diff --git a/openad/notebooks/Bio_Medical_Properties.ipynb b/openad/notebooks/Bio_Medical_Properties.ipynb
index 0977a294..2ae8efdd 100644
--- a/openad/notebooks/Bio_Medical_Properties.ipynb
+++ b/openad/notebooks/Bio_Medical_Properties.ipynb
@@ -2,12 +2,198 @@
"cells": [
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 1,
"id": "3d7c5ff1-94f6-4a37-9611-ad074587b230",
"metadata": {
"tags": []
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ ""
+ ],
+ "text/plain": [
+ ""
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"%reload_ext openad.notebooks.styles"
]
@@ -502,7 +688,7 @@
},
"outputs": [],
"source": [
- "%openadd model service status"
+ "%openad model service status"
]
},
{
@@ -1136,9 +1322,9 @@
],
"metadata": {
"kernelspec": {
- "display_name": "ad-venv",
+ "display_name": "test_venv",
"language": "python",
- "name": "ad-venv"
+ "name": "test_venv"
},
"language_info": {
"codemirror_mode": {
@@ -1150,7 +1336,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.11.11"
+ "version": "3.11.9"
}
},
"nbformat": 4,
diff --git a/openad/notebooks/Common_Client_Intro.ipynb b/openad/notebooks/Common_Client_Intro.ipynb
index 871b0194..1245933d 100644
--- a/openad/notebooks/Common_Client_Intro.ipynb
+++ b/openad/notebooks/Common_Client_Intro.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 43,
+ "execution_count": 1,
"id": "6b8a0da0-f81c-4872-8ac0-081189c73d35",
"metadata": {
"tags": []
@@ -941,7 +941,7 @@
"# %openad clear sessions\n",
"# %openad create workspace foobar\n",
"# %openad set workspace default\n",
- "%openad copy file 'imported_molecules.csv' to '~/foobar'"
+ "%openad copy 'imported_molecules.csv' to '~/foobar'"
]
},
{
@@ -1148,9 +1148,9 @@
],
"metadata": {
"kernelspec": {
- "display_name": "ad-venv",
+ "display_name": "test_venv",
"language": "python",
- "name": "ad-venv"
+ "name": "test_venv"
},
"language_info": {
"codemirror_mode": {
@@ -1162,7 +1162,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.11.11"
+ "version": "3.11.9"
}
},
"nbformat": 4,
diff --git a/openad/notebooks/Demonstration.ipynb b/openad/notebooks/Demonstration.ipynb
index 7bbdc3e6..e59ea0db 100644
--- a/openad/notebooks/Demonstration.ipynb
+++ b/openad/notebooks/Demonstration.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 47,
+ "execution_count": 1,
"id": "cfd86401-463d-4ba2-92ba-d4764ef72ee4",
"metadata": {
"tags": []
@@ -1107,9 +1107,9 @@
],
"metadata": {
"kernelspec": {
- "display_name": "ad-venv",
+ "display_name": "test_venv",
"language": "python",
- "name": "ad-venv"
+ "name": "test_venv"
},
"language_info": {
"codemirror_mode": {
@@ -1121,7 +1121,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.11.11"
+ "version": "3.11.9"
}
},
"nbformat": 4,
diff --git a/openad/notebooks/End_to_End.ipynb b/openad/notebooks/End_to_End.ipynb
index 16116e85..45b0e27f 100644
--- a/openad/notebooks/End_to_End.ipynb
+++ b/openad/notebooks/End_to_End.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 27,
+ "execution_count": 1,
"id": "684f2227-0d30-4f9f-88b2-08eade6ae0ac",
"metadata": {
"tags": []
@@ -466,9 +466,9 @@
"patented_molecules = []\n",
"for result in datasets:\n",
" for mol in result[\"0\"].to_list():\n",
- " x = %openadd search for patents containing molecule '{mol}'\n",
+ " x = %openadd ds search for patents containing molecule '{mol}'\n",
" if isinstance(x, DataFrame):\n",
- " patents_to_search.extend(x[\"PATENT ID\"].to_list())\n",
+ " patents_to_search.extend(x[\"application_id\"].to_list())\n",
" patented_molecules.append(mol)\n",
"\n",
"str(patents_to_search)"
@@ -522,10 +522,10 @@
" \"esol\",\n",
"]\n",
"\n",
- "new_props = %openadd propd get molecule property {properties_all} for {patented_molecules}\n",
+ "new_props = %openadd prop get molecule property {properties_all} for {patented_molecules}\n",
"\n",
"for x in patented_molecules:\n",
- " %openad add molecule {x} Force\n",
+ " %openad add molecule {x} force\n",
"\n",
"%openad merge molecules data using dataframe new_props\n",
"%openad enrich molecules with analysis"
@@ -579,9 +579,9 @@
],
"metadata": {
"kernelspec": {
- "display_name": "ad-venv",
+ "display_name": "test_venv",
"language": "python",
- "name": "ad-venv"
+ "name": "test_venv"
},
"language_info": {
"codemirror_mode": {
diff --git a/openad/notebooks/Generation_Models.ipynb b/openad/notebooks/Generation_Models.ipynb
index a4f296a7..22d671aa 100644
--- a/openad/notebooks/Generation_Models.ipynb
+++ b/openad/notebooks/Generation_Models.ipynb
@@ -2,12 +2,198 @@
"cells": [
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 1,
"id": "58fb5d0e-b78b-4063-88f8-9e8569eef4ce",
"metadata": {
"tags": []
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ ""
+ ],
+ "text/plain": [
+ ""
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"%reload_ext openad.notebooks.styles"
]
@@ -678,7 +864,7 @@
},
"outputs": [],
"source": [
- "%openadd gen generate with SMILESLSTMPPOGenerator data for \"{'isomer_scorer': {'target': 5.0, 'target_smile': 'NCCCCC'}}\" \\\n",
+ "%openad gen generate with SMILESLSTMPPOGenerator data for \"{'isomer_scorer': {'target': 5.0, 'target_smile': 'NCCCCC'}}\" \\\n",
"sample 20 using (num_epochs=2 episode_size=10 optimize_batch_size=2)"
]
},
@@ -699,7 +885,7 @@
},
"outputs": [],
"source": [
- "%openadd gen generate with SMILESLSTMHCGenerator data for \"{'isomer_scorer': {'target': 5.0, 'target_smile': 'NCCCCC'}}\" \\\n",
+ "%openad gen generate with SMILESLSTMHCGenerator data for \"{'isomer_scorer': {'target': 5.0, 'target_smile': 'NCCCCC'}}\" \\\n",
"sample 20 using( mols_to_sample=100 max_len=2 optimize_batch_size=3 n_epochs=2 random_start=True)"
]
},
@@ -815,7 +1001,7 @@
},
"outputs": [],
"source": [
- "%openadd gen generate with CatalystGenerator data for 1 sample 20"
+ "%openad gen generate with CatalystGenerator data for 1 sample 20"
]
},
{
@@ -827,7 +1013,7 @@
},
"outputs": [],
"source": [
- "%openadd gen generate with CatalystGenerator data for 10 sample 20 using ( number_of_points=32 number_of_steps=50 generated_length=100)"
+ "%openad gen generate with CatalystGenerator data for 10 sample 20 using ( number_of_points=32 number_of_steps=50 generated_length=100)"
]
},
{
@@ -866,9 +1052,9 @@
],
"metadata": {
"kernelspec": {
- "display_name": "ad-venv",
+ "display_name": "test_venv",
"language": "python",
- "name": "ad-venv"
+ "name": "test_venv"
},
"language_info": {
"codemirror_mode": {
diff --git a/openad/notebooks/Slide_Show.ipynb b/openad/notebooks/Slide_Show.ipynb
index dcbeb344..766aaed7 100644
--- a/openad/notebooks/Slide_Show.ipynb
+++ b/openad/notebooks/Slide_Show.ipynb
@@ -10,15 +10,198 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 1,
"id": "2fe2630a-7eb1-4914-a249-836e88883433",
"metadata": {
- "jupyter": {
- "source_hidden": true
- },
"tags": []
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ ""
+ ],
+ "text/plain": [
+ ""
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"%reload_ext openad.notebooks.styles"
]
@@ -453,9 +636,9 @@
"header": "Hello
"
},
"kernelspec": {
- "display_name": "ad-venv",
+ "display_name": "test_venv",
"language": "python",
- "name": "ad-venv"
+ "name": "test_venv"
},
"language_info": {
"codemirror_mode": {
@@ -467,7 +650,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.11.11"
+ "version": "3.11.9"
}
},
"nbformat": 4,
diff --git a/openad/notebooks/Table_of_Contents.ipynb b/openad/notebooks/Table_of_Contents.ipynb
index 2b3940f5..7a0bac76 100644
--- a/openad/notebooks/Table_of_Contents.ipynb
+++ b/openad/notebooks/Table_of_Contents.ipynb
@@ -4,19 +4,195 @@
"cell_type": "code",
"execution_count": 1,
"metadata": {
- "execution": {
- "iopub.execute_input": "2025-02-09T23:39:17.262566Z",
- "iopub.status.busy": "2025-02-09T23:39:17.262341Z",
- "iopub.status.idle": "2025-02-09T23:39:17.270720Z",
- "shell.execute_reply": "2025-02-09T23:39:17.270126Z",
- "shell.execute_reply.started": "2025-02-09T23:39:17.262545Z"
- },
- "jupyter": {
- "source_hidden": true
- },
"tags": []
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ ""
+ ],
+ "text/plain": [
+ ""
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"%reload_ext openad.notebooks.styles"
]
@@ -300,9 +476,9 @@
],
"metadata": {
"kernelspec": {
- "display_name": "ad-venv",
+ "display_name": "test_venv",
"language": "python",
- "name": "ad-venv"
+ "name": "test_venv"
},
"language_info": {
"codemirror_mode": {
@@ -314,7 +490,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.11.11"
+ "version": "3.11.9"
}
},
"nbformat": 4,
diff --git a/openad/notebooks/Untitled.ipynb b/openad/notebooks/Untitled.ipynb
deleted file mode 100644
index 8a48fc22..00000000
--- a/openad/notebooks/Untitled.ipynb
+++ /dev/null
@@ -1,63 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "code",
- "execution_count": 1,
- "id": "75826030-a7d1-4e4f-a17a-43ad67df3643",
- "metadata": {},
- "outputs": [
- {
- "data": {
- "application/vnd.jupyter.widget-view+json": {
- "model_id": "b0ae76f72c6b4b6a8779477505df7dc8",
- "version_major": 2,
- "version_minor": 0
- },
- "text/plain": [
- "Output()"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- },
- {
- "data": {
- "text/markdown": [
- "The server returned an empty response
\n",
- "{'response': {'payload': None, 'metadata': {'uiMessages': {'errors': [{'code': None, 'message': 'RESOURCE_NOT_FOUND', 'type': 'ERROR', 'description': None, 'fieldId': None, 'target': 'TOAST', 'duration': 10000}], 'infos': [], 'warnings': []}, 'extendedPagination': {}}}}
\n"
- ],
- "text/plain": [
- ""
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
- "source": [
- "%openad rxn predict retro {smiles} using (max_steps=5) use cache return df"
- ]
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "ad-venv",
- "language": "python",
- "name": "ad-venv"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.11.11"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}
diff --git a/openad/notebooks/magic_commands.ipynb b/openad/notebooks/magic_commands.ipynb
index b460c2ca..499573a4 100644
--- a/openad/notebooks/magic_commands.ipynb
+++ b/openad/notebooks/magic_commands.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": 1,
"id": "93aa997a-e74f-4412-915f-68a4ba8cd536",
"metadata": {
"tags": []
@@ -322,9 +322,9 @@
],
"metadata": {
"kernelspec": {
- "display_name": "ad-venv",
+ "display_name": "test_venv",
"language": "python",
- "name": "ad-venv"
+ "name": "test_venv"
},
"language_info": {
"codemirror_mode": {
@@ -336,7 +336,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.11.11"
+ "version": "3.11.9"
}
},
"nbformat": 4,
diff --git a/openad/notebooks/openad_magic.ipynb b/openad/notebooks/openad_magic.ipynb
index 6798c0fa..7ed99ef1 100644
--- a/openad/notebooks/openad_magic.ipynb
+++ b/openad/notebooks/openad_magic.ipynb
@@ -2,12 +2,198 @@
"cells": [
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 1,
"id": "76fef9af-5e24-4420-b7db-f8ff61a90b06",
"metadata": {
"tags": []
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ ""
+ ],
+ "text/plain": [
+ ""
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"%reload_ext openad.notebooks.styles"
]
@@ -152,9 +338,9 @@
],
"metadata": {
"kernelspec": {
- "display_name": "ad-venv",
+ "display_name": "test_venv",
"language": "python",
- "name": "ad-venv"
+ "name": "test_venv"
},
"language_info": {
"codemirror_mode": {
@@ -166,7 +352,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.11.11"
+ "version": "3.11.9"
}
},
"nbformat": 4,
diff --git a/openad/notebooks/plugin_ds_demo.ipynb b/openad/notebooks/plugin_ds_demo.ipynb
index 22fabf6f..5f1edf5c 100644
--- a/openad/notebooks/plugin_ds_demo.ipynb
+++ b/openad/notebooks/plugin_ds_demo.ipynb
@@ -2,15 +2,198 @@
"cells": [
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 1,
"id": "83f5abe4-7205-4fc1-a2bf-a75c76bbbd23",
"metadata": {
- "jupyter": {
- "source_hidden": true
- },
"tags": []
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ ""
+ ],
+ "text/plain": [
+ ""
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"%reload_ext openad.notebooks.styles"
]
@@ -912,9 +1095,9 @@
],
"metadata": {
"kernelspec": {
- "display_name": "ad-venv",
+ "display_name": "test_venv",
"language": "python",
- "name": "ad-venv"
+ "name": "test_venv"
},
"language_info": {
"codemirror_mode": {
@@ -926,7 +1109,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.11.11"
+ "version": "3.11.9"
}
},
"nbformat": 4,
diff --git a/openad/notebooks/plugin_rxn_demo.ipynb b/openad/notebooks/plugin_rxn_demo.ipynb
index a08a844f..8db5aa1e 100644
--- a/openad/notebooks/plugin_rxn_demo.ipynb
+++ b/openad/notebooks/plugin_rxn_demo.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": 1,
"id": "83f5abe4-7205-4fc1-a2bf-a75c76bbbd23",
"metadata": {
"tags": []
@@ -718,16 +718,6 @@
"%openad rxn predict retro {smiles} using (max_steps=5) use cache return df"
]
},
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "034ed2d6-0d50-447c-9367-a991c5fda461",
- "metadata": {},
- "outputs": [],
- "source": [
- "%openad predict test"
- ]
- },
{
"cell_type": "code",
"execution_count": null,
@@ -909,9 +899,9 @@
],
"metadata": {
"kernelspec": {
- "display_name": "ad-venv",
+ "display_name": "test_venv",
"language": "python",
- "name": "ad-venv"
+ "name": "test_venv"
},
"language_info": {
"codemirror_mode": {
@@ -923,7 +913,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.11.11"
+ "version": "3.11.9"
}
},
"nbformat": 4,
diff --git a/openad/notebooks/property_generation.ipynb b/openad/notebooks/property_generation.ipynb
index b2b0c4b4..7a17df46 100644
--- a/openad/notebooks/property_generation.ipynb
+++ b/openad/notebooks/property_generation.ipynb
@@ -2,12 +2,198 @@
"cells": [
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 1,
"id": "0563d9be-7898-4c39-ae8c-35dc6a0d8fc2",
"metadata": {
"tags": []
},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ ""
+ ],
+ "text/plain": [
+ ""
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"%reload_ext openad.notebooks.styles"
]
@@ -601,9 +787,9 @@
],
"metadata": {
"kernelspec": {
- "display_name": "ad-venv",
+ "display_name": "test_venv",
"language": "python",
- "name": "ad-venv"
+ "name": "test_venv"
},
"language_info": {
"codemirror_mode": {