Use KartografMapper as default in all notebooks

Author: hannahbaumann

cookbook/cofactors_rbfe.ipynb

@@ -165,7 +165,7 @@
     }
    ],
    "source": [
-    "mapper = openfe.LomapAtomMapper(max3d=1.0, element_change=False, threed=True)\n",
+    "mapper = openfe.KartografAtomMapper()\n",
     "scorer = openfe.lomap_scorers.default_lomap_score\n",
     "network_planner = openfe.ligand_network_planning.generate_minimal_spanning_network\n",
     "\n",
@@ -359,7 +359,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.12"
+   "version": "3.13.11"
   }
  },
  "nbformat": 4,

cookbook/create_alchemical_network.ipynb

@@ -68,7 +68,7 @@
     "            removeHs=False,\n",
     "        )\n",
     "    ],\n",
-    "    mappers=[openfe.setup.LomapAtomMapper()],\n",
+    "    mappers=[openfe.setup.KartografAtomMapper()],\n",
     "    scorer=openfe.lomap_scorers.default_lomap_score,\n",
     ")"
    ]

cookbook/generate_ligand_network.ipynb

@@ -99,6 +99,8 @@
    "source": [
     "from openmm import unit\n",
     "\n",
+    "kartograf_mapper = openfe.setup.KartografAtomMapper()\n",
+    "\n",
     "lomap_mapper = openfe.setup.LomapAtomMapper(\n",
     "        time=20, # Time out if MCS algorithm takes 20 seconds\n",
     "        threed=True, # Use atom positions to prune symmetric mappings\n",
@@ -107,10 +109,9 @@
     "        seed='', # Empty SMARTS string causes MCS search to start from scratch\n",
     "        shift=False, # Keep pre-aligned atom positions for 3D position checks\n",
     ")\n",
-    "kartograf_mapper = openfe.setup.KartografAtomMapper()\n",
     "\n",
     "# to demonstrate passing multiple atom mappers to the planner\n",
-    "mappers = [lomap_mapper, kartograf_mapper]"
+    "mappers = [kartograf_mapper, lomap_mapper]"
    ]
   },
   {

cookbook/hand_write_ligand_network.ipynb

@@ -102,11 +102,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mapper = openfe.setup.LomapAtomMapper(\n",
-    "    threed=True, # Use atom positions to prune symmetric mappings\n",
-    "    max3d=1.0, # Forbid mapping between atoms more than 1.0 Å apart\n",
-    "    element_change=False, # Forbid mappings that change an atoms element\n",
-    ")"
+    "mapper = openfe.setup.KartografAtomMapper()"
    ]
   },
   {

cookbook/network_from_orion_fepp.ipynb

@@ -99,11 +99,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mapper = openfe.setup.LomapAtomMapper(\n",
-    "    threed=True, # Use atom positions to prune symmetric mappings\n",
-    "    max3d=1.0, # Forbid mapping between atoms more than 1.0 Å apart\n",
-    "    element_change=False, # Forbid mappings that change an atoms element\n",
-    ")"
+    "mapper = openfe.setup.KartografAtomMapper()"
    ]
   },
   {