Merge pull request #173 from OpenFreeEnergy/cookbook_fixes

Fix cookbook rendering issues
OpenFreeEnergy · Oct 22, 2024 · 6c499cb · 6c499cb
2 parents 58fbbc1 + 07a16a4
commit 6c499cb
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diff --git a/cookbook/bespoke_parameters_showcase.ipynb b/cookbook/bespoke_parameters_showcase.ipynb
@@ -132,7 +132,7 @@
    "source": [
     "# Recap\n",
     "\n",
-    "So to recap the workflow can be reduced to the following steps:\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",

diff --git a/cookbook/user_charges.ipynb b/cookbook/user_charges.ipynb
@@ -45,7 +45,7 @@
     "\n",
     "Unfortunately charge assignment can be both, a) time consuming for large molecules, and b) non-deterministic, especially when the molecule occupies a conformation far from a local minima in the AM1 energetic landscape. The latter can be particularly problematic as this can lead to significant differences in assigned partial charges between Protocol simulation repeats.\n",
     "\n",
-    "To avoid these issues, we recommend applying `user charges` to `SmallMoleculeComponents`. In its simplest form, this is done by converting the `SmallMoleculeComponent` to an `OpenFF Molecule` calling the [OpenFF Molecule's `assign_partial_charges method`](https://docs.openforcefield.org/projects/toolkit/en/latest/api/generated/openff.toolkit.topology.Molecule.html#openff.toolkit.topology.Molecule.assign_partial_charges) and then re-loading it back into a `SmallMoleculeComponent` before further manipulation."
+    "To avoid these issues, we recommend applying `user charges` to `SmallMoleculeComponents`. In its simplest form, this is done by converting the `SmallMoleculeComponent` to an `OpenFF Molecule` calling the OpenFF Molecule's [assign_partial_charges method](https://docs.openforcefield.org/projects/toolkit/en/latest/api/generated/openff.toolkit.topology.Molecule.html#openff.toolkit.topology.Molecule.assign_partial_charges) and then re-loading it back into a `SmallMoleculeComponent` before further manipulation."
    ]
   },
   {
-Original file line number
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@@ Expand Up / @@ -45,7 +45,7 @@ @@
         "\n",
         "Unfortunately charge assignment can be both, a) time consuming for large molecules, and b) non-deterministic, especially when the molecule occupies a conformation far from a local minima in the AM1 energetic landscape. The latter can be particularly problematic as this can lead to significant differences in assigned partial charges between Protocol simulation repeats.\n",
         "\n",
-        "To avoid these issues, we recommend applying `user charges` to `SmallMoleculeComponents`. In its simplest form, this is done by converting the `SmallMoleculeComponent` to an `OpenFF Molecule` calling the [OpenFF Molecule's `assign_partial_charges method`](https://docs.openforcefield.org/projects/toolkit/en/latest/api/generated/openff.toolkit.topology.Molecule.html#openff.toolkit.topology.Molecule.assign_partial_charges) and then re-loading it back into a `SmallMoleculeComponent` before further manipulation."
+        "To avoid these issues, we recommend applying `user charges` to `SmallMoleculeComponents`. In its simplest form, this is done by converting the `SmallMoleculeComponent` to an `OpenFF Molecule` calling the OpenFF Molecule's [assign_partial_charges method](https://docs.openforcefield.org/projects/toolkit/en/latest/api/generated/openff.toolkit.topology.Molecule.html#openff.toolkit.topology.Molecule.assign_partial_charges) and then re-loading it back into a `SmallMoleculeComponent` before further manipulation."
        ]
       },
       {
@@ Expand Down @@