diff --git a/cookbook/bespoke_parameters_showcase.ipynb b/cookbook/bespoke_parameters_showcase.ipynb index 86a28e8b..8379e2bd 100644 --- a/cookbook/bespoke_parameters_showcase.ipynb +++ b/cookbook/bespoke_parameters_showcase.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# BespokeFit: Using bespoke force field parameters with OpenFE protocols\n", + "# Use bespoke parameters with BespokeFit\n", "\n", "This tutorial gives a step-by-step guide on the use of OpenFF-BespokeFit generated force field parameters with OpenFE protocols. Here we will focus on relative\n", "binding free energy (RBFE) calculations, but this strategy can be used with any OpenMM-based OpenFE protocol. \n", @@ -130,9 +130,10 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Recap\n", + "## Recap\n", + "\n", + "To recap the workflow can be reduced to the following steps:\n", "\n", - "So to recap the workflow can be reduced to the following steps:\n\n", "- Plan the RBFE network\n", "- Create a single SMIRNOFF style force field with all of the bespoke parameters for the network using the BespokeFit `combine` CLI\n", "- Store the force field as a string in the OpenFE protocol under the `settings.forcefield_settings.small_molecule_forcefield` field\n", @@ -144,7 +145,7 @@ ], "metadata": { "kernelspec": { - "display_name": "asapdiscovery", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -158,9 +159,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.6" + "version": "3.13.14" } }, "nbformat": 4, - "nbformat_minor": 2 + "nbformat_minor": 4 } diff --git a/cookbook/choose_protocol.ipynb b/cookbook/choose_protocol.ipynb index 8221d8cf..6e2c44b4 100644 --- a/cookbook/choose_protocol.ipynb +++ b/cookbook/choose_protocol.ipynb @@ -10,7 +10,7 @@ "tags": [] }, "source": [ - "# Choose and Configure a Protocol" + "# Choose and configure a protocol" ] }, { @@ -594,7 +594,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.13.10" + "version": "3.13.14" }, "widgets": { "application/vnd.jupyter.widget-state+json": { diff --git a/cookbook/create_alchemical_network.ipynb b/cookbook/create_alchemical_network.ipynb index 58ccc0b3..2803edcf 100644 --- a/cookbook/create_alchemical_network.ipynb +++ b/cookbook/create_alchemical_network.ipynb @@ -5,7 +5,7 @@ "id": "b89fdb9a-24fe-4aeb-9390-a359dae6cc9b", "metadata": {}, "source": [ - "# Create an Alchemical Network" + "# Create an `AlchemicalNetwork` manually" ] }, { diff --git a/cookbook/generate_ligand_network.ipynb b/cookbook/generate_ligand_network.ipynb index 7afe9995..3675c925 100644 --- a/cookbook/generate_ligand_network.ipynb +++ b/cookbook/generate_ligand_network.ipynb @@ -5,7 +5,7 @@ "id": "035c0099-6892-4ed2-b0d6-80b1c247c1e7", "metadata": {}, "source": [ - "# Planning a Ligand Network" + "# Plan a `LigandNetwork`" ] }, { diff --git a/cookbook/hand_write_ligand_network.ipynb b/cookbook/hand_write_ligand_network.ipynb index b603824f..cd9891ab 100644 --- a/cookbook/hand_write_ligand_network.ipynb +++ b/cookbook/hand_write_ligand_network.ipynb @@ -5,7 +5,7 @@ "id": "bf739d70-3249-42b3-a352-8a41f8f8c667", "metadata": {}, "source": [ - "# Explicitly Defining Ligand Networks" + "# Define a `LigandNetwork` explicitly" ] }, { diff --git a/cookbook/ligandnetwork_vis.ipynb b/cookbook/ligandnetwork_vis.ipynb index 13076054..3e976950 100644 --- a/cookbook/ligandnetwork_vis.ipynb +++ b/cookbook/ligandnetwork_vis.ipynb @@ -10,7 +10,7 @@ "tags": [] }, "source": [ - "# Visualizing Ligand Networks" + "# Visualize a `LigandNetwork`" ] }, { diff --git a/cookbook/loading_molecules.ipynb b/cookbook/loading_molecules.ipynb index 8e583a4b..e22783a9 100644 --- a/cookbook/loading_molecules.ipynb +++ b/cookbook/loading_molecules.ipynb @@ -13,8 +13,8 @@ "source": [ ".. _Loading Molecules:\n", "\n", - "Loading Molecules and Chemical Systems\n", - "======================================" + "Load molecules and create a ``ChemicalSystem``\n", + "==============================================" ] }, { @@ -28,7 +28,7 @@ "tags": [] }, "source": [ - "# Loading Molecules and Chemical Systems" + "# Load molecules and create a `ChemicalSystem`" ] }, { diff --git a/cookbook/network_from_orion_fepp.ipynb b/cookbook/network_from_orion_fepp.ipynb index 301058b0..4dbaaa48 100644 --- a/cookbook/network_from_orion_fepp.ipynb +++ b/cookbook/network_from_orion_fepp.ipynb @@ -5,7 +5,7 @@ "id": "4197d26d-c9e2-47ca-8d19-8372568371d8", "metadata": {}, "source": [ - "# Loading Ligand Networks Exported by Orion or FEP+" + "# Import a `LigandNetwork` from Orion or FEP+" ] }, { diff --git a/cookbook/repairing_broken_networks.ipynb b/cookbook/repairing_broken_networks.ipynb index 8fb310c4..4b4b67ed 100644 --- a/cookbook/repairing_broken_networks.ipynb +++ b/cookbook/repairing_broken_networks.ipynb @@ -5,7 +5,7 @@ "id": "ca95f143-c048-462b-9cf3-9304842c0cba", "metadata": {}, "source": [ - "# Repairing a broken ligand network\n", + "# Repair a disconnected ligand network\n", "\n", "In a relative binding free energy (RBFE) campaign, some `Transformations` may fail.\n", "If enough fail, the ligand network can become disconnected, and the ligands can no longer all be ranked against one another.\n", diff --git a/cookbook/rfe_alchemical_planners.ipynb b/cookbook/rfe_alchemical_planners.ipynb index dcdc3bf3..bbd015f2 100644 --- a/cookbook/rfe_alchemical_planners.ipynb +++ b/cookbook/rfe_alchemical_planners.ipynb @@ -5,7 +5,7 @@ "id": "b89fdb9a-24fe-4aeb-9390-a359dae6cc9b", "metadata": {}, "source": [ - "# Relative Free Energy Alchemical Network Planners" + "# Create an `AlchemicalNetwork` with a planner" ] }, { diff --git a/cookbook/user_charges.ipynb b/cookbook/user_charges.ipynb index 7919ce2a..b6bfc72d 100644 --- a/cookbook/user_charges.ipynb +++ b/cookbook/user_charges.ipynb @@ -3,15 +3,9 @@ { "cell_type": "markdown", "id": "088a1bc4-e5f3-47ac-8ebf-1a904fa82f80", - "metadata": { - "nbsphinx": "hidden", - "slideshow": { - "slide_type": "" - }, - "tags": [] - }, + "metadata": {}, "source": [ - "# Assigning partial charges to small molecules" + "# Assign partial charges to small molecules" ] }, { diff --git a/membranes/packmol_memgen_setup.ipynb b/membranes/packmol_memgen_setup.ipynb index 60e430a9..1fb6be90 100644 --- a/membranes/packmol_memgen_setup.ipynb +++ b/membranes/packmol_memgen_setup.ipynb @@ -5,7 +5,7 @@ "id": "814578a2-71ad-4d3d-9004-221a0f66fe87", "metadata": {}, "source": [ - "# Membrane Protein RBFE with packmol-memgen and OpenFE\n", + "# Prepare a membrane protein system with packmol-memgen\n", "\n", "This tutorial walks through setting up a Relative Binding Free Energy (RBFE) simulation for a membrane-embedded protein using:\n", "- `packmol-memgen`: to build the lipid bilayer system\n", @@ -717,7 +717,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.13" + "version": "3.13.14" } }, "nbformat": 4,