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@hannahbaumann
hannahbaumann committed Apr 12, 2024
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83 changes: 28 additions & 55 deletions showcase/openfe_showcase.ipynb
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"\n",
"The OpenFE toolkit provides open-source frameworks for calculating alchemical free energies. This notebook shows off the main things that you can do with OpenFE.\n",
"\n",
"Here, we will introduce different components that users can choose from during setup of free energy calculations. OpenFE allow you to mix and match different components, such as:\n",
"Throughout this showcase, we will introduce different interchangeable components that users can choose from during the setup of free energy calculations. OpenFE allow you to mix and match different components, such as:\n",
"\n",
"* Atom mappers\n",
"* Scorers (for atom mappings)\n",
"* Ligand networks\n",
"\n",
"This showcase currently focuses on relative binding free energy calculations and towards the end provides an introduction of other protocols in OpenFE, the MD protocol and absolute hydration free energy protocol.\n",
"This showcase currently focuses on relative binding free energy calculations. Towards the end it provides an introduction of other protocols that are available in OpenFE, the MD protocol and absolute hydration free energy protocol. (TODO: Remove this if we don't add it!)\n",
"\n",
"If you are planning your own calculations, please also check out our tutorials that will walk you through setup, execution and analysis of different protocols:\n",
"\n",
"* Add [links] for tutorial style notebooks"
"If you are planning your own calculations, please also check out our [tutorials](https://docs.openfree.energy/en/stable/tutorials/index.html) which will walk you through setup, execution and analysis of different protocols."
]
},
{
Expand All @@ -44,7 +42,7 @@
"\n",
"0. Setup for Google Colab\n",
"1. Overview\n",
"3. Creating a transformation network\n",
"3. Creating a network of transformations\n",
"4. Running a Relative Ligand Binding Free Energy Calculation\n",
"5. Analysis\n",
"\n",
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"id": "3128085c-db8a-4a70-89ef-0fde956fdb40",
"metadata": {},
"source": [
"Our hybrid topology RBFE protocol, an atom mapping defines which atoms are mutated during the alchemicale transformation.\n",
"In the hybrid topology RBFE protocol, an atom mapping defines which atoms are mutated during the alchemical transformation.\n",
"The user can choose between two different atom mappers:\n",
"1. `LomapAtomMapper`\n",
" * based on the maximum common substructure (MCS)\n",
"2. `KartografAtomMapper`\n",
" * based on the 3D geometries of the ligands\n",
"\n",
"Whilst we use the defaults here, please note that the various supported arguments of\n",
"While we use the defaults here, please note that the various supported arguments of\n",
"Lomap and Kartograf can be passed to the atom mapper."
]
},
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"id": "512938c0-4ec1-48f0-9351-169923319b30",
"metadata": {},
"source": [
"It is also possible to visualize the mapping in 3D:"
"It is also possible to visualize the mapping in 3D. Atoms that have the same sphere color in both ligands are mapped while atoms that do not have a coloured sphere are not mapped but are transformed to a dummy atoms."
]
},
{
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"id": "ac41ea4d"
},
"source": [
"### The OpenFE CLI\n",
"### Setup using the OpenFE CLI\n",
"\n",
"The OpenFE toolkit also has a command line interface which we plan to add several convenience methods to.\n",
"\n",
"For now functionality is limited to atom mapping, but it will be expanded upon as the project grows.\n",
"The setup, as described above, can also be carried out using the CLI command `openfe plan-rbfe-network`.\n",
"\n",
"This command plans a relative binding free energy network, saved as JSON files for the `openfe quickrun` command.\n",
"\n",
"By default, this tool makes the following choices:\n",
"\n",
"* Atom mappings performed by LOMAP, with settings max3d=1.0 and\n",
" element_change=False\n",
"* Minimal spanning network as the network planner, with LOMAP default score as the weight function\n",
"* Water as solvent, with NaCl counter ions at 0.15 M concentration.\n",
"* Protocol is the OpenMM-based relative hybrid topology protocol, with default settings.\n",
"\n",
"These choices can be customized by creating a settings yaml file, which is\n",
"passed in via the ``-s settings.yaml`` option. (TODO: Maybe add link to user guide section)\n",
"\n",
"\n",
"TODO: How about we move the CLI to the end and say \"you can do x, y, and z\" with the CLI (Or just say \"Oh we also have a CLI tool and it can do everything you just read about in this notebook) "
]
},
{
"cell_type": "code",
"execution_count": 17,
"id": "eecd0fea",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "eecd0fea",
"outputId": "c64ee46e-aada-49f0-f8e7-05c3aaa48b9d"
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Usage: openfe [OPTIONS] COMMAND [ARGS]...\n",
"\n",
" This is the command line tool to provide easy access to functionality from\n",
" the OpenFE Python library.\n",
"\n",
"Options:\n",
" --version Show the version and exit.\n",
" --log PATH logging configuration file\n",
" -h, --help Show this message and exit.\n",
"\n",
"Network Planning Commands:\n",
" view-ligand-network Visualize a ligand network\n",
" plan-rhfe-network Plan a relative hydration free energy network, saved as\n",
" JSON files for the quickrun command.\n",
" plan-rbfe-network Plan a relative binding free energy network, saved as\n",
" JSON files for the quickrun command.\n",
"\n",
"Quickrun Executor Commands:\n",
" gather Gather result jsons for network of RFE results into a TSV file\n",
" quickrun Run a given transformation, saved as a JSON file\n",
"\n",
"Miscellaneous Commands:\n",
" test Run the OpenFE test suite\n",
" fetch Fetch tutorial or other resource.\n"
]
}
],
"cell_type": "markdown",
"id": "8495f8d7-2ecf-48c0-a6fe-1750238b9a7f",
"metadata": {},
"source": [
"# Call help on the OpenFE CLI\n",
"!openfe --help"
"\n",
"`openfe plan-rbfe-network -M inputs/tyk2_ligands.sdf -p inputs/tyk2_protein.pdb -o network/`"
]
},
{
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