Modified the 1,2_NH3_elimination root group

[alongd]

*3 N cannot have 0 lone pairs, since it looses a lone pair in the recipe.

This fix prohibits species such as

<Molecule "[NH-][NH2+]NN">
1  *3 N u0 p0 c+1 {2,S} {4,S} {5,S} {6,S}
2  *2 N u0 p1 c0 {1,S} {3,S} {7,S}
3  *1 N u0 p1 c0 {2,S} {8,S} {9,S}
4     N u0 p2 c-1 {1,S} {10,S}
5     H u0 p0 c0 {1,S}
6     H u0 p0 c0 {1,S}
7  *4 H u0 p0 c0 {2,S}
8     H u0 p0 c0 {3,S}
9     H u0 p0 c0 {3,S}
10    H u0 p0 c0 {4,S}

from reacting in 1,2_NH3_elimination.

Edit: Also added a minor unrelated commit to update the structure of HON

[mjohnson541]

This looks fine. I'm happy to approve once we get the tests fixed.

[alongd]

The test fails due to the ndTorsion tearDownClass:

  File "/home/travis/build/ReactionMechanismGenerator/RMG-Py/rmgpy/statmech/ndTorsionsTest.py", line 81, in tearDownClass
    os.remove(os.path.join(os.path.dirname(cls.path),'r0','IOfiles','r0.pes'))
OSError: [Errno 2] No such file or directory: '/home/travis/build/ReactionMechanismGenerator/RMG-Py/arkane/data/CH2CHOOH/r0/IOfiles/r0.pes'

Will that be that fixed as part of the py3 branch, or in a later stage?

[mliu49]

It has been fixed on the Py3 branch. We could/should consider setting up q2dtor for RMG-database travis as well.

[alongd]

@mjohnson541, this PR should be good to go