Skip to content

consolidate instructions for creating an alchemical network #276

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
atravitz merged 5 commits into from
Dec 11, 2025
Merged

consolidate instructions for creating an alchemical network #276

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
02b0232
consolidate instructions for creating an alchemical network
atravitz Dec 10, 2025
b8c0f3b
remove redundant notebook
atravitz Dec 10, 2025
4843500
bump ci
atravitz Dec 10, 2025
b30fcdc
split imports onto separate times
atravitz Dec 10, 2025
f9bfe01
Merge branch 'main' into consolidate_preparing_alchemical_networks
atravitz Dec 10, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
85 changes: 50 additions & 35 deletions cookbook/create_alchemical_network.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,12 @@
"id": "2b11a786-0fab-4990-a2aa-242067f89287",
"metadata": {},
"source": [
"The final setup step is to compile all the different bits of information into a description of a single simulation campaign. This description takes the form of an [Alchemical Network]. Similarly to `LigandNetwork`, the `AlchemicalNetwork` class is a graph of all the transformations in the campaign; however, in an `AlchemicalNetwork`, these transformations include all the information needed to perform the transformation. By contrast, a `LigandNetwork` includes only the ligands themselves.\n",
"The final setup step is to compile all the different bits of information into a description of a single simulation campaign. This description takes the form of an [Alchemical Network].\n",
"Similar to `LigandNetwork`, the `AlchemicalNetwork` class is a graph of all the transformations in the campaign.\n",
"\n",
"However, in an `AlchemicalNetwork`, these transformations include all the information needed to perform the transformation. By contrast, a `LigandNetwork` includes only the ligands themselves.\n",
"\n",
"See the [User Guide: Alchemical Networks](https://docs.openfree.energy/en/stable/guide/setup/alchemical_network_model.html) for more background information.\n",
"\n",
"[Alchemical Network]: https://docs.openfree.energy/en/stable/reference/api/generated/openfe.AlchemicalNetwork.html"
]
Expand All @@ -28,38 +33,33 @@
"tags": []
},
"source": [
"## Setup"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "ba6d0d2f-03df-463f-8976-c15a2bdf65e5",
"metadata": {},
"outputs": [],
"source": [
"import openfe, rdkit.Chem\n",
"from openff.units import unit\n",
"from openfe.protocols.openmm_rfe import RelativeHybridTopologyProtocol"
"## Start with a `LigandNetwork`"
]
},
{
"cell_type": "markdown",
"id": "6bfee4c7-0aaf-49a6-b35a-bdbe99444bab",
"metadata": {},
"source": [
"This cookbook assumes you've already loaded a `LigandNetwork`. For more information, see [Generate a Ligand Network Automatically]:\n",
"This cookbook assumes you've already loaded a `LigandNetwork`.\n",
"\n",
"[Generate a Ligand Network Automatically]: https://docs.openfree.energy/en/stable/cookbook/generate_ligand_network.html"
"To learn how to build a `LigandNetwork`, see [Planning a Ligand Network]:\n",
"\n",
"[Planning a Ligand Network]: https://docs.openfree.energy/en/stable/cookbook/generate_ligand_network.html"
]
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 1,
"id": "4512c4d6-720f-4008-af53-a0b56b2ee1e9",
"metadata": {},
"outputs": [],
"source": [
"import openfe\n",
"import rdkit.Chem\n",
"from openff.units import unit\n",
"from openfe.protocols.openmm_rfe import RelativeHybridTopologyProtocol\n",
"\n",
"ligand_network = openfe.ligand_network_planning.generate_minimal_spanning_network(\n",
" ligands=[\n",
" openfe.SmallMoleculeComponent(mol) \n",
Expand All @@ -85,7 +85,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 2,
"id": "940e2e19-4e7d-4853-ab5e-54626b3384d8",
"metadata": {},
"outputs": [],
Expand All @@ -105,7 +105,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 3,
"id": "d3054cfc-5040-4882-b3a3-92aba7ab5d1d",
"metadata": {
"slideshow": {
Expand Down Expand Up @@ -149,7 +149,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 4,
"id": "733dee64-d23a-4eb0-87cf-c03065b8d2a6",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -181,27 +181,34 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 5,
"id": "c49f36b1-c3c1-425e-b1de-24da25ed01c3",
"metadata": {},
"outputs": [],
"source": [
"# In an RBFE, each edge includes two \"legs\": \n",
"# one for the ligand complexed to the protein, \n",
"# and the other for the ligand free in solution\n",
"\n",
"\n",
"legs = {\n",
" \"solvent\": {\n",
" # Specify the components common to all systems in this leg\n",
" 'solvent': solvent,\n",
" },\n",
" \"complex\": {\n",
" # Specify the components common to all systems in this leg\n",
" 'solvent': solvent,\n",
" 'protein': protein,\n",
" }\n",
"}\n",
"transformations = []\n",
" # Specify the components common to all systems in this leg\n",
" \"solvent\": {'solvent': solvent},\n",
" # Specify the components common to all systems in this leg\n",
" \"complex\": {'solvent': solvent, 'protein': protein}\n",
"}"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "77d71229-5dcc-40cf-a9ae-0724a7327578",
"metadata": {},
"outputs": [],
"source": [
"# create a list of transformations\n",
"\n",
"transformations = []\n",
"for mapping in ligand_network.edges:\n",
" for leg, common_components in legs.items():\n",
" system_a = openfe.ChemicalSystem(\n",
Expand Down Expand Up @@ -229,7 +236,7 @@
" name=f\"easy_rbfe_{system_a.name}_{system_b.name}\"\n",
" )\n",
" \n",
" transformations.append(transformation)"
" transformations.append(transformation)\n"
]
},
{
Expand Down Expand Up @@ -324,8 +331,16 @@
"\n",
"for n, transformation in enumerate(alchemical_network.edges):\n",
" transformation_name = transformation.name or transformation.key\n",
" transformation.dump(transformations_dir / f\"{n}_{transformation_name}.json\")"
" transformation.to_json(transformations_dir / f\"{n}_{transformation_name}.json\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "28d7af7c-0e8e-4379-91c2-c9d291c3923b",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand All @@ -344,7 +359,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.6"
"version": "3.13.11"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
Expand Down
Loading