Add wrapper for testing database

Running the function EvaluateKinetics.py will use the new checkWellFormed
database and make an output file called DatabaseWellFormedSummary.txt in
the RMG-database folder
Add output for checking for unique groups

Another check that needs to be done is if each group is unique. I have
added lines for output of that from checkWellFormed
fix AdjList in rules of Intra_R_Add_Exocyclic

Many of the adj lists in the rules did not match that of the groups. In
this family, all the groups were always more general than the rules
version, so I've changed the rule's adjList to be the same as the groups

This error was found using the checkWellFormed function
Fix child relationships in R_Addition_Csm

Some children were labelled with a "C" atom when the parent had a "Cs"
atom causing a discrepency. Probably harmless, but it's better to be
consistent
Fix errors in Disproportionation family

Errors found by checkWellFormed (and a few stumbled while making manual
corrections).

In rules.py
- O2_birad named wrong, should be O2b
-XH_Rrad_birad has been updated to a logic Or at some point, but not in
the top most node
-Same with Y_rad_birad_trirad_quadrad

In groups.py
-Deleted group N3_atom_quartet, which was an accidental duplicate group
-deleted N5dd/H_d_Rrad, which was an accidental duplicate group
-Changed atom type on N5d/H_d_Rrad, which was a typo or mistake from
recent merge
-Moved C_rad/H/O2 and C_rad/H/CsO appear to be placed under the wrong
parent. They have been moved from under C_rad/H/NonDeN to under
C_rad/H/NonDeO.
-Changed Y_rad adj list, it used to be defined R-R* for some reason, but
now I've made it just R*. This clears up several children errors.
-Added H_rad to LogicOr of Y_rad_birad_trirad_quadrad. That one seems
important.
-Made group XH_Rrad more general by allowing single or double bonds. So
that XH_d_Rrad is a child
-Many groups do not include an N atom as possible atoms, restricting
descending down to certain children. An N atom has been added to the
following groups: O_Rrad, COpri_Rrad, C/H/DeDe_Rrad, C_rad/H/OneDe,
C/H2/Nd_Rrad, Cmethyl_Rrad, C/H/NdDe_Rrad, Cdpri_Rrad, C/H2/De_Rrad,
C/H/NdNd_Rrad, Cpri_Rrad, Csec_Rrad
-Changed Ct_rad/Ct atom one from C to Ct so it is proper child
-Changed an monoradical atom type from R to R!H in NH_s_Rrad, which must
be true by definition. Also made same change for all children
-For groups N3s/H/NonDe_s_Rrad and N3s/H/Deloc_s_Rrad, changed an atom
from N to R!H based on name and consulting the creator bbuessar
Merge pull request #33 from nyee/databaseTest

Database test
Remove history fields permanently and clean up empty reference and referenceType fields.
Remove `recommended` field in databases since they have no functionality.
Remove rogue git conflict lines in R_Recombination/NIST.py
Add a list of recommended families for setting the 'default' option in RMG.

Use a dict rather than a function call to do so.
This corresponds to a commit in RMG-Py
Merge pull request #35 from connie/universalDatabase

Add list of recommended families for setting the 'default' option in RMG