diff --git a/examples/building_networks.ipynb b/examples/building_networks.ipynb index 0d5af4e..82c87d6 100644 --- a/examples/building_networks.ipynb +++ b/examples/building_networks.ipynb @@ -31,7 +31,9 @@ "outputs": [], "source": [ "# declare the charge settings and the system you want to generate the network for\n", - "CHARGE_MODEL = \"antechamber\" \n", + "CHARGE_MODEL = \"antechamber_am1bcc\" \n", + "# or\n", + "#CHARGE_MODEL = \"openeye_elf10\"\n", "SYSTEM_GROUP = \"jacs_set\"\n", "SYSTEM_NAME = \"tyk2\"" ] @@ -62,7 +64,7 @@ "network = gufe.LigandNetwork.from_graphml(system_dir.joinpath(\"lomap_network.graphml\").read_text())\n", "\n", "# load the ligands with charges\n", - "supplier = Chem.SDMolSupplier(system_dir.joinpath(f\"ligands_{CHARGE_MODEL}_am1bcc.sdf\"), removeHs=False)\n", + "supplier = Chem.SDMolSupplier(system_dir.joinpath(f\"ligands_{CHARGE_MODEL}.sdf\"), removeHs=False)\n", "ligands_by_name = {}\n", "for mol in supplier:\n", " ofe_mol = gufe.SmallMoleculeComponent.from_rdkit(mol)\n", @@ -72,7 +74,7 @@ "protein = gufe.ProteinComponent.from_pdb_file(system_dir.joinpath(\"protein.pdb\").as_posix())\n", "\n", "# check for cofactors\n", - "co_file = system_dir.joinpath(f\"cofactors_{CHARGE_MODEL}_am1bcc.sdf\")\n", + "co_file = system_dir.joinpath(f\"cofactors_{CHARGE_MODEL}.sdf\")\n", "cofactors = None\n", "if co_file.exists():\n", " cofactors = []\n", @@ -131,7 +133,7 @@ ], "metadata": { "kernelspec": { - "display_name": "openfe_env", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -145,9 +147,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.8" + "version": "3.12.10" } }, "nbformat": 4, - "nbformat_minor": 2 + "nbformat_minor": 4 }