ReactionMechanismGenerator / ReactionMechanismGenerator/RMG-database

Creating new training reaction through website does not apply starred atoms

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Dominant language
Python
Stars
127
Forks
160
Avg merge
6d 2h
Merged PRs (30d)
2

Description

The starred atoms for reaction training reactions seem to work for for families but not for others. For instance, in intra_H_migration, it does not apply starred atoms. For some other families, such as HO2_Elimination_from_PeroxyRadical, the starring of the reactants/products does occur. When there are no starred atoms for species in the training reaction, it generally produces an UndeterminableKineticsError.

We need to make sure starred atoms always appear when saving the training reaction, or allow for the fact that they aren't there. The user should only have to insert the kinetics and comments for this to work.

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  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
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Research direction

Start with the website flow that creates and saves training reactions, comparing the intra_H_migration family with HO2_Elimination_from_PeroxyRadical. Trace how starred reactants and products are applied and how UndeterminableKineticsError is raised; done means saving works with only kinetics and comments, whether starred atoms are present or absent.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend, databases
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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