Fix chem notebook formatting.

DS4SD · Jan 14, 2025 · 9835695 · 9835695
1 parent 2638ced
commit 9835695
Showing 1 changed file with 12 additions and 4 deletions.
diff --git a/examples/data_query_chemistry_patcid/chemistry_patcid.ipynb b/examples/data_query_chemistry_patcid/chemistry_patcid.ipynb
@@ -93,7 +93,7 @@
     "    CompoundsBySmarts,\n",
     "    CompoundsIn,\n",
     "    DocumentsByIds,\n",
-    "    DocumentsHaving\n",
+    "    DocumentsHaving,\n",
     ")\n",
     "from deepsearch.chemistry.queries.molecules import MolId, MolIdType, MolQueryType\n",
     "from deepsearch.cps.client.components.elastic import ElasticDataCollectionSource\n",
@@ -4538,7 +4538,9 @@
     "input_smarts = \"[#6]-[#16X3](-[#6]\"\n",
     "\n",
     "display(Markdown(\"### SMARTS\"))\n",
-    "display(Markdown(f\"We will list compounds that are described by SMARTS `{input_smarts}`\"))"
+    "display(\n",
+    "    Markdown(f\"We will list compounds that are described by SMARTS `{input_smarts}`\")\n",
+    ")"
    ]
   },
   {
@@ -8949,7 +8951,9 @@
     "\n",
     "patent_ids = [\"US10526338B%\"]\n",
     "\n",
-    "compounds = query_chemistry(api, CompoundsIn(documents=DocumentsByIds(publication_ids=patent_ids)), limit=20)\n",
+    "compounds = query_chemistry(\n",
+    "    api, CompoundsIn(documents=DocumentsByIds(publication_ids=patent_ids)), limit=20\n",
+    ")\n",
     "\n",
     "# Visualize results\n",
     "results_table = [c.model_dump() for c in compounds]\n",
@@ -10275,7 +10279,11 @@
     "\n",
     "input_smiles = \"C1(C(=C)C([O-])=C1C)=O\"\n",
     "\n",
-    "compounds = query_chemistry(api, DocumentsHaving(compounds=CompoundsBySubstructure(structure=input_smiles)), limit=20)\n",
+    "compounds = query_chemistry(\n",
+    "    api,\n",
+    "    DocumentsHaving(compounds=CompoundsBySubstructure(structure=input_smiles)),\n",
+    "    limit=20,\n",
+    ")\n",
     "\n",
     "# Visualize results\n",
     "results_table = [c.model_dump() for c in compounds]\n",