Undeterminable Kinetics Error

Friends,

It seems that in the Intra_R_Add_Endocyclic kinetic family you can bump into structures that cause RMG to crash. It seems like this should go to the top node even if there were no similar cases.

Here is the traceback...
Traceback (most recent call last): File "/home/rgillis/Code/RMG-Py/rmg.py", line 173, in <module> main() File "/home/rgillis/Code/RMG-Py/rmg.py", line 167, in main rmg.execute(**kwargs) File "/home/rgillis/Code/RMG-Py/rmgpy/rmg/main.py", line 849, in execute trimolecularReact=self.trimolecularReact) File "/home/rgillis/Code/RMG-Py/rmgpy/rmg/model.py", line 681, in enlarge unimolecularReact, bimolecularReact, trimolecularReact=trimolecularReact) File "/home/rgillis/Code/RMG-Py/rmgpy/rmg/react.py", line 143, in reactAll rxns = list(react(*spcTuples)) File "/home/rgillis/Code/RMG-Py/rmgpy/rmg/react.py", line 59, in react spcTuples) File "/home/rgillis/Code/RMG-Py/rmgpy/scoop_framework/util.py", line 154, in map_ return map(WorkerWrapper(args[0]), *args[1:], **kwargs) File "/home/rgillis/anaconda2/envs/rmg_env/lib/python2.7/site-packages/scoop-0.7.2.0-py2.7.egg/scoop/fallbacks.py", line 49, in wrapper File "/home/rgillis/Code/RMG-Py/rmgpy/scoop_framework/util.py", line 112, in __call__ return self.myfn(*args, **kwargs) File "/home/rgillis/Code/RMG-Py/rmgpy/rmg/react.py", line 75, in reactSpecies reactions = getDB('kinetics').generate_reactions_from_families(speciesTuple) File "/home/rgillis/Code/RMG-Py/rmgpy/data/kinetics/database.py", line 523, in generate_reactions_from_families reaction_list.extend(self.react_molecules(combo, products=products, only_families=only_families, prod_resonance=resonance)) File "/home/rgillis/Code/RMG-Py/rmgpy/data/kinetics/database.py", line 549, in react_molecules reaction_list.extend(family.generateReactions(molecules, products=products, prod_resonance=prod_resonance)) File "/home/rgillis/Code/RMG-Py/rmgpy/data/kinetics/family.py", line 1646, in generateReactions self.__generateReactions(reactants, products=products, forward=True, prod_resonance=prod_resonance)) File "/home/rgillis/Code/RMG-Py/rmgpy/data/kinetics/family.py", line 2160, in __generateReactions reaction.template = self.getReactionTemplateLabels(reaction) File "/home/rgillis/Code/RMG-Py/rmgpy/data/kinetics/family.py", line 2514, in getReactionTemplateLabels template = self.getReactionTemplate(reaction) File "/home/rgillis/Code/RMG-Py/rmgpy/data/kinetics/family.py", line 2344, in getReactionTemplate return self.groups.getReactionTemplate(reaction) File "/home/rgillis/Code/RMG-Py/rmgpy/data/kinetics/groups.py", line 202, in getReactionTemplate raise UndeterminableKineticsError(reaction, message=msg) rmgpy.exceptions.UndeterminableKineticsError: (TemplateReaction(reactants=[Molecule(SMILES="OOS(=C)[O]")], products=[Molecule(SMILES="OO[S]1CO1")], pairs=[[Molecule(SMILES="OOS(=C)[O]"), Molecule(SMILES="OO[S]1CO1")]], family='Intra_R_Add_Endocyclic'), 'Kinetics could not be determined. Unable to find matching template for reaction <Molecule "OOS(=C)[O]"> <=> <Molecule "OO[S]1CO1"> in reaction family <KineticsGroups "Intra_R_Add_Endocyclic/groups">.Trying to match [<Entry index=0 label="Rn">, <Entry index=1 label="multiplebond_intra">, <Entry index=2 label="radadd_intra">] but matched [<Entry index=3 label="R3">, <Entry index=396 label="radadd_intra_O">]')

Start in rmgpy/data/kinetics/groups.py at getReactionTemplate, following the traceback from rmgpy/data/kinetics/family.py. Review how the Intra_R_Add_Endocyclic family handles a reaction with no matching template and how the top node is represented. Done means the reported structure no longer crashes RMG and is routed to the top node as described.