ReactionMechanismGenerator / ReactionMechanismGenerator/ARC
Could not determine reaction family for reaction C3H6-2 + O <=> C3H6O
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- Python
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Description
Describe the bug
A reaction family could not be found for the reaction C3H6-2 + O <=> C3H6O.
How to reproduce
from arc.rmgdb import make_rmg_database_object, load_families_only
from arc.reaction import ARCReaction
from arc.species import ARCSpecies
db = make_rmg_database_object()
load_families_only(db, "all")
rxn = ARCReaction(r_species=[ARCSpecies(label="C3H6", smiles = "CC=C"),
ARCSpecies(label="O", smiles="[O]", multiplicity=1)],
p_species=[ARCSpecies(label="C3H6O", smiles = "CC1OC1")])
rxn.determine_family(db)
print(rxn.family) # result is None with errors.
This remains true even if multiplicity=3 in the [O] species. This reaction originates from the training depository of 1+2_Cycloaddition reaction family originally.
Expected behavior
print(rxn.family) -> <ReactionFamily "1+2_Cycloaddition">
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with ARCReaction.determine_family and the arc.rmgdb helpers shown in the reproduction, then investigate matching the 1+2_Cycloaddition family for C3H6-2 + O <=> C3H6O. Re-run the provided Python example with both oxygen multiplicities; done means rxn.family resolves to 1+2_Cycloaddition without errors.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Clearly specified
- Newbie friendliness
- 70/100