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fix code formatting

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Alyssa Travitz
2026-04-27 14:16:07 -07:00
parent 7b6117e738
commit 6f2154cb1d
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docs/CHANGELOG.rst
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@@ -13,16 +13,16 @@ v1.11.0
PlainMDProtocol, RelativeHybridTopologyProtocol, SepTopProtocol, and AbsoluteBindingProtocol (`PR #1561 <https://github.com/OpenFreeEnergy/openfe/pull/1561>`_).
* Added support for membrane systems to ``openfe plan-rbfe-network``.
Use ``--protein-membrane`` instead of the ``--protein`` argument, and see the tutorial on preparing membrane systems (`PR #1896 <https://github.com/OpenFreeEnergy/openfe/pull/1896>`_).
* * Added API support for resuming the PlainMDProtocol (`PR #1884 <https://github.com/OpenFreeEnergy/openfe/pull/1884>`_).
* Added API support for resuming the PlainMDProtocol (`PR #1884 <https://github.com/OpenFreeEnergy/openfe/pull/1884>`_).
* Added API support for resuming the SepTopProtocol. (`PR #1949 <https://github.com/OpenFreeEnergy/openfe/pull/1949>`_).
* The `validate` method for the SepTopProtocol has been implemented.
This means that settings and system validation can mostly be done prior to Protocol execuation by calling `SepTopProtocol.validate(stateA, stateB, mapping=None)` (`PR #1946 <https://github.com/OpenFreeEnergy/openfe/pull/1946>`_).
* The ``validate`` method for the SepTopProtocol has been implemented.
This means that settings and system validation can mostly be done prior to Protocol execuation by calling ``SepTopProtocol.validate(stateA, stateB, mapping=None)`` (`PR #1946 <https://github.com/OpenFreeEnergy/openfe/pull/1946>`_).
**Changed:**
* The SepTopProtocol now has a dedicated Analysis unit.
At the top level API, this does not change behavior, but if you are directly interfacing with th ProtocolUnits, you will have to account for this change.
The SepTopProtocolResult now solely uses the Analysis units. (`PR #1937 <https://github.com/OpenFreeEnergy/openfe/pull/1937>`_)
The SepTopProtocolResult now solely uses the Analysis units (`PR #1937 <https://github.com/OpenFreeEnergy/openfe/pull/1937>`_).
* Updated the chemical systems user guide and the defining protocols user guide to reflect recent protocol updates, including adding membrane support (`PR #1933 <https://github.com/OpenFreeEnergy/openfe/pull/1933>`_).
**Deprecated:**