T,P) values at 1 bar from the paper instead of
the k(T,P -> infinity) values listed just a few lines below it in the
same table in the source paper.
Fixed A factor error for two entries in R_Addition_MultipleBond NIST.

These A factors were off by an Avogadro number (and this despite having
units of s^-1).
Removed several entries from R_Addition_MultipleBond NIST depository.

These entries did not contain high-pressure-limit Arrhenius parameters,
but instead k(T,P) values for 1 bar.