Add `aromatic_matching=False` to isometry check

[mattwthompson]

Description

Taking @lilyminium's suggestion in #255 and just seeing what happens in tests.

Not squatting on this at all; if somebody wants to move this forward please feel free to use this branch/PR.

Todos

Notable points that this PR has either accomplished or will accomplish.

• [x] Add aromatic_matching=False to isometry check
• [x] Add test reproducing #255

Status

• [x] Ready to go

[codecov[bot]]

Codecov Report

Merging #260 (d48e333) into main (60f4210) will not change coverage. Report is 1 commits behind head on main. The diff coverage is n/a.

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Additional details and impacted files

[j-wags]

I looked through the code to make sure that this wouldn't cause any unanticipated surprises and it looks good at a first pass. I'd approve this PR if a test is added.

[mattwthompson]

Just a note to myself: adding a test like test_componentresult_deduplication_iso (or some others in the same file) with an appropriate molecule should cover this change. IIUC the key behavior is that two molecules (or two representations of, or two tautomers of, depending on your view)

• have the same InChi key
• are viewed by the toolkit as isomorphic when aromatic_matching=False
• are not viewed by the toolkit as isomorphic when aromatic_matching=True (the current behavior, and the toolkit's default)

The molecule in the linked issue appears to trigger these conditions via having a proton hop around within an aromatic ring

[mattwthompson]

Test added! If I revert the aromatic_matching=False change this test fails; with the change, the test passes.

[jthorton]

Great job guys!