add -q flag

showcase/openfe_showcase.ipynb

@@ -113,7 +113,7 @@
     "    import condacolab\n",
     "    import locale\n",
     "    locale.getpreferredencoding = lambda: \"UTF-8\"\n",
-    "    !mamaba install openfe\n",
+    "    !mamba -q install openfe\n",
     "    !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
     "    for _ in range(3):\n",
     "      # Sometimes we have to re-run the check\n",

showcase/showcase.py

@@ -0,0 +1,36 @@
+import openfe
+from rdkit import Chem
+from rdkit.Chem import AllChem
+from openfe import SmallMoleculeComponent
+from openfe.setup import LomapAtomMapper
+# from openfe.setup.ligand_network_planning import generate_lomap_network
+
+import lomap
+
+# Extract the contents of the sdf file and visualise it
+ligands_rdmol = [
+    mol for mol in Chem.SDMolSupplier("inputs/tyk2_ligands.sdf", removeHs=False)
+]
+
+for ligand in ligands_rdmol:
+    AllChem.Compute2DCoords(ligand)
+
+Chem.Draw.MolsToGridImage(ligands_rdmol)
+
+
+# Load ligands using RDKit
+ligands_sdf = Chem.SDMolSupplier("inputs/tyk2_ligands.sdf", removeHs=False)
+
+# Now pass these to form a list of Molecules
+ligand_mols = [SmallMoleculeComponent(sdf) for sdf in ligands_sdf]
+
+mapper = LomapAtomMapper()
+lomap_mapping = next(mapper.suggest_mappings(ligand_mols[0], ligand_mols[4]))
+
+lomap_network = lomap.generate_lomap_network(
+    molecules=ligand_mols,
+    scorer=openfe.lomap_scorers.default_lomap_score,
+    mappers=[
+        LomapAtomMapper(),
+    ],
+)