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diff --git a/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL/index.html b/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL/index.html index f7ac7fa..0da2ef5 100644 --- a/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL/index.html +++ b/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL/index.html @@ -1,8 +1,8 @@ -<!DOCTYPE html><html lang="en"><head><meta charset="UTF-8"/><meta name="og:site_name" content="Navan Chauhan"/><link rel="canonical" href="https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL"/><meta name="twitter:url" content="https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL"/><meta name="og:url" content="https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL"/><title>Workflow for Lightning Fast Molecular Docking Part One | Navan Chauhan</title><meta name="twitter:title" content="Workflow for Lightning Fast Molecular Docking Part One | Navan Chauhan"/><meta name="og:title" content="Workflow for Lightning Fast Molecular Docking Part One | Navan Chauhan"/><meta name="description" content="This is my workflow for lightning fast molecular docking."/><meta name="twitter:description" content="This is my workflow for lightning fast molecular docking."/><meta name="og:description" content="This is my workflow for lightning fast molecular docking."/><meta name="twitter:card" content="summary"/><link rel="stylesheet" href="/styles.css" type="text/css"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><link rel="shortcut icon" href="/images/favicon.png" type="image/png"/><link rel="alternate" href="/feed.rss" type="application/rss+xml" title="Subscribe to Navan Chauhan"/><meta name="twitter:image" content="https://navanchauhan.github.io/images/logo.png"/><meta name="og:image" content="https://navanchauhan.github.io/images/logo.png"/></head><head><script src="https://www.googletagmanager.com/gtag/js?id=UA-108635191-1v"></script><script>window.dataLayer = window.dataLayer || [];function gtag(){dataLayer.push(arguments);}gtag('js', new Date());gtag('config', 'UA-108635191-1');</script></head><body class="item-page"><header><div class="wrapper"><a class="site-name" href="/">Navan Chauhan</a><nav><ul><li><a href="/about">About Me</a></li><li><a class="selected" href="/posts">Posts</a></li><li><a href="/publications">Publications</a></li><li><a href="/assets/résumé.pdf">Résumé</a></li><li><a href="https://navanchauhan.github.io/repo">Repo</a></li></ul></nav></div></header><div class="wrapper"><article><div class="content"><span class="reading-time">2 minute read</span><span class="reading-time">Created on June 1, 2020</span><h1>Workflow for Lightning Fast Molecular Docking Part One</h1><h2>My Setup</h2><ul><li>macOS Catalina ( RIP 32bit app)</li><li>PyMOL</li><li>AutoDock Vina</li><li>Open Babel</li></ul><h2>One Command Docking</h2><pre><code><div class="highlight"><span></span>obabel -:<span class="s2">"</span><span class="k">$(</span>pbpaste<span class="k">)</span><span class="s2">"</span> --gen3d -opdbqt -Otest.pdbqt <span class="o">&&</span> vina --receptor lu.pdbqt --center_x -9.7 --center_y <span class="m">11</span>.4 --center_z <span class="m">68</span>.9 --size_x <span class="m">19</span>.3 --size_y <span class="m">29</span>.9 --size_z <span class="m">21</span>.3 --ligand test.pdbqt +<!DOCTYPE html><html lang="en"><head><meta charset="UTF-8"/><meta name="og:site_name" content="Navan Chauhan"/><link rel="canonical" href="https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL"/><meta name="twitter:url" content="https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL"/><meta name="og:url" content="https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL"/><title>Workflow for Lightning Fast Molecular Docking Part One | Navan Chauhan</title><meta name="twitter:title" content="Workflow for Lightning Fast Molecular Docking Part One | Navan Chauhan"/><meta name="og:title" content="Workflow for Lightning Fast Molecular Docking Part One | Navan Chauhan"/><meta name="description" content="This is my workflow for lightning fast molecular docking."/><meta name="twitter:description" content="This is my workflow for lightning fast molecular docking."/><meta name="og:description" content="This is my workflow for lightning fast molecular docking."/><meta name="twitter:card" content="summary"/><link rel="stylesheet" href="/styles.css" type="text/css"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><link rel="shortcut icon" href="/images/favicon.png" type="image/png"/><link rel="alternate" href="/feed.rss" type="application/rss+xml" title="Subscribe to Navan Chauhan"/><meta name="twitter:image" content="https://navanchauhan.github.io/images/logo.png"/><meta name="og:image" content="https://navanchauhan.github.io/images/logo.png"/></head><head><script src="https://www.googletagmanager.com/gtag/js?id=UA-108635191-1v"></script><script>window.dataLayer = window.dataLayer || [];function gtag(){dataLayer.push(arguments);}gtag('js', new Date());gtag('config', 'UA-108635191-1');</script></head><body class="item-page"><header><div class="wrapper"><a class="site-name" href="/">Navan Chauhan</a><nav><ul><li><a href="/about">About Me</a></li><li><a class="selected" href="/posts">Posts</a></li><li><a href="/publications">Publications</a></li><li><a href="/assets/résumé.pdf">Résumé</a></li><li><a href="https://navanchauhan.github.io/repo">Repo</a></li></ul></nav></div></header><div class="wrapper"><article><div class="content"><span class="reading-time">2 minute read</span><span class="reading-time">Created on June 1, 2020</span><span class="reading-time">Last modified on June 2, 2020</span><h1>Workflow for Lightning Fast Molecular Docking Part One</h1><h2>My Setup</h2><ul><li>macOS Catalina ( RIP 32bit app)</li><li>PyMOL</li><li>AutoDock Vina</li><li>Open Babel</li></ul><h2>One Command Docking</h2><pre><code><div class="highlight"><span></span>obabel -:<span class="s2">"</span><span class="k">$(</span>pbpaste<span class="k">)</span><span class="s2">"</span> --gen3d -opdbqt -Otest.pdbqt <span class="o">&&</span> vina --receptor lu.pdbqt --center_x -9.7 --center_y <span class="m">11</span>.4 --center_z <span class="m">68</span>.9 --size_x <span class="m">19</span>.3 --size_y <span class="m">29</span>.9 --size_z <span class="m">21</span>.3 --ligand test.pdbqt </div></code></pre><p>To run this command you simple copy the SMILES structure of the ligand you want an it automatically takes it from your clipboard, generates the 3D structure in the AutoDock PDBQT format using Open Babel and then docks it with your receptor using AutoDock Vina, all with just one command.</p><p>Let me break down the commands</p><pre><code><div class="highlight"><span></span>obabel -:<span class="s2">"</span><span class="k">$(</span>pbpaste<span class="k">)</span><span class="s2">"</span> --gen3d -opdbqt -Otest.pdbqt </div></code></pre><p><code>pbpaste</code> and <code>pbcopy</code> are macOS commands for pasting and copying from and to the clipboard. Linux users may install the <code>xclip</code> and <code>xsel</code> packages from their respective package managers and then insert these aliases into their bash_profile, zshrc e.t.c</p><pre><code><div class="highlight"><span></span><span class="nb">alias</span> <span class="nv">pbcopy</span><span class="o">=</span><span class="s1">'xclip -selection clipboard'</span> <span class="nb">alias</span> <span class="nv">pbpaste</span><span class="o">=</span><span class="s1">'xclip -selection clipboard -o'</span> </div></code></pre><pre><code><div class="highlight"><span></span><span class="k">$(</span>pbpaste<span class="k">)</span> </div></code></pre><p>This is used in bash to evaluate the results of a command. In this scenario we are using it to get the contents of the clipboard.</p><p>The rest of the command is a normal Open Babel command to generate a 3D structure in PDBQT format and then save it as <code>test.pdbqt</code></p><pre><code><div class="highlight"><span></span><span class="o">&&</span> </div></code></pre><p>This tells the termianl to only run the next part if the previous command runs succesfuly without any errors.</p><pre><code><div class="highlight"><span></span>vina --receptor lu.pdbqt --center_x -9.7 --center_y <span class="m">11</span>.4 --center_z <span class="m">68</span>.9 --size_x <span class="m">19</span>.3 --size_y <span class="m">29</span>.9 --size_z <span class="m">21</span>.3 --ligand test.pdbqt -</div></code></pre><p>This is just the docking command for AutoDock Vina. In the next part I will tell how to use PyMOL and a plugin to directly generate the coordinates in Vina format <code> --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3</code> without needing to type them manually.</p></div><span>Tagged with: </span><ul class="tag-list"><li><a href="/tags/codesnippet">Code-Snippet</a></li><li><a href="/tags/moleculardocking">Molecular-Docking</a></li><li><a href="/tags/cheminformatics">Cheminformatics</a></li><li><a href="/tags/openbabel">Open-Babel</a></li></ul><div id="disqus_thread"></div><script src="/assets/disqus.js"></script><noscript>Please enable JavaScript to view the comments</noscript></article></div><footer><p>Made with ❤️ using <a href="https://github.com/johnsundell/publish">Publish</a></p><p><a href="/feed.rss">RSS feed</a></p></footer></body></html>
\ No newline at end of file +</div></code></pre><p>This is just the docking command for AutoDock Vina. In the next part I will tell how to use PyMOL and a plugin to directly generate the coordinates in Vina format <code> --center_x -9.7 --center_y 11.4 --center_z 68.9 --size_x 19.3 --size_y 29.9 --size_z 21.3</code> without needing to type them manually.</p></div><span>Tagged with: </span><ul class="tag-list"><li><a href="/tags/codesnippet">Code-Snippet</a></li><li><a href="/tags/moleculardocking">Molecular-Docking</a></li><li><a href="/tags/cheminformatics">Cheminformatics</a></li><li><a href="/tags/openbabel">Open-Babel</a></li><li><a href="/tags/autodock-vina">AutoDock Vina</a></li></ul><div id="disqus_thread"></div><script src="/assets/disqus.js"></script><noscript>Please enable JavaScript to view the comments</noscript></article></div><footer><p>Made with ❤️ using <a href="https://github.com/johnsundell/publish">Publish</a></p><p><a href="/feed.rss">RSS feed</a></p></footer></body></html>
\ No newline at end of file diff --git a/posts/2020-06-02-Compiling-AutoDock-Vina-on-iOS/index.html b/posts/2020-06-02-Compiling-AutoDock-Vina-on-iOS/index.html index 2265b38..e160e76 100644 --- a/posts/2020-06-02-Compiling-AutoDock-Vina-on-iOS/index.html +++ b/posts/2020-06-02-Compiling-AutoDock-Vina-on-iOS/index.html @@ -26,4 +26,4 @@ include ../../makefile_common std::cerr << <span class="s2">"\n\nParse error on line "</span> <span class="s"><< e.line</span> << <span class="s2">" in file \""</span> <span class="s"><< e.file</span>.native_file_string<span class="o">()</span> << <span class="s2">"\": "</span> <span class="s"><< e.re</span>ason <span class="s"><< '\n';</span> <span class="s"> ~~~~~~ ^</span> <span class="s">2 errors gen</span>erated. -</div></code></pre><p>Turns out <code>native_file_string</code> was deprecated in Boost 1.57 and replaced with just <code>string</code></p><h3>Error 3 - Library Not Found</h3><p>This one still boggles me because there was no reason for it to not work, as a workaround I downloaded the DEB, extracted it and used that path for compiling.</p><h3>Error 4 - No Member Named 'native<em>file</em>string' Again.</h3><p>But, this time in another file and I quickle fixed it</p><h2>Moment of Truth</h2><p>Obviously it was working on my iPad, but would it work on another device? I transfered the compiled binary and</p><img src="/assets/posts/autodock-vina/s1.png" alt=""AutoDock Vina running on my iPhone""/><p>The package is available on my repository and only depends on boost. ( Both, Vina and Vina-Split are part of the package)</p></div><span>Tagged with: </span><ul class="tag-list"><li><a href="/tags/ios">iOS</a></li><li><a href="/tags/jailbreak">Jailbreak</a></li><li><a href="/tags/cheminformatics">Cheminformatics</a></li><li><a href="/tags/autodock-vina">AutoDock Vina</a></li></ul><div id="disqus_thread"></div><script src="/assets/disqus.js"></script><noscript>Please enable JavaScript to view the comments</noscript></article></div><footer><p>Made with ❤️ using <a href="https://github.com/johnsundell/publish">Publish</a></p><p><a href="/feed.rss">RSS feed</a></p></footer></body></html>
\ No newline at end of file +</div></code></pre><p>Turns out <code>native_file_string</code> was deprecated in Boost 1.57 and replaced with just <code>string</code></p><h3>Error 3 - Library Not Found</h3><p>This one still boggles me because there was no reason for it to not work, as a workaround I downloaded the DEB, extracted it and used that path for compiling.</p><h3>Error 4 - No Member Named 'native<em>file</em>string' Again.</h3><p>But, this time in another file and I quickle fixed it</p><h2>Moment of Truth</h2><p>Obviously it was working on my iPad, but would it work on another device? I transfered the compiled binary and</p><img src="/assets/posts/autodock-vina/s1.png" alt=""AutoDock Vina running on my iPhone""/><p>The package is available on my repository and only depends on boost. ( Both, Vina and Vina-Split are part of the package)</p></div><span>Tagged with: </span><ul class="tag-list"><li><a href="/tags/ios">iOS</a></li><li><a href="/tags/jailbreak">Jailbreak</a></li><li><a href="/tags/cheminformatics">Cheminformatics</a></li><li><a href="/tags/autodock-vina">AutoDock Vina</a></li><li><a href="/tags/moleculardocking">Molecular-Docking</a></li></ul><div id="disqus_thread"></div><script src="/assets/disqus.js"></script><noscript>Please enable JavaScript to view the comments</noscript></article></div><footer><p>Made with ❤️ using <a href="https://github.com/johnsundell/publish">Publish</a></p><p><a href="/feed.rss">RSS feed</a></p></footer></body></html>
\ No newline at end of file diff --git a/posts/index.html b/posts/index.html index ff943f0..52f4112 100644 --- a/posts/index.html +++ b/posts/index.html @@ -1 +1 @@ -<!DOCTYPE html><html lang="en"><head><meta charset="UTF-8"/><meta name="og:site_name" content="Navan Chauhan"/><link rel="canonical" href="https://navanchauhan.github.io/posts"/><meta name="twitter:url" content="https://navanchauhan.github.io/posts"/><meta name="og:url" content="https://navanchauhan.github.io/posts"/><title>Posts | Navan Chauhan</title><meta name="twitter:title" content="Posts | Navan Chauhan"/><meta name="og:title" content="Posts | Navan Chauhan"/><meta name="description" content="Welcome to my personal fragment of the internet. Majority of the posts should be complete."/><meta name="twitter:description" content="Welcome to my personal fragment of the internet. Majority of the posts should be complete."/><meta name="og:description" content="Welcome to my personal fragment of the internet. Majority of the posts should be complete."/><meta name="twitter:card" content="summary"/><link rel="stylesheet" href="/styles.css" type="text/css"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><link rel="shortcut icon" href="/images/favicon.png" type="image/png"/><link rel="alternate" href="/feed.rss" type="application/rss+xml" title="Subscribe to Navan Chauhan"/><meta name="twitter:image" content="https://navanchauhan.github.io/images/logo.png"/><meta name="og:image" content="https://navanchauhan.github.io/images/logo.png"/></head><head><script src="https://www.googletagmanager.com/gtag/js?id=UA-108635191-1v"></script><script>window.dataLayer = window.dataLayer || [];function gtag(){dataLayer.push(arguments);}gtag('js', new Date());gtag('config', 'UA-108635191-1');</script></head><body><header><div class="wrapper"><a class="site-name" href="/">Navan Chauhan</a><nav><ul><li><a href="/about">About Me</a></li><li><a class="selected" href="/posts">Posts</a></li><li><a href="/publications">Publications</a></li><li><a href="/assets/résumé.pdf">Résumé</a></li><li><a href="https://navanchauhan.github.io/repo">Repo</a></li></ul></nav></div></header><div class="wrapper"><h1>Posts</h1><p>Tips, tricks and tutorials which I think might be useful.</p><ul class="item-list"><li><article><h1><a href="/posts/2010-01-24-experiments">Experiments</a></h1><ul class="tag-list"><li><a href="/tags/experiment">Experiment</a></li></ul><span>🕑 1 minute read. January 24, 2010</span><p>Just a markdown file for all experiments related to the website</p></article></li><li><article><h1><a href="/posts/2019-05-05-Custom-Snowboard-Anemone-Theme">Creating your own custom theme for Snowboard or Anemone</a></h1><ul class="tag-list"><li><a href="/tags/tutorial">Tutorial</a></li><li><a href="/tags/jailbreak">Jailbreak</a></li><li><a href="/tags/designing">Designing</a></li><li><a href="/tags/snowboard">Snowboard</a></li><li><a href="/tags/anemone">Anemone</a></li></ul><span>🕑 5 minute read. May 5, 2019</span><p>Tutorial on creating your own custom theme for Snowboard or Anemone</p></article></li><li><article><h1><a href="/posts/2019-12-04-Google-Teachable-Machines">Image Classifier With Teachable Machines</a></h1><ul class="tag-list"><li><a href="/tags/tutorial">Tutorial</a></li></ul><span>🕑 2 minute read. December 4, 2019</span><p>Tutorial on creating a custom image classifier quickly with Google Teachanle Machines</p></article></li><li><article><h1><a href="/posts/2019-12-08-Image-Classifier-Tensorflow">Creating a Custom Image Classifier using Tensorflow 2.x and Keras for Detecting Malaria</a></h1><ul class="tag-list"><li><a href="/tags/tutorial">Tutorial</a></li><li><a href="/tags/tensorflow">Tensorflow</a></li><li><a href="/tags/colab">Colab</a></li></ul><span>🕑 4 minute read. December 8, 2019</span><p>Tutorial on creating an image classifier model using TensorFlow which detects malaria</p></article></li><li><article><h1><a href="/posts/2019-12-08-Splitting-Zips">Splitting ZIPs into Multiple Parts</a></h1><ul class="tag-list"><li><a href="/tags/codesnippet">Code-Snippet</a></li><li><a href="/tags/tutorial">Tutorial</a></li></ul><span>🕑 1 minute read. December 8, 2019</span><p>Short code snippet for splitting zips.</p></article></li><li><article><h1><a href="/posts/2019-12-10-TensorFlow-Model-Prediction">Making Predictions using Image Classifier (TensorFlow)</a></h1><ul class="tag-list"><li><a href="/tags/tutorial">Tutorial</a></li><li><a href="/tags/tensorflow">Tensorflow</a></li><li><a href="/tags/codesnippet">Code-Snippet</a></li></ul><span>🕑 1 minute read. December 10, 2019</span><p>Making predictions for image classification models built using TensorFlow</p></article></li><li><article><h1><a href="/posts/2019-12-16-TensorFlow-Polynomial-Regression">Polynomial Regression Using TensorFlow</a></h1><ul class="tag-list"><li><a href="/tags/tutorial">Tutorial</a></li><li><a href="/tags/tensorflow">Tensorflow</a></li><li><a href="/tags/colab">Colab</a></li></ul><span>🕑 17 minute read. December 16, 2019</span><p>Polynomial regression using TensorFlow</p></article></li><li><article><h1><a href="/posts/2019-12-22-Fake-News-Detector">Building a Fake News Detector with Turicreate</a></h1><ul class="tag-list"><li><a href="/tags/tutorial">Tutorial</a></li><li><a href="/tags/colab">Colab</a></li><li><a href="/tags/swiftui">SwiftUI</a></li><li><a href="/tags/turicreate">Turicreate</a></li></ul><span>🕑 7 minute read. December 22, 2019</span><p>In this tutorial we will build a fake news detecting app from scratch, using Turicreate for the machine learning model and SwiftUI for building the app</p></article></li><li><article><h1><a href="/posts/2020-01-14-Converting-between-PIL-NumPy">Converting between image and NumPy array</a></h1><ul class="tag-list"><li><a href="/tags/codesnippet">Code-Snippet</a></li><li><a href="/tags/tutorial">Tutorial</a></li></ul><span>🕑 1 minute read. January 14, 2020</span><p>Short code snippet for converting between PIL image and NumPy arrays.</p></article></li><li><article><h1><a href="/posts/2020-01-15-Setting-up-Kaggle-to-use-with-Colab">Setting up Kaggle to use with Google Colab</a></h1><ul class="tag-list"><li><a href="/tags/tutorial">Tutorial</a></li><li><a href="/tags/colab">Colab</a></li><li><a href="/tags/turicreate">Turicreate</a></li><li><a href="/tags/kaggle">Kaggle</a></li></ul><span>🕑 1 minute read. January 15, 2020</span><p>Tutorial on setting up kaggle, to use with Google Colab</p></article></li><li><article><h1><a href="/posts/2020-01-16-Image-Classifier-Using-Turicreate">Creating a Custom Image Classifier using Turicreate to detect Smoke and Fire</a></h1><ul class="tag-list"><li><a href="/tags/tutorial">Tutorial</a></li><li><a href="/tags/colab">Colab</a></li><li><a href="/tags/turicreate">Turicreate</a></li></ul><span>🕑 6 minute read. January 16, 2020</span><p>Tutorial on creating a custom Image Classifier using Turicreate and a dataset from Kaggle</p></article></li><li><article><h1><a href="/posts/2020-01-19-Connect-To-Bluetooth-Devices-Linux-Terminal">How to setup Bluetooth on a Raspberry Pi</a></h1><ul class="tag-list"><li><a href="/tags/codesnippet">Code-Snippet</a></li><li><a href="/tags/tutorial">tutorial</a></li><li><a href="/tags/raspberrypi">Raspberry-Pi</a></li><li><a href="/tags/linux">Linux</a></li></ul><span>🕑 1 minute read. January 19, 2020</span><p>Connecting to Bluetooth Devices using terminal, tested on Raspberry Pi Zero W</p></article></li><li><article><h1><a href="/posts/2020-03-03-Playing-With-Android-TV">Tinkering with an Android TV</a></h1><ul class="tag-list"><li><a href="/tags/androidtv">Android-TV</a></li><li><a href="/tags/android">Android</a></li></ul><span>🕑 1 minute read. March 3, 2020</span><p>Tinkering with an Android TV</p></article></li><li><article><h1><a href="/posts/2020-03-08-Making-Vaporwave-Track">Making My First Vaporwave Track (Remix)</a></h1><ul class="tag-list"><li><a href="/tags/vaporwave">Vaporwave</a></li><li><a href="/tags/music">Music</a></li></ul><span>🕑 2 minute read. March 8, 2020</span><p>I made my first vaporwave remix</p></article></li><li><article><h1><a href="/posts/2020-04-13-Fixing-X11-Error-AmberTools-macOS">Fixing X11 Error on macOS Catalina for AmberTools 18/19</a></h1><ul class="tag-list"><li><a href="/tags/moleculardynamics">Molecular-Dynamics</a></li><li><a href="/tags/macos">macOS</a></li></ul><span>🕑 2 minute read. April 13, 2020</span><p>Fixing Could not find the X11 libraries; you may need to edit config.h, AmberTools macOS Catalina</p></article></li><li><article><h1><a href="/posts/2020-05-31-compiling-open-babel-on-ios">Compiling Open Babel on iOS</a></h1><ul class="tag-list"><li><a href="/tags/ios">iOS</a></li><li><a href="/tags/jailbreak">Jailbreak</a></li><li><a href="/tags/cheminformatics">Cheminformatics</a></li><li><a href="/tags/openbabel">Open-Babel</a></li></ul><span>🕑 5 minute read. May 31, 2020</span><p>Compiling Open Babel on iOS</p></article></li><li><article><h1><a href="/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL">Workflow for Lightning Fast Molecular Docking Part One</a></h1><ul class="tag-list"><li><a href="/tags/codesnippet">Code-Snippet</a></li><li><a href="/tags/moleculardocking">Molecular-Docking</a></li><li><a href="/tags/cheminformatics">Cheminformatics</a></li><li><a href="/tags/openbabel">Open-Babel</a></li></ul><span>🕑 2 minute read. June 1, 2020</span><p>This is my workflow for lightning fast molecular docking.</p></article></li><li><article><h1><a href="/posts/2020-06-02-Compiling-AutoDock-Vina-on-iOS">Compiling AutoDock Vina on iOS</a></h1><ul class="tag-list"><li><a href="/tags/ios">iOS</a></li><li><a href="/tags/jailbreak">Jailbreak</a></li><li><a href="/tags/cheminformatics">Cheminformatics</a></li><li><a href="/tags/autodock-vina">AutoDock Vina</a></li></ul><span>🕑 3 minute read. June 2, 2020</span><p>Compiling AutoDock Vina on iOS</p></article></li><li><article><h1><a href="/posts/hello-world">Hello World</a></h1><ul class="tag-list"><li><a href="/tags/helloworld">hello-world</a></li></ul><span>🕑 1 minute read. April 16, 2019</span><p>My first post.</p></article></li></ul></div><footer><p>Made with ❤️ using <a href="https://github.com/johnsundell/publish">Publish</a></p><p><a href="/feed.rss">RSS feed</a></p></footer></body></html>
\ No newline at end of file +<!DOCTYPE html><html lang="en"><head><meta charset="UTF-8"/><meta name="og:site_name" content="Navan Chauhan"/><link rel="canonical" href="https://navanchauhan.github.io/posts"/><meta name="twitter:url" content="https://navanchauhan.github.io/posts"/><meta name="og:url" content="https://navanchauhan.github.io/posts"/><title>Posts | Navan Chauhan</title><meta name="twitter:title" content="Posts | Navan Chauhan"/><meta name="og:title" content="Posts | Navan Chauhan"/><meta name="description" content="Welcome to my personal fragment of the internet. Majority of the posts should be complete."/><meta name="twitter:description" content="Welcome to my personal fragment of the internet. Majority of the posts should be complete."/><meta name="og:description" content="Welcome to my personal fragment of the internet. Majority of the posts should be complete."/><meta name="twitter:card" content="summary"/><link rel="stylesheet" href="/styles.css" type="text/css"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><link rel="shortcut icon" href="/images/favicon.png" type="image/png"/><link rel="alternate" href="/feed.rss" type="application/rss+xml" title="Subscribe to Navan Chauhan"/><meta name="twitter:image" content="https://navanchauhan.github.io/images/logo.png"/><meta name="og:image" content="https://navanchauhan.github.io/images/logo.png"/></head><head><script src="https://www.googletagmanager.com/gtag/js?id=UA-108635191-1v"></script><script>window.dataLayer = window.dataLayer || [];function gtag(){dataLayer.push(arguments);}gtag('js', new Date());gtag('config', 'UA-108635191-1');</script></head><body><header><div class="wrapper"><a class="site-name" href="/">Navan Chauhan</a><nav><ul><li><a href="/about">About Me</a></li><li><a class="selected" href="/posts">Posts</a></li><li><a href="/publications">Publications</a></li><li><a href="/assets/résumé.pdf">Résumé</a></li><li><a href="https://navanchauhan.github.io/repo">Repo</a></li></ul></nav></div></header><div class="wrapper"><h1>Posts</h1><p>Tips, tricks and tutorials which I think might be useful.</p><ul class="item-list"><li><article><h1><a href="/posts/2010-01-24-experiments">Experiments</a></h1><ul class="tag-list"><li><a href="/tags/experiment">Experiment</a></li></ul><span>🕑 1 minute read. January 24, 2010</span><p>Just a markdown file for all experiments related to the website</p></article></li><li><article><h1><a href="/posts/2019-05-05-Custom-Snowboard-Anemone-Theme">Creating your own custom theme for Snowboard or Anemone</a></h1><ul class="tag-list"><li><a href="/tags/tutorial">Tutorial</a></li><li><a href="/tags/jailbreak">Jailbreak</a></li><li><a href="/tags/designing">Designing</a></li><li><a href="/tags/snowboard">Snowboard</a></li><li><a href="/tags/anemone">Anemone</a></li></ul><span>🕑 5 minute read. May 5, 2019</span><p>Tutorial on creating your own custom theme for Snowboard or Anemone</p></article></li><li><article><h1><a href="/posts/2019-12-04-Google-Teachable-Machines">Image Classifier With Teachable Machines</a></h1><ul class="tag-list"><li><a href="/tags/tutorial">Tutorial</a></li></ul><span>🕑 2 minute read. December 4, 2019</span><p>Tutorial on creating a custom image classifier quickly with Google Teachanle Machines</p></article></li><li><article><h1><a href="/posts/2019-12-08-Image-Classifier-Tensorflow">Creating a Custom Image Classifier using Tensorflow 2.x and Keras for Detecting Malaria</a></h1><ul class="tag-list"><li><a href="/tags/tutorial">Tutorial</a></li><li><a href="/tags/tensorflow">Tensorflow</a></li><li><a href="/tags/colab">Colab</a></li></ul><span>🕑 4 minute read. December 8, 2019</span><p>Tutorial on creating an image classifier model using TensorFlow which detects malaria</p></article></li><li><article><h1><a href="/posts/2019-12-08-Splitting-Zips">Splitting ZIPs into Multiple Parts</a></h1><ul class="tag-list"><li><a href="/tags/codesnippet">Code-Snippet</a></li><li><a href="/tags/tutorial">Tutorial</a></li></ul><span>🕑 1 minute read. December 8, 2019</span><p>Short code snippet for splitting zips.</p></article></li><li><article><h1><a href="/posts/2019-12-10-TensorFlow-Model-Prediction">Making Predictions using Image Classifier (TensorFlow)</a></h1><ul class="tag-list"><li><a href="/tags/tutorial">Tutorial</a></li><li><a href="/tags/tensorflow">Tensorflow</a></li><li><a href="/tags/codesnippet">Code-Snippet</a></li></ul><span>🕑 1 minute read. December 10, 2019</span><p>Making predictions for image classification models built using TensorFlow</p></article></li><li><article><h1><a href="/posts/2019-12-16-TensorFlow-Polynomial-Regression">Polynomial Regression Using TensorFlow</a></h1><ul class="tag-list"><li><a href="/tags/tutorial">Tutorial</a></li><li><a href="/tags/tensorflow">Tensorflow</a></li><li><a href="/tags/colab">Colab</a></li></ul><span>🕑 17 minute read. December 16, 2019</span><p>Polynomial regression using TensorFlow</p></article></li><li><article><h1><a href="/posts/2019-12-22-Fake-News-Detector">Building a Fake News Detector with Turicreate</a></h1><ul class="tag-list"><li><a href="/tags/tutorial">Tutorial</a></li><li><a href="/tags/colab">Colab</a></li><li><a href="/tags/swiftui">SwiftUI</a></li><li><a href="/tags/turicreate">Turicreate</a></li></ul><span>🕑 7 minute read. December 22, 2019</span><p>In this tutorial we will build a fake news detecting app from scratch, using Turicreate for the machine learning model and SwiftUI for building the app</p></article></li><li><article><h1><a href="/posts/2020-01-14-Converting-between-PIL-NumPy">Converting between image and NumPy array</a></h1><ul class="tag-list"><li><a href="/tags/codesnippet">Code-Snippet</a></li><li><a href="/tags/tutorial">Tutorial</a></li></ul><span>🕑 1 minute read. January 14, 2020</span><p>Short code snippet for converting between PIL image and NumPy arrays.</p></article></li><li><article><h1><a href="/posts/2020-01-15-Setting-up-Kaggle-to-use-with-Colab">Setting up Kaggle to use with Google Colab</a></h1><ul class="tag-list"><li><a href="/tags/tutorial">Tutorial</a></li><li><a href="/tags/colab">Colab</a></li><li><a href="/tags/turicreate">Turicreate</a></li><li><a href="/tags/kaggle">Kaggle</a></li></ul><span>🕑 1 minute read. January 15, 2020</span><p>Tutorial on setting up kaggle, to use with Google Colab</p></article></li><li><article><h1><a href="/posts/2020-01-16-Image-Classifier-Using-Turicreate">Creating a Custom Image Classifier using Turicreate to detect Smoke and Fire</a></h1><ul class="tag-list"><li><a href="/tags/tutorial">Tutorial</a></li><li><a href="/tags/colab">Colab</a></li><li><a href="/tags/turicreate">Turicreate</a></li></ul><span>🕑 6 minute read. January 16, 2020</span><p>Tutorial on creating a custom Image Classifier using Turicreate and a dataset from Kaggle</p></article></li><li><article><h1><a href="/posts/2020-01-19-Connect-To-Bluetooth-Devices-Linux-Terminal">How to setup Bluetooth on a Raspberry Pi</a></h1><ul class="tag-list"><li><a href="/tags/codesnippet">Code-Snippet</a></li><li><a href="/tags/tutorial">tutorial</a></li><li><a href="/tags/raspberrypi">Raspberry-Pi</a></li><li><a href="/tags/linux">Linux</a></li></ul><span>🕑 1 minute read. January 19, 2020</span><p>Connecting to Bluetooth Devices using terminal, tested on Raspberry Pi Zero W</p></article></li><li><article><h1><a href="/posts/2020-03-03-Playing-With-Android-TV">Tinkering with an Android TV</a></h1><ul class="tag-list"><li><a href="/tags/androidtv">Android-TV</a></li><li><a href="/tags/android">Android</a></li></ul><span>🕑 1 minute read. March 3, 2020</span><p>Tinkering with an Android TV</p></article></li><li><article><h1><a href="/posts/2020-03-08-Making-Vaporwave-Track">Making My First Vaporwave Track (Remix)</a></h1><ul class="tag-list"><li><a href="/tags/vaporwave">Vaporwave</a></li><li><a href="/tags/music">Music</a></li></ul><span>🕑 2 minute read. March 8, 2020</span><p>I made my first vaporwave remix</p></article></li><li><article><h1><a href="/posts/2020-04-13-Fixing-X11-Error-AmberTools-macOS">Fixing X11 Error on macOS Catalina for AmberTools 18/19</a></h1><ul class="tag-list"><li><a href="/tags/moleculardynamics">Molecular-Dynamics</a></li><li><a href="/tags/macos">macOS</a></li></ul><span>🕑 2 minute read. April 13, 2020</span><p>Fixing Could not find the X11 libraries; you may need to edit config.h, AmberTools macOS Catalina</p></article></li><li><article><h1><a href="/posts/2020-05-31-compiling-open-babel-on-ios">Compiling Open Babel on iOS</a></h1><ul class="tag-list"><li><a href="/tags/ios">iOS</a></li><li><a href="/tags/jailbreak">Jailbreak</a></li><li><a href="/tags/cheminformatics">Cheminformatics</a></li><li><a href="/tags/openbabel">Open-Babel</a></li></ul><span>🕑 5 minute read. May 31, 2020</span><p>Compiling Open Babel on iOS</p></article></li><li><article><h1><a href="/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL">Workflow for Lightning Fast Molecular Docking Part One</a></h1><ul class="tag-list"><li><a href="/tags/codesnippet">Code-Snippet</a></li><li><a href="/tags/moleculardocking">Molecular-Docking</a></li><li><a href="/tags/cheminformatics">Cheminformatics</a></li><li><a href="/tags/openbabel">Open-Babel</a></li><li><a href="/tags/autodock-vina">AutoDock Vina</a></li></ul><span>🕑 2 minute read. June 1, 2020</span><p>This is my workflow for lightning fast molecular docking.</p></article></li><li><article><h1><a href="/posts/2020-06-02-Compiling-AutoDock-Vina-on-iOS">Compiling AutoDock Vina on iOS</a></h1><ul class="tag-list"><li><a href="/tags/ios">iOS</a></li><li><a href="/tags/jailbreak">Jailbreak</a></li><li><a href="/tags/cheminformatics">Cheminformatics</a></li><li><a href="/tags/autodock-vina">AutoDock Vina</a></li><li><a href="/tags/moleculardocking">Molecular-Docking</a></li></ul><span>🕑 3 minute read. June 2, 2020</span><p>Compiling AutoDock Vina on iOS</p></article></li><li><article><h1><a href="/posts/hello-world">Hello World</a></h1><ul class="tag-list"><li><a href="/tags/helloworld">hello-world</a></li></ul><span>🕑 1 minute read. April 16, 2019</span><p>My first post.</p></article></li></ul></div><footer><p>Made with ❤️ using <a href="https://github.com/johnsundell/publish">Publish</a></p><p><a href="/feed.rss">RSS feed</a></p></footer></body></html>
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