updates user charges notebook

OpenFreeEnergy · Dec 4, 2023 · 00b34c3 · 00b34c3
1 parent 0873718
commit 00b34c3
Showing 1 changed file with 8 additions and 81 deletions.
diff --git a/cookbook/user_charges.ipynb b/cookbook/user_charges.ipynb
@@ -1,23 +1,5 @@
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-    ".. _User Charges:\n",
-    "\n",
-    "Assining partial Charges to Small Molecule Components\n",
-    "====================================================="
-   ]
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@@ -30,23 +12,7 @@
     "tags": []
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    "source": [
-    "# Assigning partial charges to Small Molecule Components"
-   ]
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-   "source": [
-    "On partial charge assignment\n",
-    "----------------------------"
+    "# Selecting partial charge assigment methods when loading small molecules"
    ]
   },
   {
@@ -82,25 +48,7 @@
     "\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/0.9.2/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."
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-    ".. _Loading small molecules and converting them to OpenFF Molecules:\n",
-    "\n",
-    "Loading small molecules and converting them to OpenFF Molecules\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."
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@@ -175,14 +123,11 @@
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    "source": [
-    ".. _Assigning partial charges to an OpenFF Molecule:\n",
-    "\n",
-    "Assigning partial charges to an OpenFF Molecule\n",
-    "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+    "### Assigning partial charges to an OpenFF Molecule"
    ]
   },
   {
@@ -242,7 +187,7 @@
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-    "Alternative partial charge methods can be used. For example one could ask for `am1-mulliken` charges. Please see the [OpenFF documentation](https://docs.openforcefield.org/projects/toolkit/en/stable/) for more information."
+    "Alternative partial charge methods can be used. For example one could ask for `am1-mulliken` charges. Please see the [OpenFF documentation](https://docs.openforcefield.org/projects/toolkit/en/latest/api/generated/openff.toolkit.topology.Molecule.html#openff.toolkit.topology.Molecule.assign_partial_charges) for more information."
    ]
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@@ -274,24 +219,6 @@
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-   "source": [
-    ".. _Converting to OpenFE SmallMoleculeComponents:\n",
-    "\n",
-    "Converting to OpenFE SmallMoleculeComponents\n",
-    "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-   ]
-  },
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@@ -338,7 +265,7 @@
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-      "/home/ialibay/software/mambaforge/install/envs/alchemiscale-client-0.2.1/lib/python3.10/site-packages/gufe/components/explicitmoleculecomponent.py:79: UserWarning: Partial charges have been provided, these will preferentially be used instead of generating new partial charges\n",
+      "/Users/dwhs/mambaforge/envs/openfe/lib/python3.11/site-packages/gufe/components/explicitmoleculecomponent.py:79: UserWarning: Partial charges have been provided, these will preferentially be used instead of generating new partial charges\n",
       "  warnings.warn(wmsg)\n"
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@@ -379,7 +306,7 @@
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