Tree gen SubstitutionS

[ChrisBNEU]

Autogenerated tree for SubstitutionS family. DB tests pass for first commit where we change the logic nodes and setup the reverse map. fails after the tree is generated, with the following error:

======================================================================
ERROR: Kinetics family SubstitutionS: Entry is accessible?
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Traceback (most recent call last):
  File "/Users/blais.ch/anaconda3/envs/rmg_env/lib/python3.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/Users/blais.ch/_01_code/RMG_env_1/RMG-Py/testing/databaseTest.py", line 149, in <lambda>
    test = lambda x: self.kinetics_check_sample_descends_to_group(family_name)
  File "/Users/blais.ch/_01_code/RMG_env_1/RMG-Py/testing/databaseTest.py", line 1290, in kinetics_check_sample_descends_to_group
    raise ValueError("Error Occurred")
ValueError: Error Occurred

======================================================================
ERROR: Kinetics family SubstitutionS: Recipe applies to group entry?
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Traceback (most recent call last):
  File "/Users/blais.ch/_01_code/RMG_env_1/RMG-Py/testing/databaseTest.py", line 1354, in kinetics_check_sample_can_react
    sample_molecule = entry.item.make_sample_molecule()
  File "rmgpy/molecule/group.py", line 2632, in rmgpy.molecule.group.Group.make_sample_molecule
    def make_sample_molecule(self):
  File "rmgpy/molecule/group.py", line 2723, in rmgpy.molecule.group.Group.make_sample_molecule
    raise UnexpectedChargeError(graph=new_molecule)
rmgpy.exceptions.UnexpectedChargeError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/blais.ch/anaconda3/envs/rmg_env/lib/python3.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/Users/blais.ch/_01_code/RMG_env_1/RMG-Py/testing/databaseTest.py", line 155, in <lambda>
    test = lambda x: self.kinetics_check_sample_can_react(family_name)
  File "/Users/blais.ch/_01_code/RMG_env_1/RMG-Py/testing/databaseTest.py", line 1364, in kinetics_check_sample_can_react
    tst3.append((False, """
NameError: name 'tst3' is not defined

----------------------------------------------------------------------
Ran 1515 tests in 281.878s

FAILED (errors=2)
make: *** [test-database] Error 1

[kspieks]

Thanks for the PR! Changes look good
@mjohnson541 should be able to merge this :)

[ChrisBNEU]

rebased for hack-a-thon