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Merged
PhillipDowney merged 8 commits into from
May 29, 2025
Merged

Notebook edits #144

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6de1d1c
demo service wip
themoenen May 21, 2025
1a6dad6
Merge branch 'main' of github.com:acceleratedscience/openad-toolkit
themoenen May 22, 2025
6680dcb
merge
themoenen May 23, 2025
a7a2b98
Merge branch 'main' of github.com:acceleratedscience/openad-toolkit
themoenen May 28, 2025
efa830a
Fixed notebooks
themoenen May 28, 2025
696eb56
cleanup for PR
themoenen May 29, 2025
84253ab
styling & cleanup
themoenen May 29, 2025
7557873
Replace %openadd with %openad in Generation.ipynb
themoenen May 29, 2025
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198 changes: 192 additions & 6 deletions openad/notebooks/Bio_Medical_Properties.ipynb
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10 changes: 5 additions & 5 deletions openad/notebooks/Common_Client_Intro.ipynb
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Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 43,
"execution_count": 1,
"id": "6b8a0da0-f81c-4872-8ac0-081189c73d35",
"metadata": {
"tags": []
Expand Down Expand Up @@ -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'"
]
},
{
Expand Down Expand Up @@ -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": {
Expand All @@ -1162,7 +1162,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.11"
"version": "3.11.9"
}
},
"nbformat": 4,
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8 changes: 4 additions & 4 deletions openad/notebooks/Demonstration.ipynb
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Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 47,
"execution_count": 1,
"id": "cfd86401-463d-4ba2-92ba-d4764ef72ee4",
"metadata": {
"tags": []
Expand Down Expand Up @@ -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": {
Expand All @@ -1121,7 +1121,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.11"
"version": "3.11.9"
}
},
"nbformat": 4,
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14 changes: 7 additions & 7 deletions openad/notebooks/End_to_End.ipynb
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Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 27,
"execution_count": 1,
"id": "684f2227-0d30-4f9f-88b2-08eade6ae0ac",
"metadata": {
"tags": []
Expand Down Expand Up @@ -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)"
Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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": {
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202 changes: 194 additions & 8 deletions openad/notebooks/Generation_Models.ipynb
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199 changes: 191 additions & 8 deletions openad/notebooks/Slide_Show.ipynb
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204 changes: 190 additions & 14 deletions openad/notebooks/Table_of_Contents.ipynb
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63 changes: 0 additions & 63 deletions openad/notebooks/Untitled.ipynb
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8 changes: 4 additions & 4 deletions openad/notebooks/magic_commands.ipynb
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Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 1,
"id": "93aa997a-e74f-4412-915f-68a4ba8cd536",
"metadata": {
"tags": []
Expand Down Expand Up @@ -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": {
Expand All @@ -336,7 +336,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.11"
"version": "3.11.9"
}
},
"nbformat": 4,
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196 changes: 191 additions & 5 deletions openad/notebooks/openad_magic.ipynb
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199 changes: 191 additions & 8 deletions openad/notebooks/plugin_ds_demo.ipynb
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18 changes: 4 additions & 14 deletions openad/notebooks/plugin_rxn_demo.ipynb
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Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 1,
"id": "83f5abe4-7205-4fc1-a2bf-a75c76bbbd23",
"metadata": {
"tags": []
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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": {
Expand All @@ -923,7 +913,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.11"
"version": "3.11.9"
}
},
"nbformat": 4,
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