Return every atom map per reaction and cluster them into distinct reaction channels - #1024

Merged

calvinp0 merged 13 commits into

mainfrom

atom_map_clustering

Sep 5, 2026

Commits on Sep 5, 2026

Return every superimposable atom map instead of only the best-scoring one
kfir4444
committed
0393faa
Cluster atom maps into distinct reaction channels by their Aut(R) orbit
kfir4444
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9fc0417
Expose the distinct reaction channels as ARCReaction.atom_map_clusters
kfir4444
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c2d07cb
Seed the flipped reaction with a family when enumerating atom maps
kfir4444
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6db0da1
Compute reaction path degeneracy exactly from the reaction center orbit
kfir4444
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6179019
Test that sec-butyl to n-butyl resolves into its two migration channels
kfir4444
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448b3ff
Skip atom maps that are not a bijection instead of aborting clustering
kfir4444
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51880b3
Report an empty channel enumeration once, not on every property access
kfir4444
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a7f7e63
fix: increment the values of a dict atom map, not its keys, for inc_vals
kfir4444
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640070b
Import unittest.mock without mixing the two import styles
kfir4444
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6909774
Divide out interchangeable hydrogens when counting reaction path degeneracy
kfir4444
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b32ebf6
Handle resonance symmetry, duplicated template labels and order-only reactions
kfir4444
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ad726ec
fix: create job directories without a check-then-create race
kfir4444
committed
b7aa476