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@@ -1,4 +1,4 @@ -<?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>Tue, 2 Jun 2020 23:25:41 +0530</lastBuildDate><pubDate>Tue, 2 Jun 2020 23:25:41 +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/2020-06-02-Compiling-AutoDock-Vina-on-iOS</guid><title>Compiling AutoDock Vina on iOS</title><description>Compiling AutoDock Vina on iOS</description><link>https://navanchauhan.github.io/posts/2020-06-02-Compiling-AutoDock-Vina-on-iOS</link><pubDate>Tue, 2 Jun 2020 23:23:00 +0530</pubDate><content:encoded><![CDATA[<h1>Compiling AutoDock Vina on iOS</h1><p>Why? Because I can.</p><h2>Installing makedepend</h2><p><code>makedepend</code> is a Unix tool used to generate dependencies of C source files. Most modern programes do not use this anymore, but then again AutoDock Vina's source code hasn't been changed since 2011. The first hurdle came when I saw that there was no makedepend command, neither was there any package on any development repository for iOS. So, I tracked down the original source code for <code>makedepend</code> (https://github.com/DerellLicht/makedepend). According to the repository this is actually the source code for the makedepend utility that came with some XWindows distribution back around Y2K. I am pretty sure there is a problem with my current compiler configuration because I had to manually edit the <code>Makefile</code> to provide the path to the iOS SDKs using the <code>-isysroot</code> flag.</p><h2>Editting the Makefile</h2><p>Original Makefile ( I used the provided mac Makefile base )</p><pre><code><div class="highlight"><span></span><span class="nv">BASE</span><span class="o">=</span>/usr/local +<?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>Thu, 25 Jun 2020 18:17:35 +0530</lastBuildDate><pubDate>Thu, 25 Jun 2020 18:17:35 +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/2020-06-02-Compiling-AutoDock-Vina-on-iOS</guid><title>Compiling AutoDock Vina on iOS</title><description>Compiling AutoDock Vina on iOS</description><link>https://navanchauhan.github.io/posts/2020-06-02-Compiling-AutoDock-Vina-on-iOS</link><pubDate>Tue, 2 Jun 2020 23:23:00 +0530</pubDate><content:encoded><![CDATA[<h1>Compiling AutoDock Vina on iOS</h1><p>Why? Because I can.</p><h2>Installing makedepend</h2><p><code>makedepend</code> is a Unix tool used to generate dependencies of C source files. Most modern programes do not use this anymore, but then again AutoDock Vina's source code hasn't been changed since 2011. The first hurdle came when I saw that there was no makedepend command, neither was there any package on any development repository for iOS. So, I tracked down the original source code for <code>makedepend</code> (https://github.com/DerellLicht/makedepend). According to the repository this is actually the source code for the makedepend utility that came with some XWindows distribution back around Y2K. I am pretty sure there is a problem with my current compiler configuration because I had to manually edit the <code>Makefile</code> to provide the path to the iOS SDKs using the <code>-isysroot</code> flag.</p><h2>Editting the Makefile</h2><p>Original Makefile ( I used the provided mac Makefile base )</p><pre><code><div class="highlight"><span></span><span class="nv">BASE</span><span class="o">=</span>/usr/local <span class="nv">BOOST_VERSION</span><span class="o">=</span>1_41 <span class="nv">BOOST_INCLUDE</span> <span class="o">=</span> <span class="k">$(</span>BASE<span class="k">)</span>/include <span class="nv">C_PLATFORM</span><span class="o">=</span>-arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min<span class="o">=</span><span class="m">10</span>.4 @@ -33,7 +33,8 @@ include ../../makefile_common </div></code></pre><pre><code><div class="highlight"><span></span><span class="k">$(</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>]]></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 23:30:00 +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 +</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 23:30:00 +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 SDKs to my iPad</p><pre><code><div class="highlight"><span></span>scp -r /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk root@192.168.1.8:/var/sdks/ +</div></code></pre><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: |