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61 lines
2.6 KiB
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61 lines
2.6 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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Below is a collection of tutorials that demonstrate key elements of OpenFE tooling.
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You can clone the `Example Notebooks Repository <https://github.com/OpenFreeEnergy/ExampleNotebooks>`_ to explore any of these tutorials interactively.
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Relative Free Energies
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----------------------
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- :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.
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- :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.
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- :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.
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Absolute Free Energies
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----------------------
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- :any:`Absolute Absolute Free Energy Protocol <abfe_tutorial>`: A walk-through of calculating the absolute binding free energy of toluene to T4 Lysozyme.
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- :any:`Absolute Solvation Free Energy Protocol <ahfe_tutorial>`: A walk-through of calculating the hydration free energy of a benzene ligand.
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Relative Free Energies using Separated Topologies
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-------------------------------------------------
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- :any:`SepTop Protocol <septop_tutorial>`: A walk-through of calculating the relative binding free energy between TYK2 ligands using a Separated Topologies approach.
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Molecular Dynamics (MD)
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-----------------------
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- :any:`MD protocol <md_tutorial>`: A walk-through of running a conventional (non-alchemical) MD simulation of benzene bound to T4-lysozyme L99A.
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Post-Simulation Analysis
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------------------------
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- :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.
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Generating Partial Charges
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--------------------------
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.. todo: this should be in cookbook
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- :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.
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.. toctree::
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:maxdepth: 1
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:hidden:
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showcase_notebook
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rbfe_python_tutorial
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rbfe_cli_tutorial
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abfe_tutorial
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abfe_analysis_tutorial
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ahfe_tutorial
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septop_tutorial
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septop_analysis_tutorial
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md_tutorial
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plotting_with_cinnabar
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charge_molecules_cli_tutorial
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