[WIP] Correct elements for hybrid topology transformations that undergo element changes#108
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hannahbaumann wants to merge 62 commits into
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[WIP] Correct elements for hybrid topology transformations that undergo element changes#108hannahbaumann wants to merge 62 commits into
hannahbaumann wants to merge 62 commits into
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Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: Josh Horton <joshua.horton@openforcefield.org>
hannahbaumann
commented
May 26, 2026
jthorton
reviewed
May 27, 2026
Comment on lines
+91
to
+95
| def correct_elements( | ||
| atomgroup: mda.AtomGroup, | ||
| rdmol: Chem.Mol, | ||
| atom_mapping: dict[int, int] | None = None, | ||
| ) -> None: |
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This looks great, it might be worthing checking you can round trip a ligand, so for a real Htop output fix stateB which uses different elements and connectivity, then compare the input SMC with the fixed atomgroup and check that the atoms and bonds match exactly.
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #108 +/- ##
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+ Coverage 98.05% 98.13% +0.08%
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Files 9 9
Lines 462 482 +20
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+ Hits 453 473 +20
Misses 9 9 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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This functionality may also be better in openfe.