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-<?xml version="1.0" encoding="UTF-8"?><rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom" xmlns:content="http://purl.org/rss/1.0/modules/content"><channel><title>Navan Chauhan</title><description>Welcome to my personal fragment of the internet. Majority of the posts should be complete.</description><link>https://navanchauhan.github.io/</link><language>en</language><lastBuildDate>Mon, 1 Jun 2020 00:48:18 +0530</lastBuildDate><pubDate>Mon, 1 Jun 2020 00:48:18 +0530</pubDate><ttl>250</ttl><atom:link href="https://navanchauhan.github.io/feed.rss" rel="self" type="application/rss+xml"/><item><guid isPermaLink="true">https://navanchauhan.github.io/posts/2020-05-31-compiling-open-babel-on-ios</guid><title>Compiling Open Babel on iOS</title><description>Compiling Open Babel on iOS</description><link>https://navanchauhan.github.io/posts/2020-05-31-compiling-open-babel-on-ios</link><pubDate>Sun, 31 May 2020 11:30:00 +0530</pubDate><content:encoded><![CDATA[<h1>Compiling Open Babel on iOS</h1><p>Due to the fact that my summer vacations started today, I had the brilliant idea of trying to run open babel on my iPad. To give a little background, I had tried to compile AutoDock Vina using a cross-compiler but I had miserably failed.</p><p>I am running the Checkr1n jailbreak on my iPad and the Unc0ver jailbreak on my phone.</p><h2>But Why?</h2><p>Well, just because I can. This is literally the only reason I tried compiling it and also partially because in the long run I want to compile AutoDock Vina so I can do Molecular Docking on the go.</p><h2>Let's Go!</h2><p>How hard can it be to compile open babel right? It is just a simple software with clear and concise build instructions. I just need to use <code>cmake</code> to build and the <code>make</code> to install.</p><p>It is 11 AM in the morning. I install <code>clang, cmake and make</code> from the Sam Bingner's repository, fired up ssh, downloaded the source code and ran the build command.`clang</p><h3>Fail No. 1</h3><p>I couldn't even get cmake to run, I did a little digging arond StackOverflow and founf that I needed the iOS SDK, sure no problem. I waited for Xcode to update and transfered the <code>/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk</code> to <code>/var/sdks/</code> on my iPad</p><p>Them I told cmake that this is the location for my SDK 😠. Succesful! Now I just needed to use make.</p><h3>Fail No. 2</h3><p>It was giving the error that thread-local-storage was not supported on this device.</p><pre><code><div class="highlight"><span></span><span class="o">[</span>  <span class="m">0</span>%<span class="o">]</span> Building CXX object src/CMakeFiles/openbabel.dir/alias.cpp.o
+<?xml version="1.0" encoding="UTF-8"?><rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom" xmlns:content="http://purl.org/rss/1.0/modules/content"><channel><title>Navan Chauhan</title><description>Welcome to my personal fragment of the internet. Majority of the posts should be complete.</description><link>https://navanchauhan.github.io/</link><language>en</language><lastBuildDate>Mon, 1 Jun 2020 12:27:03 +0530</lastBuildDate><pubDate>Mon, 1 Jun 2020 12:27:03 +0530</pubDate><ttl>250</ttl><atom:link href="https://navanchauhan.github.io/feed.rss" rel="self" type="application/rss+xml"/><item><guid isPermaLink="true">https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL</guid><title>Workflow for Lightning Fast Molecular Docking Part One</title><description>This is my workflow for lightning fast molecular docking.</description><link>https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL</link><pubDate>Mon, 1 Jun 2020 13:10:00 +0530</pubDate><content:encoded><![CDATA[<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">&quot;</span><span class="k">$(</span>pbpaste<span class="k">)</span><span class="s2">&quot;</span> --gen3d -opdbqt -Otest.pdbqt <span class="o">&amp;&amp;</span> vina --receptor lu.pdbqt --center_x -9.7 --center_y <span class="m">11</span>.4 --center_z <span class="m">68</span>.9 --size_x <span class="m">19</span>.3 --size_y <span class="m">29</span>.9 --size_z <span class="m">21</span>.3  --ligand test.pdbqt
+</div></code></pre><p>To run this command you simple copy the SMILES structure of the ligand you want an it automatically takes it from your clipboard, generates the 3D structure in the AutoDock PDBQT format using Open Babel and then docks it with your receptor using AutoDock Vina, all with just one command.</p><p>Let me break down the commands</p><pre><code><div class="highlight"><span></span>obabel -:<span class="s2">&quot;</span><span class="k">$(</span>pbpaste<span class="k">)</span><span class="s2">&quot;</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">&#39;xclip -selection clipboard&#39;</span>
+<span class="nb">alias</span> <span class="nv">pbpaste</span><span class="o">=</span><span class="s1">&#39;xclip -selection clipboard -o&#39;</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">&amp;&amp;</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>]]></content:encoded></item><item><guid isPermaLink="true">https://navanchauhan.github.io/posts/2020-05-31-compiling-open-babel-on-ios</guid><title>Compiling Open Babel on iOS</title><description>Compiling Open Babel on iOS</description><link>https://navanchauhan.github.io/posts/2020-05-31-compiling-open-babel-on-ios</link><pubDate>Sun, 31 May 2020 11:30:00 +0530</pubDate><content:encoded><![CDATA[<h1>Compiling Open Babel on iOS</h1><p>Due to the fact that my summer vacations started today, I had the brilliant idea of trying to run open babel on my iPad. To give a little background, I had tried to compile AutoDock Vina using a cross-compiler but I had miserably failed.</p><p>I am running the Checkr1n jailbreak on my iPad and the Unc0ver jailbreak on my phone.</p><h2>But Why?</h2><p>Well, just because I can. This is literally the only reason I tried compiling it and also partially because in the long run I want to compile AutoDock Vina so I can do Molecular Docking on the go.</p><h2>Let's Go!</h2><p>How hard can it be to compile open babel right? It is just a simple software with clear and concise build instructions. I just need to use <code>cmake</code> to build and the <code>make</code> to install.</p><p>It is 11 AM in the morning. I install <code>clang, cmake and make</code> from the Sam Bingner's repository, fired up ssh, downloaded the source code and ran the build command.`clang</p><h3>Fail No. 1</h3><p>I couldn't even get cmake to run, I did a little digging arond StackOverflow and founf that I needed the iOS SDK, sure no problem. I waited for Xcode to update and transfered the <code>/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk</code> to <code>/var/sdks/</code> on my iPad</p><p>Them I told cmake that this is the location for my SDK 😠. Succesful! Now I just needed to use make.</p><h3>Fail No. 2</h3><p>It was giving the error that thread-local-storage was not supported on this device.</p><pre><code><div class="highlight"><span></span><span class="o">[</span>  <span class="m">0</span>%<span class="o">]</span> Building CXX object src/CMakeFiles/openbabel.dir/alias.cpp.o
 <span class="o">[</span>  <span class="m">1</span>%<span class="o">]</span> Building CXX object src/CMakeFiles/openbabel.dir/atom.cpp.o
 In file included from /var/root/obabel/ob-src/src/atom.cpp:28:
 In file included from /var/root/obabel/ob-src/include/openbabel/ring.h:29: