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Demonstrating using chembl_downloader to get SDF path #12

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Demonstrating using chembl_downloader to get SDF path #12

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b608412
Demonstrating using chembl_downloader to get SDF path
cthoyt Dec 21, 2021
b9624ff
Update 2021-12-20-substructlibrary-search-order.ipynb
cthoyt Dec 21, 2021
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11 changes: 7 additions & 4 deletions _notebooks/2021-12-20-substructlibrary-search-order.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -61,15 +61,17 @@
"metadata": {},
"source": [
"Here's the code to build the `SubstructLibrary` from the sdf file distributed by the ChEMBL team. \n",
"This uses a feature added in RDKit v2021.09 to allow a molecule key (or name) to be stored with the molecules in a `SubstructLibrary`.\n",
"This uses a feature added in RDKit v2021.09 to allow a molecule key (or name) to be stored with the molecules in a `SubstructLibrary`. Note you'll need to `pip install chembl_downloader` to run this block.\n",
"\n",
"Executing this takes about 45 minutes on my machine."
]
},
{
"cell_type": "raw",
"cell_type": "markdown",
"metadata": {},
"source": [
"```python\n",
"import chembl_downloader\n",
"RDLogger.DisableLog(\"rdApp.warning\")\n",
"\n",
"molholder = rdSubstructLibrary.CachedTrustedSmilesMolHolder()\n",
Expand All @@ -79,7 +81,8 @@
"keys = rdSubstructLibrary.KeyFromPropHolder() \n",
"slib = rdSubstructLibrary.SubstructLibrary(molholder,patts,keys)\n",
"t1 = time.time()\n",
"with gzip.GzipFile('/home/glandrum/Downloads/chembl_29.sdf.gz') as gz, Chem.ForwardSDMolSupplier(gz) as suppl:\n",
"sdf_path = chembl_downloader.download_sdf(version=\"29\")\n",
"with gzip.open(sdf_path) as gz, Chem.ForwardSDMolSupplier(gz) as suppl:\n",
" nDone = 0\n",
" for m in suppl:\n",
" if m is None:\n",
Expand All @@ -96,7 +99,7 @@
"print(f'That took {time.time()-t1:.2f}s in total.')\n",
"with open('./results/chembl29_ssslib.pkl','wb+') as outf:\n",
" pickle.dump(slib,outf)\n",
" "
"```"
]
},
{
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