[ WIP ] Support for charge changes in the HybTop protocol for explicitly solvated systems#1978
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hannahbaumann wants to merge 5 commits into
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[ WIP ] Support for charge changes in the HybTop protocol for explicitly solvated systems#1978hannahbaumann wants to merge 5 commits into
hannahbaumann wants to merge 5 commits into
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…for explicitly solvated systems
hannahbaumann
commented
May 18, 2026
| """ | ||
| Infer positive and negative ion residue names from a topology by | ||
| finding the most common monovalent ion of each charge type. | ||
| Falls back to NA/CL if none are found. |
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I'm doing this mostly because e.g. maestro doesn't always add ions (in the a2a example there were no negative ions in the system).
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hannahbaumann
commented
May 20, 2026
| system_mapping: dict, | ||
| charge_difference: int, | ||
| solvent_component: SolventComponent, | ||
| positive_ion_resname: str, |
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use element or formal charge instead?
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No API break detected ✅ |
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1978 +/- ##
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- Coverage 94.94% 90.54% -4.40%
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Files 216 216
Lines 20481 20547 +66
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- Hits 19445 18604 -841
- Misses 1036 1943 +907
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This is just a first idea (and the
_get_ion_resnames_from_topologywas written together with Claude). This is mostly just to show the different things we have to consider, but I don't like the dictionary idea of known ions yet. Maybe it would also be ok to always use Cl and Na ions for explicitly solvated systems, no matter if other ion types were used as counterions?Checklist
newsentry, or the changes are not user-facing.pre-commit.ci autofix.Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).
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