RMG-Py cannot find multiple transition states

[connie]

This issue came up after investigations for issue #140 RMG-Py cannot find multiple transition states when reactants and products are identical. For instance in the following reaction between tertiary and primary isobutyl radical we only find one reaction rate (RMG-Java will predict both transition state and generate duplicate reactions):

http://dev.rmg.mit.edu/database/kinetics/reaction/reactant1=1%20C%200%20%7B2,S%7D%20%7B3,S%7D%20%7B4,S%7D;2%20C%200%20%7B1,S%7D;3%20C%200%20%7B1,S%7D;4%20C%201%20%7B1,S%7D;__reactant2=1%20C%200%20%7B4,S%7D;2%20C%200%20%7B4,S%7D;3%20C%200%20%7B4,S%7D;4%20C%201%20%7B1,S%7D%20%7B2,S%7D%20%7B3,S%7D;__product1=1%20C%200%20%7B2,S%7D%20%7B3,S%7D%20%7B4,S%7D;2%20C%200%20%7B1,S%7D;3%20C%200%20%7B1,S%7D;4%20C%200%20%7B1,S%7D;__product2=1%20C%200%20%7B3,S%7D;2%20C%200%20%7B3,S%7D;3%20C%200%20%7B1,S%7D%20%7B2,S%7D%20%7B4,D%7D;4%20C%200%20%7B3,D%7D;

I believe this is due to the reaction degeneracy being increased after checking that reactants and products are identical without regard to different atom labels leading to potentially different reaction templates. (https://github.com/GreenGroup/RMG-Py/blob/master/rmgpy/data/kinetics/family.py#L1437) After the degeneracy is counted, only the very first retained reaction's template gets used to fetch kinetics.

[rwest]

A better plan would be to fetch kinetics for every match, then group them and increase degeneracy for ones with identical kinetics (same matching nodes) leaving duplicate reactions when necessary (different temperature dependencies)?

[connie]

Attempted a preliminary fix here: connie@82b4098, going with keeping the different reaction paths as separate reactions rather than combining the kinetics into an MultiArrhenius reaction like in Java. There's still several issues:

• How to identify the correct reverse reaction when having multiple TS's.
  My solution is to match the correct reaction pairs- but this only works in
  the case of a bimolecular A+B=C+D reaction. If the reaction is unimolecular,
  the reaction pairs will be the same and the correct path cannot be distinguished.
• If kinetics are identical, they should be combined through degeneracy, in this
  commit they remain as duplicates.
• A lot of 'duplicate' reactions are not true transition state differences, but simply matching
  to separate templates due to assymetry like the propene + CH2 = cyclopropane reaction from Degeneracy on asymmetrical groups (1+2_Cycloaddition) #140.

[rwest]

Any thoughts, @jwallen?

[goldmanm]

fixed with #1055