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75 lines
2.1 KiB
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75 lines
2.1 KiB
ReStructuredText
Tutorials
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=========
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.. todo: make sure we can inline the tutorial, for now we only provide links
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OpenFE has several tutorial notebooks which are maintained on our
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`Example Notebooks repository <https://github.com/OpenFreeEnergy/ExampleNotebooks>`_.
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Here is a list of key tutorials which cover the different aspects of the
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OpenFE tooling:
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Relative Free Energies
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----------------------
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Python API Showcase
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~~~~~~~~~~~~~~~~~~~
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Our :any:`shocase notebook <showcase_notebook>` walks users through
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how to use the main Python API components of OpenFE to create a
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relative binding free energy calculation.
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Relative Free Energies CLI tutorial
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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The :ref:`Relative Free Energies with the OpenFE CLI <rbfe_cli_tutorial>`
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tutorial walks users through how to use the OpenFE command line to calculate
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relative binding free energies of various ligands against the TYK2 target.
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Associated with it is also a :any:`notebook <rbfe_python_tutorial>`
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for how to achieve the same outcomes using the Python API.
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Absolute Free Energies
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----------------------
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Absolute Solvation Free Energies
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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The :any:`Absolute Solvation Free Energy Protocol <ahfe_tutorial>` tutorial
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walks users through how to calculate the hydration free energy of a benzene
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ligand.
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Molecular Dynamics (MD)
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-----------------------
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The :any:`MD protocol <md_tutorial>`
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tutorial walks users through how to run a conventional (non-alchemical) MD
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simulation of benzene bound to T4-lysozyme L99A in OpenFE.
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Post Simulation Analysis
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------------------------
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Analyzing and Plotting RFE Networks with Cinnabar
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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The :any:`Cinnabar tutorial <plotting_with_cinnabar>` demonstrates how to
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use the `Cinnabar Python package <https://github.com/OpenFreeEnergy/cinnabar>`_
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to analyze (e.g. generating MLE estimates of absolute free energies)
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and plot networks of relative free energy results.
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.. toctree::
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:maxdepth: 1
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:hidden:
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rbfe_cli_tutorial
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rbfe_python_tutorial
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showcase_notebook
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md_tutorial
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ahfe_tutorial
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plotting_with_cinnabar
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