mirror of
https://github.com/OpenFreeEnergy/openfe.git
synced 2026-06-04 14:14:22 +08:00
8d229cffe3
* 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>
63 lines
2.8 KiB
ReStructuredText
63 lines
2.8 KiB
ReStructuredText
Tutorials
|
|
=========
|
|
|
|
.. todo: make sure we can inline the tutorial, for now we only provide links
|
|
|
|
Below is a collection of tutorials that demonstrate key elements of OpenFE tooling.
|
|
|
|
You can clone the `Example Notebooks Repository <https://github.com/OpenFreeEnergy/ExampleNotebooks>`_ to explore any of these tutorials interactively.
|
|
|
|
|
|
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 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
|
|
----------------------
|
|
|
|
- :any:`Absolute Absolute Free Energy Protocol <abfe_tutorial>`: A walk-through of calculating the absolute binding free energy of toluene to T4 Lysozyme.
|
|
- :any:`Absolute Solvation Free Energy Protocol <ahfe_tutorial>`: A walk-through of calculating the hydration free energy of a benzene ligand.
|
|
|
|
Relative Free Energies using Separated Topologies
|
|
-------------------------------------------------
|
|
|
|
- :any:`SepTop Protocol <septop_tutorial>`: A walk-through of calculating the relative binding free energy between TYK2 ligands using a Separated Topologies approach.
|
|
|
|
Molecular Dynamics (MD)
|
|
-----------------------
|
|
|
|
- :any:`MD protocol <md_tutorial>`: A walk-through of running a conventional (non-alchemical) MD simulation of benzene bound to T4-lysozyme L99A.
|
|
|
|
Post-Simulation Analysis
|
|
------------------------
|
|
|
|
- :any:`Cinnabar tutorial <plotting_with_cinnabar>`: A tutorial for using the `cinnabar <https://github.com/OpenFreeEnergy/cinnabar>`_ Python package to analyze (e.g. generating MLE estimates of absolute free energies) and plot networks of relative free energy results.
|
|
|
|
Generating Partial Charges
|
|
--------------------------
|
|
|
|
.. todo: this should be in cookbook
|
|
|
|
- :ref:`Generating Partial Charges CLI tutorial <charge_molecules_cli_tutorial>`: how to use the CLI to assign and store partial charges for mall molecules which can be used throughout the OpenFE ecosystem.
|
|
|
|
.. toctree::
|
|
:maxdepth: 1
|
|
:hidden:
|
|
|
|
showcase_notebook
|
|
rbfe_python_tutorial
|
|
rbfe_cli_tutorial
|
|
rbfe_membrane_protein
|
|
abfe_tutorial
|
|
abfe_analysis_tutorial
|
|
ahfe_tutorial
|
|
septop_tutorial
|
|
septop_analysis_tutorial
|
|
md_tutorial
|
|
plotting_with_cinnabar
|
|
charge_molecules_cli_tutorial
|