docs/posts/2020-07-01-Install-rdkit-colab.html


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	<h1>Installing RDKit on Google Colab</h1>

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

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

</code></pre>

<h2>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="sd">&quot;&quot;&quot;install rdkit from miniconda</span>
<span class="sd">    ```</span>
<span class="sd">    import rdkit_installer</span>
<span class="sd">    rdkit_installer.install()</span>
<span class="sd">    ```</span>
<span class="sd">    &quot;&quot;&quot;</span>

    <span class="n">python_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">join</span><span class="p">(</span>
        <span class="n">conda_path</span><span class="p">,</span>
        <span class="s2">&quot;lib&quot;</span><span class="p">,</span>
        <span class="s2">&quot;python</span><span class="si">{0}</span><span class="s2">.</span><span class="si">{1}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">*</span><span class="n">sys</span><span class="o">.</span><span class="n">version_info</span><span class="p">),</span>
        <span class="s2">&quot;site-packages&quot;</span><span class="p">,</span>
    <span class="p">)</span>

    <span class="k">if</span> <span class="n">add_python_path</span> <span class="ow">and</span> <span class="n">python_path</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="p">:</span>
        <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;add </span><span class="si">{}</span><span class="s2"> to PYTHONPATH&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">python_path</span><span class="p">))</span>
        <span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">python_path</span><span class="p">)</span>

    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</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="n">python_path</span><span class="p">,</span> <span class="s2">&quot;rdkit&quot;</span><span class="p">)):</span>
        <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;rdkit is already installed&quot;</span><span class="p">)</span>
        <span class="k">if</span> <span class="ow">not</span> <span class="n">force</span><span class="p">:</span>
            <span class="k">return</span>

        <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;force re-install&quot;</span><span class="p">)</span>

    <span class="n">url</span> <span class="o">=</span> <span class="n">url_base</span> <span class="o">+</span> <span class="n">file_name</span>
    <span class="n">python_version</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="si">{0}</span><span class="s2">.</span><span class="si">{1}</span><span class="s2">.</span><span class="si">{2}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">*</span><span class="n">sys</span><span class="o">.</span><span class="n">version_info</span><span class="p">)</span>

    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;python version: </span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">python_version</span><span class="p">))</span>

    <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">conda_path</span><span class="p">):</span>
        <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">&quot;remove current miniconda&quot;</span><span class="p">)</span>
        <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">conda_path</span><span class="p">)</span>
    <span class="k">elif</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">conda_path</span><span class="p">):</span>
        <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">&quot;remove </span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">conda_path</span><span class="p">))</span>
        <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">conda_path</span><span class="p">)</span>

    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s1">&#39;fetching installer from </span><span class="si">{}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">url</span><span class="p">))</span>
    <span class="n">res</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">url</span><span class="p">,</span> <span class="n">stream</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
    <span class="n">res</span><span class="o">.</span><span class="n">raise_for_status</span><span class="p">()</span>
    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_name</span><span class="p">,</span> <span class="s1">&#39;wb&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
        <span class="k">for</span> <span class="n">chunk</span> <span class="ow">in</span> <span class="n">res</span><span class="o">.</span><span class="n">iter_content</span><span class="p">(</span><span class="n">chunk_size</span><span class="p">):</span>
            <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">chunk</span><span class="p">)</span>
    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s1">&#39;done&#39;</span><span class="p">)</span>

    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s1">&#39;installing miniconda to </span><span class="si">{}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">conda_path</span><span class="p">))</span>
    <span class="n">subprocess</span><span class="o">.</span><span class="n">check_call</span><span class="p">([</span><span class="s2">&quot;bash&quot;</span><span class="p">,</span> <span class="n">file_name</span><span class="p">,</span> <span class="s2">&quot;-b&quot;</span><span class="p">,</span> <span class="s2">&quot;-p&quot;</span><span class="p">,</span> <span class="n">conda_path</span><span class="p">])</span>
    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s1">&#39;done&#39;</span><span class="p">)</span>

    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;installing rdkit&quot;</span><span class="p">)</span>
    <span class="n">subprocess</span><span class="o">.</span><span class="n">check_call</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="n">conda_path</span><span class="p">,</span> <span class="s2">&quot;bin&quot;</span><span class="p">,</span> <span class="s2">&quot;conda&quot;</span><span class="p">),</span>
        <span class="s2">&quot;install&quot;</span><span class="p">,</span>
        <span class="s2">&quot;--yes&quot;</span><span class="p">,</span>
        <span class="s2">&quot;-c&quot;</span><span class="p">,</span> <span class="s2">&quot;rdkit&quot;</span><span class="p">,</span>
        <span class="s2">&quot;python==</span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">python_version</span><span class="p">),</span>
        <span class="s2">&quot;rdkit&quot;</span> <span class="k">if</span> <span class="n">rdkit_version</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="s2">&quot;rdkit==</span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">rdkit_version</span><span class="p">)])</span>
    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;done&quot;</span><span class="p">)</span>

    <span class="kn">import</span> <span class="nn">rdkit</span>
    <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;rdkit-</span><span class="si">{}</span><span class="s2"> installation finished!&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">rdkit</span><span class="o">.</span><span class="n">__version__</span><span class="p">))</span>


<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
    <span class="n">install</span><span class="p">()</span>
</code></pre></div>

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