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membrane CLI support (#1896)

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* initial cli ideas

* clean up names

* add test

* update docstrings and fix imports

* fix tests

* use gufe gzip branch

* clean up fixtures

* update fixtures

* adding membrane component to tests

* add membrane barostat check

* make output more consistent and add membrane args test

* error messages

* revert some out of scope typing things

* tidying fixtures

* update protein arg parsing

* clearer var naming

* add protein validate

* add validation

* fix handling for membrane solvents

* update docstring

* point to membrane tutorial branch

* linking

* remove redundant validation

* remove unneeded type hints

* Update src/openfecli/commands/plan_rbfe_network.py

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

* Update src/openfecli/parameters/protein.py

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

* clean up suggestions

* use click BadParameter

* testing arg errors

* update examplenotebook branch

* add news item

* use BadParameter

* fix test comments

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
This commit is contained in:
Alyssa Travitz
2026-04-27 09:05:43 -07:00
committed by GitHub
parent dd7b9febbc
commit 8d229cffe3
14 changed files with 260 additions and 145 deletions
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6
docs/tutorials/index.rst
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@@ -12,8 +12,9 @@ Relative Free Energies
----------------------
- :any:`Python API Showcase <showcase_notebook>`: Start here! An introduction to OpenFE's Python API and approach to performing a relative binding free energy calculation.
- :any:`RBFE with the Python API <rbfe_python_tutorial>`: A step-by-step tutorial for using the Python API to calculate relative binding free energies for TYK2.
- :ref:`RBFE with the CLI <rbfe_cli_tutorial>`: A step-by-step tutorial for using the OpenFE command line interface (CLI) to calculate relative binding free energies for TYK2.
- :any:`RBFE using the Python API <rbfe_python_tutorial>`: A step-by-step tutorial for using the Python API to calculate relative binding free energies for TYK2.
- :ref:`RBFE using the CLI <rbfe_cli_tutorial>`: A step-by-step tutorial for using the OpenFE command line interface (CLI) to calculate relative binding free energies for TYK2.
- :any:`RBFE with membrane systems <rbfe_membrane_protein>`: A step-by-step guide to setting up an RBFE calculation with special considerations for membrane systems.
Absolute Free Energies
----------------------
@@ -50,6 +51,7 @@ Generating Partial Charges
showcase_notebook
rbfe_python_tutorial
rbfe_cli_tutorial
rbfe_membrane_protein
abfe_tutorial
abfe_analysis_tutorial
ahfe_tutorial

3
docs/tutorials/rbfe_membrane_protein.nblink Normal file
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@@ -0,0 +1,3 @@
{
"path": "../ExampleNotebooks/membranes/rbfe_membrane_protein.ipynb"
}