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Pattern equality should normalize bond labels (or document the limitation) #73

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Pattern equality should normalize bond labels (or document the limitation)#73

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@wshlavacek
wshlavacek
opened on May 9, 2026

Location:bionetgen/modelapi/pattern.py:626

Original marker:

# TODO: try to decide if A(b!1).B(a!1) is the same
# as A(b!2).B(a!2), if so, the bond check is much harder

Component.__eq__ (and through it, Molecule/Pattern equality) compares bonds as raw label tokens. Two BNGL patterns that differ only in the labels of their bonds are semantically identical — A(b!1).B(a!1) and A(b!2).B(a!2) represent the same complex — but the equality check returns False. The author's commented-out attempt to compare bonds as sets sits below the marker.

Recent context:421bac9 (Fix Pattern/Molecule equality and mutable defaults) addressed the worst case (mutable defaults causing unrelated patterns to compare equal). This issue is the remaining correctness gap.

What would unblock this: decide between two resolutions:

  1. Normalize bond labels. Relabel each pattern's bonds in canonical order before comparing. Adds correctness but means equality is no longer a string-identity check.
  2. Document the limitation. Keep the current label-sensitive equality, add a docstring explaining that callers should canonicalize first.

If a current consumer depends on label-normalized equality (e.g. structural pattern dedup in the simulator bridge), please note it on this issue so the resolution scope is clear.

Discovered during: non-Atomizer TODO/FIXME triage sweep, 2026-05-08.

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