1,2_NH3_elimination calls decrementLonePairs on atom without any lone pairs?

[rwest]

Bug Description

A job crashed with:

Error: Could not generate product structures for reaction family 1,2_NH3_elimination in forward direction
Reactant structures:
<Molecule "NN[NH+](N)[O-]">
1     O u0 p3 c-1 {2,S}
2  *3 N u0 p0 c+1 {1,S} {3,S} {4,S} {6,S}
3  *2 N u0 p1 c0 {2,S} {5,S} {7,S}
4     N u0 p1 c0 {2,S} {8,S} {9,S}
5  *1 N u0 p1 c0 {3,S} {10,S} {11,S}
6     H u0 p0 c0 {2,S}
7  *4 H u0 p0 c0 {3,S}
8     H u0 p0 c0 {4,S}
9     H u0 p0 c0 {4,S}
10    H u0 p0 c0 {5,S}
11    H u0 p0 c0 {5,S}


Traceback (most recent call last):
  File "/Users/rwest/Code/Cat/RMG-Py/rmg.py", line 185, in <module>
    main()
  File "/Users/rwest/Code/Cat/RMG-Py/rmg.py", line 170, in main
    cProfile.runctx(command, global_vars, local_vars, stats_file)
  File "/Users/rwest/anaconda/envs/rmg241/lib/python2.7/cProfile.py", line 49, in runctx
    prof = prof.runctx(statement, globals, locals)
  File "/Users/rwest/anaconda/envs/rmg241/lib/python2.7/cProfile.py", line 140, in runctx
    exec cmd in globals, locals
  File "<string>", line 1, in <module>
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/rmg/main.py", line 866, in execute
    trimolecularReact=self.trimolecularReact)
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/rmg/model.py", line 590, in enlarge
    procnum=procnum)
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/rmg/react.py", line 172, in react_all
    return react(spc_fam_tuples, procnum), [fam_tuple[0] for fam_tuple in spc_fam_tuples]
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/rmg/react.py", line 66, in react
    reactions = map(_react_species_star, spc_fam_tuples)
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/rmg/react.py", line 79, in _react_species_star
    return react_species(*args)
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/rmg/react.py", line 94, in react_species
    reactions = getDB('kinetics').generate_reactions_from_families(species_tuple, only_families=only_families)
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/data/kinetics/database.py", line 527, in generate_reactions_from_families
    reaction_list = find_degenerate_reactions(reaction_list, same_reactants, kinetics_database=self)
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/data/kinetics/common.py", line 344, in find_degenerate_reactions
    rxn.degeneracy = family.calculateDegeneracy(rxn)
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/data/kinetics/family.py", line 1821, in calculateDegeneracy
    react_non_reactive=True))
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/data/kinetics/family.py", line 1908, in __generateReactions
    productStructures = self.__generateProductStructures(reactantStructures, [map], forward)
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/data/kinetics/family.py", line 1560, in __generateProductStructures
    productStructures = self.applyRecipe(reactantStructures, forward=forward)
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/data/kinetics/family.py", line 1349, in applyRecipe
    self.forwardRecipe.applyForward(reactantStructure, unique)
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/data/kinetics/family.py", line 379, in applyForward
    return self.__apply(struct, True, unique)
  File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/data/kinetics/family.py", line 369, in __apply
    atom.applyAction(['LOSE_PAIR', label, 1])
  File "rmgpy/molecule/molecule.py", line 458, in rmgpy.molecule.molecule.Atom.applyAction
  File "rmgpy/molecule/molecule.py", line 422, in rmgpy.molecule.molecule.Atom.decrementLonePairs
rmgpy.exceptions.ActionError: Unable to update Atom due to LOSE_PAIR action: Invalid lone electron pairs set "-1".

The species NN[NH+](N)[O-] was made via radical recombination of NN[O] + N[NH]:
NH2NHOJ(36) + NH2NHJ(37) <=> NN[NH+](N)[O-](1574)

How To Reproduce

Try to generate reactions of NN[NH+](N)[O-].
(A quick kinetics search on the website will confirm the error)

Expected Behavior

It wouldn't crash.

Installation Information

Describe your installation method and system information.

• OS: Mac OS Mojave 10.14.5
• Installation method: anaconda, from source
• RMG version information:
  • RMG-database: 2.4.0-14-ge461edb9 commit e461edb]
  • RMG-Py: commit cc2716c (HEAD -> catfix, official/catfix) which is pr Fix a few bugs and add tests: KineticsModel and uncertainty handling. #1705
    (but the bug occurs also on rmg.mit.edu)

[alongd]

Thanks!
The fix should be this: ReactionMechanismGenerator/RMG-database#350. @mjohnson541, let's get it in

[rwest]

Thanks! I should have checked the database for issues.

[github-actions]

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