Rename all cookbook links to how-to guides

abfe_tutorial/abfe_tutorial.ipynb

@@ -130,7 +130,7 @@
     "\n",
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Learn more:** To assign partial charges to your own ligands, see the cookbook on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/cookbook/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Learn more:** To assign partial charges to your own ligands, see the how-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]

ahfe_tutorial/ahfe_tutorial.ipynb

@@ -122,7 +122,7 @@
    "source": [
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Partial charges:** The ligand in `benzene_am1bcc.sdf` already has AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the cookbook on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/cookbook/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Partial charges:** The ligand in `benzene_am1bcc.sdf` already has AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the how-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]

cookbook/cofactors_rbfe.ipynb

@@ -7,7 +7,7 @@
    "source": [
     "# Defining Cofactors\n",
     "\n",
-    "This cookbook demonstrates how to define cofactors (any small molecules that are not the bound ligand) with 1) the ``openfe`` CLI during the planning phase and 2) directly using the Python API.\n",
+    "This how-to guide demonstrates how to define cofactors (any small molecules that are not the bound ligand) with 1) the ``openfe`` CLI during the planning phase and 2) directly using the Python API.\n",
     "\n",
     "Similar to `ligand` definition, `cofactors` can be loaded from in SDF file format, and multiple molecules can be defined in a single file."
    ]
@@ -65,7 +65,7 @@
     "\n",
     "\n",
     "<div class=\"alert alert-warning\">\n",
-    "Note that partial charges are already assigned for both the ligands and cofactors. See <a href=\"https://docs.openfree.energy/en/latest/cookbook/user_charges.html\">Assigning partial charges to an OpenFF Molecule</a> or and <a href=\" https://docs.openfree.energy/en/latest/reference/cli/charge_molecules.html\">charge-molecules CLI command</a> for information on assigning partial charges.\n",
+    "Note that partial charges are already assigned for both the ligands and cofactors. See <a href=\"https://docs.openfree.energy/en/latest/how_to_guides/user_charges.html\">Assigning partial charges to an OpenFF Molecule</a> or and <a href=\" https://docs.openfree.energy/en/latest/reference/cli/charge_molecules.html\">charge-molecules CLI command</a> for information on assigning partial charges.\n",
     "\n",
     "Supplying cofactors as SmallMoleculeCompoents means they will be parameterized using the small molecule force field, which might not be applicable in all situations.\n",
     "</div>\n"
@@ -359,7 +359,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.11"
+   "version": "3.13.14"
   }
  },
  "nbformat": 4,

cookbook/create_alchemical_network.ipynb

@@ -51,8 +51,8 @@
    "id": "6bfee4c7-0aaf-49a6-b35a-bdbe99444bab",
    "metadata": {},
    "source": [
-    "This cookbook assumes you've already loaded a `LigandNetwork`.\n",
-    "To learn how to build a `LigandNetwork`, see [Planning a Ligand Network](https://docs.openfree.energy/en/stable/cookbook/generate_ligand_network.html)."
+    "This how-to guide assumes you've already loaded a `LigandNetwork`.\n",
+    "To learn how to build a `LigandNetwork`, see [Planning a Ligand Network](https://docs.openfree.energy/en/stable/how_to_guides/generate_ligand_network.html)."
    ]
   },
   {
@@ -85,7 +85,7 @@
    "source": [
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Partial charges:** The ligands in `somebenzenes_am1bcc.sdf` already have AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the cookbook on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/cookbook/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Partial charges:** The ligands in `somebenzenes_am1bcc.sdf` already have AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the how-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]
@@ -95,9 +95,9 @@
    "id": "405fe819-b4a6-408b-8623-041492c84dfb",
    "metadata": {},
    "source": [
-    "This cookbook assumes you've already loaded a `Protocol`. For more information, see [Choose and Configure a Protocol]:\n",
+    "This how-to guide assumes you've already loaded a `Protocol`. For more information, see [Choose and Configure a Protocol]:\n",
     "\n",
-    "[Choose and Configure a Protocol]: https://docs.openfree.energy/en/stable/cookbook/choose_protocol.html"
+    "[Choose and Configure a Protocol]: https://docs.openfree.energy/en/stable/how_to_guides/choose_protocol.html"
    ]
   },
   {
@@ -117,9 +117,9 @@
    "id": "0908d2b2-421d-4b51-8b35-d2cca5e25a95",
    "metadata": {},
    "source": [
-    "This cookbook assumes you've already loaded a solvent and all the other chemical components of the system, including any proteins or cofactors. For more information, see [Loading your data into Components]:\n",
+    "This how-to guide assumes you've already loaded a solvent and all the other chemical components of the system, including any proteins or cofactors. For more information, see [Loading your data into Components]:\n",
     "\n",
-    "[Loading your data into Components]: https://docs.openfree.energy/en/stable/cookbook/loading_molecules.html"
+    "[Loading your data into Components]: https://docs.openfree.energy/en/stable/how_to_guides/loading_molecules.html"
    ]
   },
   {
@@ -167,7 +167,7 @@
    "source": [
     "To create an `AlchemicalNetwork` loop over the `LigandNetwork` edges and manually create the `Transformation` objects for each of them. This gives you full control over the entire network. For more information, see [Under the Hood]:\n",
     "\n",
-    "[Under the Hood]: https://docs.openfree.energy/en/stable/cookbook/under_the_hood.html"
+    "[Under the Hood]: https://docs.openfree.energy/en/stable/how_to_guides/under_the_hood.html"
    ]
   },
   {
@@ -282,9 +282,9 @@
     "tags": []
    },
    "source": [
-    "While the `AlchemicalNetwork` class itself has no on-disk representation, the `Transformation` instances that compose it do. Write an alchemical network to disk by iterating over its edges. For more information, see [Dumping a Transformation to JSON]:\n",
+    "While the `AlchemicalNetwork` class itself has no on-disk representation, the `Transformation` instances that compose it do. Write an alchemical network to disk by iterating over its edges. For more information, see [Writing a Transformation to JSON].\n",
     "\n",
-    "[Dumping a Transformation to JSON]: https://docs.openfree.energy/en/stable/cookbook/dumping_transformation.html"
+    "[Writing a Transformation to JSON]: https://docs.openfree.energy/en/stable/how_to_guides/dumping_transformation.html"
    ]
   },
   {

cookbook/generate_ligand_network.ipynb

@@ -29,9 +29,9 @@
    "id": "7f1a272a-ffe7-4397-a8a6-c590d3a210bc",
    "metadata": {},
    "source": [
-    "This cookbook assumes you have already loaded a collection of `SmallMoleculeComponent` objects into an iterable called `ligands`.\n",
+    "This how-to guide assumes you have already loaded a collection of `SmallMoleculeComponent` objects into an iterable called `ligands`.\n",
     "\n",
-    "For more information, see the [Loading Small Molecules Cookbook](https://docs.openfree.energy/en/stable/cookbook/loading_molecules.html#loading-small-molecules)."
+    "For more information, see the [Loading Small Molecules how-to guide](https://docs.openfree.energy/en/stable/how_to_guides/loading_molecules.html#loading-small-molecules)."
    ]
   },
   {
@@ -979,7 +979,7 @@
    "source": [
     "For more ways to visualize a `LigandNetwork`, see [Visualizing Ligand Networks].\n",
     "\n",
-    "[Visualizing Ligand Networks]: https://docs.openfree.energy/en/stable/cookbook/ligandnetwork_vis.html"
+    "[Visualizing Ligand Networks]: https://docs.openfree.energy/en/stable/how_to_guides/ligandnetwork_vis.html"
    ]
   },
   {

cookbook/hand_write_ligand_network.ipynb

@@ -21,8 +21,8 @@
     "\n",
     "Although this is the most flexible way to define a ``LigandNetwork``, we encourage you to use **openfe** helper functionality when possible for performance, reproducibility, and ease of use:\n",
     "\n",
-    "  - [Loading Ligand Networks Exported by Orion or FEP+](https://docs.openfree.energy/en/stable/cookbook/network_from_orion_fepp.html)\n",
-    "  - [Planning a Ligand Network](https://docs.openfree.energy/en/stable/cookbook/generate_ligand_network.html)\n"
+    "  - [Loading Ligand Networks Exported by Orion or FEP+](https://docs.openfree.energy/en/stable/how_to_guides/network_from_orion_fepp.html)\n",
+    "  - [Planning a Ligand Network](https://docs.openfree.energy/en/stable/how_to_guides/generate_ligand_network.html)\n"
    ]
   },
   {
@@ -38,9 +38,9 @@
    "id": "39e64f74-337e-4a88-b253-ab051820d5e3",
    "metadata": {},
    "source": [
-    "This cookbook assumes you've already loaded a collection of `SmallMoleculeComponent` objects into an iterable called `ligands`.\n",
+    "This how-to guide assumes you've already loaded a collection of `SmallMoleculeComponent` objects into an iterable called `ligands`.\n",
     "\n",
-    "For more information, see [Loading Small Molecules](https://docs.openfree.energy/en/stable/cookbook/loading_molecules.html#loading-small-molecules)."
+    "For more information, see [Loading Small Molecules](https://docs.openfree.energy/en/stable/how_to_guides/loading_molecules.html#loading-small-molecules)."
    ]
   },
   {
@@ -92,7 +92,7 @@
    "source": [
     "As we will only specify the topology of the network, OpenFE must generate atom mappings for us. For this, it needs an atom mapper; for more information, see [Choose an Atom Mapper]:\n",
     "\n",
-    "[Choose an Atom Mapper]: https://docs.openfree.energy/en/stable/cookbook/generate_ligand_network.html#Choose-an-atom-mapper"
+    "[Choose an Atom Mapper]: https://docs.openfree.energy/en/stable/how_to_guides/generate_ligand_network.html#Choose-an-atom-mapper"
    ]
   },
   {
@@ -240,7 +240,7 @@
    "source": [
     "For more ways to visualize a `LigandNetwork`, see [Visualizing Ligand Networks].\n",
     "\n",
-    "[Visualizing Ligand Networks]: https://docs.openfree.energy/en/stable/cookbook/ligandnetwork_vis.html"
+    "[Visualizing Ligand Networks]: https://docs.openfree.energy/en/stable/how_to_guides/ligandnetwork_vis.html"
    ]
   },
   {

cookbook/ligandnetwork_vis.ipynb

@@ -39,7 +39,7 @@
    "id": "0d405db9-1ab5-43e1-aa51-89b5bdb283d7",
    "metadata": {},
    "source": [
-    "You will need to create a `LigandNetwork` for your system of interest. For more information, see [Generating a Ligand Network](https://docs.openfree.energy/en/stable/cookbook/generate_ligand_network.html)."
+    "You will need to create a `LigandNetwork` for your system of interest. For more information, see [Generating a Ligand Network](https://docs.openfree.energy/en/stable/how_to_guides/generate_ligand_network.html)."
    ]
   },
   {

cookbook/loading_molecules.ipynb

@@ -246,7 +246,7 @@
    "source": [
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Partial charges:** Any partial charges stored in an SDF file are read along with the molecules, and are used in simulations instead of generating new ones. The files used here already have AM1-BCC partial charges. To assign partial charges to your own molecules, see the cookbook on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/cookbook/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Partial charges:** Any partial charges stored in an SDF file are read along with the molecules, and are used in simulations instead of generating new ones. The files used here already have AM1-BCC partial charges. To assign partial charges to your own molecules, see the how-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/chow_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]

cookbook/network_from_orion_fepp.ipynb

@@ -35,7 +35,7 @@
    "source": [
     "Both FEP+ `.edge` and Orion `.dat` files identify molecules by name, so to load the network OpenFE requires a list of named ligands.\n",
     "\n",
-    "Load the ligands used by the network into instances of `SmallMoleculeComponent`. For more information, see [Loading Small Molecules](https://docs.openfree.energy/en/stable/cookbook/loading_molecules.html#loading-small-molecules)."
+    "Load the ligands used by the network into instances of `SmallMoleculeComponent`. For more information, see [Loading Small Molecules](https://docs.openfree.energy/en/stable/how_to_guides/loading_molecules.html#loading-small-molecules)."
    ]
   },
   {
@@ -87,7 +87,7 @@
    "source": [
     "Both formats encode only the network itself, leaving mappings between atoms in each edge undefined. OpenFE needs an atom mapper to produce atom mappings; for more information, see [Choose an Atom Mapper]:\n",
     "\n",
-    "[Choose an Atom Mapper]: https://docs.openfree.energy/en/stable/cookbook/generate_ligand_network.html#Choose-an-atom-mapper"
+    "[Choose an Atom Mapper]: https://docs.openfree.energy/en/stable/how_to_guides/generate_ligand_network.html#Choose-an-atom-mapper"
    ]
   },
   {
@@ -170,7 +170,7 @@
     "\n",
     "For more ways to visualize a `LigandNetwork`, see [Visualizing Ligand Networks].\n",
     "\n",
-    "[Visualizing Ligand Networks]: https://docs.openfree.energy/en/stable/cookbook/ligandnetwork_vis.html"
+    "[Visualizing Ligand Networks]: https://docs.openfree.energy/en/stable/how_to_guides/ligandnetwork_vis.html"
    ]
   },
   {
@@ -249,7 +249,7 @@
    "source": [
     "See [Creating an Alchemical Network] for how to use these defined `ligand_network` objects to create an AlchemicalNetwork, which can then be executed using the OpenFE CLI.\n",
     "\n",
-    "[Creating an Alchemical Network]: https://docs.openfree.energy/en/stable/cookbook/create_alchemical_network.html"
+    "[Creating an Alchemical Network]: https://docs.openfree.energy/en/stable/how_to_guides/create_alchemical_network.html"
    ]
   }
  ],

cookbook/repairing_broken_networks.ipynb

@@ -10,7 +10,7 @@
     "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",
     "\n",
-    "This cookbook follows the repair workflow end to end:\n",
+    "This how-to guide follows the repair workflow end to end:\n",
     "\n",
     "1. **Identify failures** from campaign results and reconstruct the broken network.\n",
     "2. **Repair the ligand network**, either manually or automatically by edge score.\n",

cookbook/rfe_alchemical_planners.ipynb

@@ -101,7 +101,7 @@
    "source": [
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "**Partial charges:** The ligands in `somebenzenes_am1bcc.sdf` already have AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the cookbook on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/cookbook/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
+    "**Partial charges:** The ligands in `somebenzenes_am1bcc.sdf` already have AM1-BCC partial charges, so the same charges are used in every repeat. To assign partial charges to your own ligands, see the how-to guide on [assigning partial charges with the Python API](https://docs.openfree.energy/en/stable/how_to_guides/user_charges.html) or the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html).\n",
     "\n",
     "</div>"
    ]

cookbook/user_charges.ipynb

@@ -27,7 +27,7 @@
    "id": "717f695e-7841-4168-b820-87fe2eb29c72",
    "metadata": {},
    "source": [
-    "`SmallMoleculeComponent`s are usually loaded into OpenFE without partial charges, for example when loading from [SDF files](https://docs.openfree.energy/en/stable/cookbook/loading_molecules.html#Loading-small-molecules).\n",
+    "`SmallMoleculeComponent`s are usually loaded into OpenFE without partial charges, for example when loading from [SDF files](https://docs.openfree.energy/en/stable/how_to_guides/loading_molecules.html#Loading-small-molecules).\n",
     "\n",
     "In that case, partial charges are assigned by the `Protocol`, using the method defined in its `partial_charge_settings`. By default, this is AM1-BCC charges from AmberTools, using the input conformer.\n",
     "\n",
@@ -38,7 +38,7 @@
     "\n",
     "Both apply to the AM1-BCC-based methods. To avoid these issues, we recommend assigning partial charges once, before setting up any simulations, and storing them with your molecules. Any partial charges present on a `SmallMoleculeComponent` are used by the `Protocol` instead of generating new ones.\n",
     "\n",
-    "This cookbook shows how to do this with the Python API. To do the same from the command line, see the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html)."
+    "This how-to guide shows how to do this with the Python API. To do the same from the command line, see the [partial charges CLI tutorial](https://docs.openfree.energy/en/stable/tutorials/charge_molecules_cli_tutorial.html)."
    ]
   },
   {

execution/task_based_execution_python_api.ipynb

@@ -70,7 +70,7 @@
     "\n",
     "The input to a task-based campaign is an `AlchemicalNetwork`. If you don't\n",
     "have one yet, see the\n",
-    "[Create an `AlchemicalNetwork` cookbook](https://docs.openfree.energy/en/stable/cookbook/create_alchemical_network.html),\n",
+    "[Create an `AlchemicalNetwork` how-to guide](https://docs.openfree.energy/en/stable/how_to_guides/create_alchemical_network.html),\n",
     "or add `--networks-only` to an `openfe plan-rbfe-network` call.\n",
     "\n",
     "Here we use a small MCL-1 network with pre-charged ligands and two edges,\n",
@@ -1639,7 +1639,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.16"
+   "version": "3.13.14"
   }
  },
  "nbformat": 4,