feat: Chemistry Queries for PatCID2 (#76)

* Update patcid examples with new query methods. Signed-off-by: DKL <[email protected]> * Fix chem notebook formatting. Signed-off-by: DKL <[email protected]> * feat!: Update examples with new toolkit version (#77) * updated examples with new conversion changes in toolkit. Signed-off-by: Tiago Santana <[email protected]> * fix conversion settings example in upload_explore_donwlad_pdfs Signed-off-by: Tiago Santana <[email protected]> * Small fixes to upload_and_explore example Signed-off-by: Viktor Kuropiatnyk <[email protected]> * fix download of kg and add validation of file exists. few typo fix Signed-off-by: Tiago Santana <[email protected]> * changed deepsearch-toolkit dep to version 2.0.0 Signed-off-by: Tiago Santana <[email protected]> --------- Signed-off-by: Tiago Santana <[email protected]> Signed-off-by: Viktor Kuropiatnyk <[email protected]> Co-authored-by: Viktor Kuropiatnyk <[email protected]> Signed-off-by: DKL <[email protected]> * Update patcid examples with new query methods. Signed-off-by: DKL <[email protected]> --------- Signed-off-by: DKL <[email protected]> Signed-off-by: Tiago Santana <[email protected]> Signed-off-by: Viktor Kuropiatnyk <[email protected]> Co-authored-by: Tiago Santana <[email protected]> Co-authored-by: Viktor Kuropiatnyk <[email protected]>
DS4SD · Jan 29, 2025 · 1ab45f1 · 1ab45f1
1 parent 1f13c27
commit 1ab45f1
Showing 1 changed file with 11 additions and 7 deletions.
diff --git a/examples/data_query_chemistry_patcid/chemistry_patcid.ipynb b/examples/data_query_chemistry_patcid/chemistry_patcid.ipynb
@@ -37,7 +37,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 17,
    "id": "4a9b4de7-bace-4c39-a4e7-b563292a2a30",
    "metadata": {},
    "outputs": [],
@@ -68,7 +68,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 18,
    "id": "1ea3cd26",
    "metadata": {},
    "outputs": [],
@@ -86,10 +86,14 @@
     "import deepsearch as ds\n",
     "from deepsearch.cps.client.api import CpsApi\n",
     "from deepsearch.cps.client.components.elastic import ElasticDataCollectionSource\n",
-    "from deepsearch.chemistry.queries.molecules import (\n",
-    "    MoleculeQuery,\n",
-    "    MoleculesInPatentsQuery,\n",
-    "    PatentsWithMoleculesQuery,\n",
+    "from deepsearch.chemistry.queries import (\n",
+    "    query_chemistry,\n",
+    "    CompoundsBySubstructure,\n",
+    "    CompoundsBySimilarity,\n",
+    "    CompoundsBySmarts,\n",
+    "    CompoundsIn,\n",
+    "    DocumentsByIds,\n",
+    "    DocumentsHaving,\n",
     ")\n",
     "from deepsearch.chemistry.queries import (\n",
     "    query_chemistry,\n",
@@ -119,7 +123,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 19,
    "id": "fae4dee3",
    "metadata": {},
    "outputs": [