\n",
"
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n",
" jupyter labextension install jupyterlab_3dmol
\n",
"
\n",
""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"viewer = py3Dmol.view(width=300, height=300)\n",
"viewer.addModel(Chem.MolToMolBlock(imatinib), 'mol')\n",
"viewer.addModel(Chem.MolToMolBlock(mol_new), 'mol')\n",
"viewer.setStyle({\"stick\":{}})\n",
"viewer.zoomTo()\n",
"viewer.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Note you can perform a fragment grafting instead of embedding. See https://pschmidtke.github.io/blog/rdkit/3d-editor/2021/01/23/grafting-fragments.html"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.4"
}
},
"nbformat": 4,
"nbformat_minor": 4
}