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Use KartografMapper as default in all notebooks #326

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Use KartografMapper as default in all notebooks #326

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62e96ce
Use KartografMapper as default in all notebooks
hannahbaumann Sep 10, 2026
8d3d444
Shorten lomap example showcase
hannahbaumann Sep 10, 2026
0ea9171
Another lomap switch
hannahbaumann Sep 10, 2026
1e844b5
small fix
hannahbaumann Sep 10, 2026
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4 changes: 2 additions & 2 deletions cookbook/cofactors_rbfe.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -359,7 +359,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.12"
"version": "3.13.11"
}
},
"nbformat": 4,
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2 changes: 1 addition & 1 deletion cookbook/create_alchemical_network.ipynb
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Expand Up @@ -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",
")"
]
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5 changes: 3 additions & 2 deletions cookbook/generate_ligand_network.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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]"
]
},
{
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6 changes: 1 addition & 5 deletions cookbook/hand_write_ligand_network.ipynb
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Expand Up @@ -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()"
]
},
{
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6 changes: 1 addition & 5 deletions cookbook/network_from_orion_fepp.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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()"
]
},
{
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53 changes: 27 additions & 26 deletions openmm_septop/septop_tutorial.ipynb
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76 changes: 42 additions & 34 deletions rbfe_tutorial/rbfe_python_tutorial.ipynb
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2,110 changes: 1,810 additions & 300 deletions showcase/openfe_showcase.ipynb
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