Add training reactions from library

[davidfarinajr]

Motivation or Problem

I was working on a script to add training reactions from a library, then I found this awesome python notebook that already does this :). This PR adds some features and bug fixes to the library to training notebook and tools.

Description of Changes

1. Skip over kinetics in library not suitable for training reactions (Pdep, MultiArrhenius, etc)
2. change A units only for gas phase kinetics
3. search for isomorphic reactions already in training, skip the library reactions if identical (isomorphic with same kinetics) and compare kinetics with isomorphic training reactions
4. option to manually selection in step 1 while we are comparing kinetics.
5. do not relabel the products while getting the species labels for a reaction. Without this option, for some families, like H_Abstraction, the products are relabeled with reactant labels to match with forbidden species for the family.
6. option to save unmatched reaction to a new library, perhaps to use as seed mechanism or to save for later to figure out if new families are needed

Testing

Added training reactions from a 2-BTP kinetic library

Reviewer Tips

Give it a try.

Unresolved issues

• A forbidden species in your library (like CH) will cause this code to crash, we may need to just skip over these reactions or add an allowed species option
• we may want to load all thermo libraries by default. If your thermo is bad and the training reaction is in reverse, the kinetics can be ugly

[lgtm-com[bot]]

This pull request introduces 1 alert when merging 1922d691719b26913edf28e6a354fa0dab5df26f into 1e21621d3a7cf75dc7085b7ada330941021018d2 - view on LGTM.com

new alerts:

• 1 for Except block handles 'BaseException'

[codecov[bot]]

Codecov Report

Merging #2061 (fd82ade) into master (209d194) will increase coverage by 0.04%. The diff coverage is 86.79%.

@@            Coverage Diff             @@
##           master    #2061      +/-   ##
==========================================
+ Coverage   47.54%   47.59%   +0.04%     
==========================================
  Files          89       89              
  Lines       23565    23574       +9     
  Branches     6131     6135       +4     
==========================================
+ Hits        11204    11219      +15     
+ Misses      11177    11173       -4     
+ Partials     1184     1182       -2     

Impacted Files	Coverage Δ
rmgpy/data/kinetics/family.py	48.61% <86.79%> (-0.10%)	:arrow_down:
arkane/kinetics.py	12.24% <0.00%> (ø)
rmgpy/molecule/draw.py	53.09% <0.00%> (+1.11%)	:arrow_up:

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[rwest]

I nominated @hwpang as a reviewer, because it looks like she recently worked on this tool.

[lgtm-com[bot]]

This pull request introduces 3 alerts when merging 6512be5556093ec96d4ee425b62202209272fa75 into 773564358a141fbe7384d27ae5fac69ef3ff39ac - view on LGTM.com

new alerts:

• 2 for Except block handles 'BaseException'
• 1 for Non-callable called

[lgtm-com[bot]]

This pull request introduces 3 alerts when merging fd82ade12f34b9f25da0e2ff22979fb731afeedb into 209d194ddde989b93369ec6c7e875c966c430893 - view on LGTM.com

new alerts:

• 3 for Except block handles 'BaseException'

[lgtm-com[bot]]

This pull request introduces 3 alerts when merging b399343101a0bcad53834c26fd42b7d5118d2822 into f07039c3c86a02c667a273d1a33910da3c51ce8e - view on LGTM.com

new alerts:

• 3 for Except block handles 'BaseException'

[github-actions[bot]]

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