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hannahbaumann merged 11 commits into from
Nov 4, 2026
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Update cookbook titles for docs display #351

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Update cookbook titles for docs display
hannahbaumann Nov 2, 2026
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Update cookbook/bespoke_parameters_showcase.ipynb
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13 changes: 7 additions & 6 deletions cookbook/bespoke_parameters_showcase.ipynb
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"cell_type": "markdown",

@jthorton jthorton Nov 2, 2026 •
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Maybe we could hit part of OpenFreeEnergy/openfe#2283 with this change as well and drop bespokefit from the title? I can then update the introduction in another PR to say BespokeFit is just one example of the input files we can use.

What about "Using custom force field parameters" as a more general title?


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@hannahbaumann hannahbaumann Nov 3, 2026

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I like the idea of changing the title and the explanation to make it more broad, but I would suggest we can maybe change the title together with the text in a follow up PR?

"metadata": {},
"source": [
"# BespokeFit: Using bespoke force field parameters with OpenFE protocols\n",
"# Use bespoke parameters with BespokeFit\n",

@IAlibay IAlibay Nov 2, 2026

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I notice you're changing the text away from present participle - is this intentional?

@hannahbaumann hannahbaumann Nov 2, 2026

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Yes, this was intentional, mostly to shorten titles, and also because if now it's How-to ... it works better I thought. But if others think the other version is better, I can also switch to that.

@IAlibay IAlibay Nov 2, 2026

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Ah I see, so it's "How to X"? That makes a lot of sense, thanks!

"\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",
Expand Down Expand Up @@ -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",
Expand All @@ -144,7 +145,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "asapdiscovery",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -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
}
4 changes: 2 additions & 2 deletions cookbook/choose_protocol.ipynb
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"tags": []
},
"source": [
"# Choose and Configure a Protocol"
"# Choose and configure a protocol"
]
},
{
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"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.13.10"
"version": "3.13.14"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
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2 changes: 1 addition & 1 deletion cookbook/create_alchemical_network.ipynb
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"id": "b89fdb9a-24fe-4aeb-9390-a359dae6cc9b",
"metadata": {},
"source": [
"# Create an Alchemical Network"
"# Create an `AlchemicalNetwork` manually"
]
},
{
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2 changes: 1 addition & 1 deletion cookbook/generate_ligand_network.ipynb
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"id": "035c0099-6892-4ed2-b0d6-80b1c247c1e7",

@jthorton jthorton Nov 2, 2026 •
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Should it be -> Plan a LigandNetwork to match the use of the AlchemicalNetwork in the other cookbook titles?


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@hannahbaumann hannahbaumann Nov 3, 2026

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Done!

"metadata": {},
"source": [
"# Planning a Ligand Network"
"# Plan a `LigandNetwork`"
]
},
{
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2 changes: 1 addition & 1 deletion cookbook/hand_write_ligand_network.ipynb
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"id": "bf739d70-3249-42b3-a352-8a41f8f8c667",
"metadata": {},
"source": [
"# Explicitly Defining Ligand Networks"
"# Define a `LigandNetwork` explicitly"
]
},
{
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2 changes: 1 addition & 1 deletion cookbook/ligandnetwork_vis.ipynb
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"tags": []
},
"source": [
"# Visualizing Ligand Networks"
"# Visualize a `LigandNetwork`"
]
},
{
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6 changes: 3 additions & 3 deletions cookbook/loading_molecules.ipynb
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"source": [
".. _Loading Molecules:\n",
"\n",
"Loading Molecules and Chemical Systems\n",
"======================================"
"Load molecules and create a ``ChemicalSystem``\n",
"=============================================="
]
},
{
Expand All @@ -28,7 +28,7 @@
"tags": []
},
"source": [
"# Loading Molecules and Chemical Systems"
"# Load molecules and create a `ChemicalSystem`"
]
},
{
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2 changes: 1 addition & 1 deletion cookbook/network_from_orion_fepp.ipynb
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"id": "4197d26d-c9e2-47ca-8d19-8372568371d8",
"metadata": {},
"source": [
"# Loading Ligand Networks Exported by Orion or FEP+"
"# Import a `LigandNetwork` from Orion or FEP+"
]
},
{
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2 changes: 1 addition & 1 deletion cookbook/repairing_broken_networks.ipynb
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"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",
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2 changes: 1 addition & 1 deletion cookbook/rfe_alchemical_planners.ipynb
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"id": "b89fdb9a-24fe-4aeb-9390-a359dae6cc9b",
"metadata": {},
"source": [
"# Relative Free Energy Alchemical Network Planners"
"# Create an `AlchemicalNetwork` with a planner"
]
},
{
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10 changes: 2 additions & 8 deletions cookbook/user_charges.ipynb
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{
"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"
]
},
{
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4 changes: 2 additions & 2 deletions membranes/packmol_memgen_setup.ipynb
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"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",
Expand Down Expand Up @@ -717,7 +717,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.13"
"version": "3.13.14"
}
},
"nbformat": 4,
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