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Navan Chauhan <br> <a href="/feed.rss">RSS</a></p></div> - </div> -</div> - -<script> -let phrases = [ - "Something Funny", "Veni, vidi, vici", "Alea iacta est", "In vino veritas", "Acta, non verba", "Castigat ridendo mores", - "Cui bono?", "Memento vivere", "अहम् ब्रह्मास्मि", "अनुगच्छतु प्रवाहं", "चरन्मार्गान्विजानाति", "coq de cheval", "我愛啤酒" - ]; - -let new_phrase = phrases[Math.floor(Math.random()*phrases.length)]; - -let lead = document.getElementById("random-lead"); -lead.innerText = new_phrase; -</script> - <div class="content container"> - - <div class="post"> - <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">"Miniconda3-latest-Linux-x86_64.sh"</span><span class="p">,</span> - <span class="n">url_base</span><span class="o">=</span><span class="s2">"https://repo.continuum.io/miniconda/"</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">"~"</span><span class="p">,</span> <span class="s2">"miniconda"</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">"""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> - - </div> - <blockquote>If you have scrolled this far, consider subscribing to my mailing list <a href="https://listmonk.navan.dev/subscription/form">here.</a> You can subscribe to either a specific type of post you are interested in, or subscribe to everything with the "Everything" list.</blockquote> - <script data-isso="https://comments.navan.dev/" - src="https://comments.navan.dev/js/embed.min.js"></script> - <div id="isso-thread"> - <noscript>Javascript needs to be activated to view comments.</noscript> - </div> - - </div> - <script src="assets/manup.min.js"></script> - <script src="/pwabuilder-sw-register.js"></script> -</body> -</html>
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