\n",
- "Note: When using results from relative binding afinity calculations, the derived absolute binding afinites will be centered around zero rather than the experimental mean. Thus an offset should be applied to the calculated results before comparing them.\n",
- "
\n",
- "\n",
- "You can read more about absolute estimators in the [cinnabar guide](https://cinnabar.openfree.energy/en/latest/concepts/estimators.html#centering-of-results)\n",
- "\n",
- "Next, we will use the ``cinnabar`` API to gather the experimental and calculated results into a single object:"
- ],
- "id": "8781f5c4ff6493c1"
- },
- {
- "metadata": {},
- "cell_type": "code",
- "outputs": [],
- "execution_count": null,
- "source": [
- "# Create FEMap\n",
- "fe_map = FEMap()\n",
- "\n",
- "# add the experimental data\n",
- "for index, row in experimental_data.iterrows():\n",
- " fe_map.add_experimental_measurement(\n",
- " label=row['ligand'],\n",
- " value=row['estimate (kcal/mol)'] * unit.kilocalories_per_mole,\n",
- " uncertainty=row['uncertainty (kcal/mol)'] * unit.kilocalories_per_mole,\n",
- " source=\"Experimental\"\n",
- " )\n",
- "\n",
- "# add the computed data\n",
- "for index, row in calculated_data.iterrows():\n",
- " fe_map.add_absolute_calculation(\n",
- " label=row['ligand'],\n",
- " value=row[\"DG(MLE) (kcal/mol)\"] * unit.kilocalories_per_mole,\n",
- " uncertainty=row[\"uncertainty (kcal/mol)\"] * unit.kilocalories_per_mole,\n",
- " source=\"openfe\"\n",
- " )"
- ],
- "id": "c3a96a00cabbd790"
- },
- {
- "metadata": {},
- "cell_type": "markdown",
- "source": "We can then check that the absolute measurements were added correctly:",
- "id": "883ce05e186f631d"
- },
- {
- "metadata": {},
- "cell_type": "code",
- "outputs": [],
- "execution_count": null,
- "source": "fe_map.get_absolute_dataframe()",
- "id": "9f5f9ff2b2628be8"
- },
- {
- "metadata": {},
- "cell_type": "markdown",
- "source": "Finally, we can use ``cinnabar`` to plot the calculated vs. experimental results with some accuracy and ranking metrics:",
- "id": "bf9d8fcff63cc1e7"
- },
- {
- "metadata": {},
- "cell_type": "code",
- "outputs": [],
- "execution_count": null,
- "source": [
- "plotting.plot_DGs(\n",
- " fe_map, \n",
- " source=\"openfe\", # the name of the computational source to plot\n",
- " figsize=5, \n",
- " shift=experimental_data[\"estimate (kcal/mol)\"].mean(), # shift the computed values by the mean of the experimental values to put them on a similar scale\n",
- " xy_lim=[-15, -5]\n",
- " )"
- ],
- "id": "641c870dbd8a0021"
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "b7a7fa721a373142",
- "metadata": {},
- "outputs": [],
- "source": []
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "openfe_dev",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.12.9"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}
diff --git a/plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb b/cookbook/plot_results_with_cinnabar.ipynb
similarity index 71%
rename from plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb
rename to cookbook/plot_results_with_cinnabar.ipynb
index 955cc0d8..00899eae 100644
--- a/plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb
+++ b/cookbook/plot_results_with_cinnabar.ipynb
@@ -5,9 +5,20 @@
"id": "ddae61fd-fa15-4be9-9160-ba3e195c67dc",
"metadata": {},
"source": [
- "# Plotting OpenFE results against experiment using Cinnabar v0.6.0\n",
+ "# Plot results against experiment with cinnabar\n",
"\n",
- "This notebook shows how one would go about creating a ``cinnabar`` style plot of OpenFE results against known experimental values. For more information on the ``cinnabar`` API and the available plot styles, see the [tutorials](https://cinnabar.openfree.energy/en/latest/tutorials/index.html)."
+ "Here, we show how to plot OpenFE free energy results against experimental values with [cinnabar](https://github.com/OpenFreeEnergy/cinnabar). It covers:\n",
+ "\n",
+ "1. **relative free energies**, from the table written by `openfe gather --report ddg`, and the absolute free energies derived from them, and\n",
+ "2. **absolute free energies**, from the table written by `openfe gather --report dg`, `openfe gather-abfe --report dg` or `openfe gather-septop --report dg`.\n",
+ "\n",
+ "For more on the `cinnabar` API and the available plot styles, see the [cinnabar tutorials](https://cinnabar.openfree.energy/en/latest/tutorials/index.html).\n",
+ "\n",
+ "
\n",
+ "\n",
+ "**Note:** This notebook requires `cinnabar` 0.6 or later, which is installed with openfe. With older versions, the plotting functions fail with errors such as `'FEMap' object has no attribute 'edges'`.\n",
+ "\n",
+ "
"
]
},
{
@@ -36,7 +47,7 @@
" \n",
" !pip install -q condacolab\n",
" import condacolab\n",
- " condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.7.0/OpenFEforge-1.7.0-Linux-x86_64.sh\")"
+ " condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.13.0/OpenFEforge-1.13.0-Linux-x86_64.sh\")"
]
},
{
@@ -81,16 +92,12 @@
"\n",
"```\n",
"ligand estimate (kcal/mol) uncertainty (kcal/mol)\n",
- "```\n",
- "\n",
- "**Important note:**\n",
- "Please note that for now you must have an experimental entry for every ligand involved in your free energy network.\n",
- "In future versions of cinnabar this will no longer be needed."
+ "```"
]
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 1,
"id": "6abcaae7-f5fd-483c-972f-5bb5b6d4908a",
"metadata": {},
"outputs": [],
@@ -105,7 +112,7 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 2,
"id": "8b80f592-f1a3-4c7f-8757-58a88c2e8ee7",
"metadata": {},
"outputs": [
@@ -235,14 +242,14 @@
"12 lig_jmc_28 -11.01 0.18"
]
},
- "execution_count": 4,
+ "execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# read in the experimental data\n",
- "experimental_data = pd.read_csv('experimental.tsv', sep=\"\\t\")\n",
+ "experimental_data = pd.read_csv('assets/experimental.tsv', sep=\"\\t\")\n",
"experimental_data"
]
},
@@ -251,16 +258,22 @@
"id": "aca5ede7-3741-4cc1-97ba-9115d90abd96",
"metadata": {},
"source": [
- "## Loading free energy results\n",
+ "## Plotting relative free energy results\n",
+ "\n",
+ "### Loading the results\n",
"\n",
"Next we load in results from the TSV file created by running `openfe gather --report ddg` on a network of results from [relative binding free energy calculations](https://docs.openfree.energy/en/latest/guide/protocols/relativehybridtopology.html#overview).\n",
"\n",
- "Please see the full [RBFE gather command tutorial](https://github.com/OpenFreeEnergy/ExampleNotebooks/blob/main/rbfe_tutorial/cli_tutorial.md) for more information."
+ "Please see the full [RBFE gather command tutorial](https://github.com/OpenFreeEnergy/ExampleNotebooks/blob/main/rbfe_tutorial/cli_tutorial.md) for more information.\n",
+ "\n",
+ "
\n",
+ "Note: Each openfe gather command only reads the results of one protocol. For networks that combine protocols, for example hybrid topology and Separated Topologies edges, load the results in Python and add them to a single FEMap, as shown in the Mixed Protocol Networks tutorial.\n",
+ "
\n",
+ "Note: As above, absolute free energies derived from relative calculations (gather --report dg and gather-septop --report dg) are centred around zero, so we shift them by the mean of the experimental values. Results from absolute binding free energy calculations (gather-abfe) do not need this shift.\n",
+ "