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* Membrane support prototype start * Point to corresponding branch in gufe * Make plain md protocol membrane ready * Dry run for membrane system for debugging * Add box vectors to modeller * Adapt htf to allow for membrane barostat * Fix test * Add test files membrane * Change test to cpu * Prints for debugging * Some more debugginh stuff, remove later * Small fix * Temporarily use branches for openmmtools and openmmforcefield * Small fixes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * support membrane in gather * First pass membrane support for SepTop protocol * Change validation solvent * Move changes in solvent validation to validate_solvent * Some small fixes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add membrane test septop * Change box vector units for handling membrane barostat * Test box vectors SepTop more * First pass at ABFE membrane prototype * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove some prints * Revert box changes * Some fixes in SepTop to fix tests * Apply suggestion from @hannahbaumann * Add tests for system creation * FIx test * Add ABFE membrane tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * More tests membrane septop and more dry outputs in septop * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add validation for box vector in ProteinMembraneComponent * Adapt gather for membranes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small changes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify box vectors plain md * Address review comments * Remove unnecessary prints * Subclass membrane test * Small fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove unnecessary import * Remove prints * Small fix * Small fix * Larger change to checks for BaseSolventComponent, SolvatedPDBComponent, and adding barostat settings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Some more changes * Small fix * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * ABFE enforce timestep complex solvent the same * Update test files * Update environment.yaml with new openmmtools and openmmforcefield versions * Remove unnecessary checks for box_vectors which are handled in gufe * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update openfe/protocols/openmm_afe/equil_binding_afe_method.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Attempt at rewriting validate_solvent * Move get barostat to self * Simplify mapping in test * Add validator for surface_tension and membrane barostat * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add membrane barostat to adaptive settings rfe protocol * Add validation/warning for barostat component mismatch * Fix tests (except CLI) * More merge fixes * Remove unnecessary imports * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add test files * Update tests * Add lipid ff in adaptive settings * remove commented out lines * Update test abfe * Update ABFE results with new settings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix solvent validation * change env to gufe main * Apply suggestion from @hannahbaumann * Remove files from before src layout change * Update tests * Small fix * mark slow tests * Update env file * Small fix * Update src/openfe/protocols/openmm_afe/equil_binding_afe_method.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Update src/openfe/protocols/openmm_afe/equil_binding_afe_method.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Update src/openfe/protocols/openmm_rfe/_rfe_utils/relative.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Update src/openfe/protocols/openmm_utils/system_validation.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Address review comments 1 * update doc string * Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Address review comments 2 * Address review comments 3 * fix mypy * Fix system creation tests * Roundtrip box vectors to remove vec3 issues * Roundtrip box vectors to remove vec3 issues * Remove unnecessary imports * Apply suggestion from @hannahbaumann * Test mypy failure * Test mypy failure 2 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * some fixes * small fixes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update test files * Update SepTop results settings * add more tests for adaptive settings and others * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add news entry * Fix for box vectors hybtop * Make test slow again * Make mypy happy * try to make mypy happy again * Adapt gather RFE membrane component types * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * use reference platform for the membrane energy test * Add ChemicalSystem Component validation to Protocols * Add test for chemicalsystem validation * Apply suggestions from code review Co-authored-by: Josh Horton <joshua.horton@openforcefield.org> * Update with slight variation to @jthorton 's suggestion * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * point gufe back at main * Drop lipid17 from adaptive settings * just a tiny nit change * fix typo * Add extra class to openfecli check * Add total particle checks to abfe protocol tests * remove lipid17 check from adaptive settings * remove lipid17 check from adaptive settings * Add some checks for number of particles & residues * Fix up some tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Minimized protein * Update protein * Revert back to old protein * Apply suggestion from @hannahbaumann * Remove box roundtrip and fix solvent from get_components * Merge conflicts * Update src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix merge conflict * Forgot another one * Move box roundtrip to _pre_equilibrate * First go at modifying the user guide for membranes and ABFE and SepTop * some small fixes * Add adaptive_settings to user guide * Add example code loading protein membrane * Add box vector explanation * Some smaller changes * Make adaptive settings subheading * Some more changes * Add warning adaptive settings * Update docs/guide/setup/defining_protocols.rst Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> * Addressing review comments * some more updates * Test out subheadings * Restructure user guide * merge conflicts * Small fix * some small updates * addressing review comments * Small fix * address review comments * small fix * Add news entry * Update docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> * Update docs/guide/setup/defining_protocols.rst Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> * Update docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> * Addres review comment * Update docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk> * Update docs/guide/setup/chemical_systems_and_thermodynamic_cycles.rst Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk> * Address review comment --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com> Co-authored-by: Josh Horton <Josh.Horton@newcastle.ac.uk> Co-authored-by: Josh Horton <joshua.horton@openforcefield.org>
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* Updated the chemical systems user guide and the defining protocols user guide to reflect recent protocol updates, including adding membrane support.
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