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	<h1 id="installing-rdkit-on-google-colab">Installing RDKit on Google Colab</h1>

<p><strong>Update: March 2024</strong> </p>

<p><code>rdkit-pypi</code> has been deprecated in favour of <code>rdkit</code></p>

<p>You can simply run:</p>

<pre><code>!pip install rdkit
</code></pre>

<p><strong>EDIT:</strong> Try installing RDKit using pip</p>

<pre><code>!pip install rdkit-pypi

</code></pre>

<h2 id="old-method-still-works">Old Method (Still Works)</h2>

<p>RDKit is one of the most integral part of any Cheminfomatic specialist's toolkit but it is notoriously difficult to install unless you already have <code>conda</code> installed. I originally found this in a GitHub Gist but I have not been able to find that gist again :/ </p>

<p>Just copy and paste this in a Colab cell and it will install it 👍</p>

<div class="codehilite">
<pre><span></span><code><span class="kn">import</span> <span class="nn">sys</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">requests</span>
<span class="kn">import</span> <span class="nn">subprocess</span>
<span class="kn">import</span> <span class="nn">shutil</span>
<span class="kn">from</span> <span class="nn">logging</span> <span class="kn">import</span> <span class="n">getLogger</span><span class="p">,</span> <span class="n">StreamHandler</span><span class="p">,</span> <span class="n">INFO</span>


<span class="n">logger</span> <span class="o">=</span> <span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
<span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">StreamHandler</span><span class="p">())</span>
<span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">INFO</span><span class="p">)</span>


<span class="k">def</span> <span class="nf">install</span><span class="p">(</span>
        <span class="n">chunk_size</span><span class="o">=</span><span class="mi">4096</span><span class="p">,</span>
        <span class="n">file_name</span><span class="o">=</span><span class="s2">&quot;Miniconda3-latest-Linux-x86_64.sh&quot;</span><span class="p">,</span>
        <span class="n">url_base</span><span class="o">=</span><span class="s2">&quot;https://repo.continuum.io/miniconda/&quot;</span><span class="p">,</span>
        <span class="n">conda_path</span><span class="o">=</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expanduser</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s2">&quot;~&quot;</span><span class="p">,</span> <span class="s2">&quot;miniconda&quot;</span><span class="p">)),</span>
        <span class="n">rdkit_version</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
        <span class="n">add_python_path</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
        <span class="n">force</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
    <span class="s2">&quot;&quot;&quot;install rdkit from miniconda</span>
<span class="s2">   </span>
</code></pre>
</div>

<pre><code>import rdkit_installer
rdkit_installer.install()
```
"""

python_path = os.path.join(
    conda_path,
    "lib",
    "python{0}.{1}".format(*sys.version_info),
    "site-packages",
)

if add_python_path and python_path not in sys.path:
    logger.info("add {} to PYTHONPATH".format(python_path))
    sys.path.append(python_path)

if os.path.isdir(os.path.join(python_path, "rdkit")):
    logger.info("rdkit is already installed")
    if not force:
        return

    logger.info("force re-install")

url = url_base + file_name
python_version = "{0}.{1}.{2}".format(*sys.version_info)

logger.info("python version: {}".format(python_version))

if os.path.isdir(conda_path):
    logger.warning("remove current miniconda")
    shutil.rmtree(conda_path)
elif os.path.isfile(conda_path):
    logger.warning("remove {}".format(conda_path))
    os.remove(conda_path)

logger.info('fetching installer from {}'.format(url))
res = requests.get(url, stream=True)
res.raise_for_status()
with open(file_name, 'wb') as f:
    for chunk in res.iter_content(chunk_size):
        f.write(chunk)
logger.info('done')

logger.info('installing miniconda to {}'.format(conda_path))
subprocess.check_call(["bash", file_name, "-b", "-p", conda_path])
logger.info('done')

logger.info("installing rdkit")
subprocess.check_call([
    os.path.join(conda_path, "bin", "conda"),
    "install",
    "--yes",
    "-c", "rdkit",
    "python=={}".format(python_version),
    "rdkit" if rdkit_version is None else "rdkit=={}".format(rdkit_version)])
logger.info("done")

import rdkit
logger.info("rdkit-{} installation finished!".format(rdkit.__version__))
</code></pre>

<p>if <strong>name</strong> == "<strong>main</strong>":
    install()
```</p>

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