Update cookbooks for openfe 1.0

OpenFreeEnergy · Apr 3, 2024 · ea738ba · ea738ba
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Showing 9 changed files with 192 additions and 289 deletions.
diff --git a/cookbook/choose_protocol.ipynb b/cookbook/choose_protocol.ipynb
diff --git a/cookbook/create_alchemical_network.ipynb b/cookbook/create_alchemical_network.ipynb
@@ -22,7 +22,6 @@
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@@ -109,7 +108,6 @@
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@@ -225,7 +223,7 @@
     "        transformation = openfe.Transformation(\n",
     "            stateA=system_a,\n",
     "            stateB=system_b,\n",
-    "            mapping={'ligand': mapping},\n",
+    "            mapping=mapping,\n",
     "            protocol=protocol,\n",
     "            # Using the same name as to_rbfe_alchemical_network()\n",
     "            name=f\"easy_rbfe_{system_a.name}_{system_b.name}\"\n",
@@ -265,7 +263,6 @@
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@@ -350,7 +344,7 @@
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diff --git a/cookbook/generate_ligand_network.ipynb b/cookbook/generate_ligand_network.ipynb
diff --git a/cookbook/generate_lomap_network.ipynb b/cookbook/generate_lomap_network.ipynb
diff --git a/cookbook/hand_write_ligand_network.ipynb b/cookbook/hand_write_ligand_network.ipynb
diff --git a/cookbook/ligandnetwork_vis.ipynb b/cookbook/ligandnetwork_vis.ipynb
diff --git a/cookbook/loading_molecules.ipynb b/cookbook/loading_molecules.ipynb
@@ -4,7 +4,6 @@
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diff --git a/cookbook/network_from_orion_fepp.ipynb b/cookbook/network_from_orion_fepp.ipynb