ReactionMechanismGenerator / ReactionMechanismGenerator/ARC
Issue with deremining reaction family under the new functionality
Open
Nobody has claimed this yet.
Type: Bug
- Dominant language
- Python
- Stars
- 51
- Forks
- 25
- Avg merge
- 4d 5h
- Merged PRs (30d)
- 15
Description
Describe the bug
I am trying to determine the reaction family of a reaction:
[CH2] + C=C <=> C1CC1
Which is the most basic 1,2 cycloaddition. This fails for some reason.
How to reproduce
from arc.reaction import ARCReaction
from arc.species import ARCSpecies
rxn = ARCReaction(r_species = [ARCSpecies(label="r1", smiles="[CH2]"),
ARCSpecies(label="r2", smiles="C=C")],
p_species = [ARCSpecies(label="p1", smiles="C1CC1")])
rxn.determine_family() # (output: (None, None))
rxn.determine_family(rmg_family_set="all") # fails with KeyError: "RCH(OOH)CH2C(O)R'"
Expected behavior
Not to fail or crash
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
Reproduce the example using ARCReaction, ARCSpecies, and determine_family(), first with the default family set and then with rmg_family_set="all". Trace the KeyError for "RCH(OOH)CH2C(O)R'" and verify that the cycloaddition case completes without failing or crashing.
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
- Mostly clear
- Newbie friendliness
- 48/100