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<!DOCTYPE HTML>
<html lang>
<head>
<!-- Generated by javadoc (21) -->
<title>Source code</title>
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="description" content="source: package: demo, class: CookBook">
<meta name="generator" content="javadoc/SourceToHTMLConverter">
<link rel="stylesheet" type="text/css" href="../../stylesheet.css" title="Style">
</head>
<body class="source-page">
<main role="main">
<div class="source-container">
<pre><span class="source-line-no">001</span><span id="line-1">/*</span>
<span class="source-line-no">002</span><span id="line-2"> * BioJava development code</span>
<span class="source-line-no">003</span><span id="line-3"> *</span>
<span class="source-line-no">004</span><span id="line-4"> * This code may be freely distributed and modified under the</span>
<span class="source-line-no">005</span><span id="line-5"> * terms of the GNU Lesser General Public Licence. This should</span>
<span class="source-line-no">006</span><span id="line-6"> * be distributed with the code. If you do not have a copy,</span>
<span class="source-line-no">007</span><span id="line-7"> * see:</span>
<span class="source-line-no">008</span><span id="line-8"> *</span>
<span class="source-line-no">009</span><span id="line-9"> * http://www.gnu.org/copyleft/lesser.html</span>
<span class="source-line-no">010</span><span id="line-10"> *</span>
<span class="source-line-no">011</span><span id="line-11"> * Copyright for this code is held jointly by the individual</span>
<span class="source-line-no">012</span><span id="line-12"> * authors. These should be listed in @author doc comments.</span>
<span class="source-line-no">013</span><span id="line-13"> *</span>
<span class="source-line-no">014</span><span id="line-14"> * For more information on the BioJava project and its aims,</span>
<span class="source-line-no">015</span><span id="line-15"> * or to join the biojava-l mailing list, visit the home page</span>
<span class="source-line-no">016</span><span id="line-16"> * at:</span>
<span class="source-line-no">017</span><span id="line-17"> *</span>
<span class="source-line-no">018</span><span id="line-18"> * http://www.biojava.org/</span>
<span class="source-line-no">019</span><span id="line-19"> *</span>
<span class="source-line-no">020</span><span id="line-20"> * Created on Mar 11, 2010</span>
<span class="source-line-no">021</span><span id="line-21"> * Author: Andreas Prlic</span>
<span class="source-line-no">022</span><span id="line-22"> *</span>
<span class="source-line-no">023</span><span id="line-23"> */</span>
<span class="source-line-no">024</span><span id="line-24"></span>
<span class="source-line-no">025</span><span id="line-25">package demo;</span>
<span class="source-line-no">026</span><span id="line-26"></span>
<span class="source-line-no">027</span><span id="line-27"></span>
<span class="source-line-no">028</span><span id="line-28">import org.biojava.nbio.structure.Atom;</span>
<span class="source-line-no">029</span><span id="line-29">import org.biojava.nbio.structure.Structure;</span>
<span class="source-line-no">030</span><span id="line-30">import org.biojava.nbio.structure.StructureTools;</span>
<span class="source-line-no">031</span><span id="line-31">import org.biojava.nbio.structure.align.StructureAlignment;</span>
<span class="source-line-no">032</span><span id="line-32">import org.biojava.nbio.structure.align.StructureAlignmentFactory;</span>
<span class="source-line-no">033</span><span id="line-33">import org.biojava.nbio.structure.align.fatcat.FatCatFlexible;</span>
<span class="source-line-no">034</span><span id="line-34">import org.biojava.nbio.structure.align.gui.DisplayAFP;</span>
<span class="source-line-no">035</span><span id="line-35">import org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay;</span>
<span class="source-line-no">036</span><span id="line-36">import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;</span>
<span class="source-line-no">037</span><span id="line-37">import org.biojava.nbio.structure.align.model.AFPChain;</span>
<span class="source-line-no">038</span><span id="line-38">import org.biojava.nbio.structure.align.model.AfpChainWriter;</span>
<span class="source-line-no">039</span><span id="line-39">import org.biojava.nbio.structure.align.util.AtomCache;</span>
<span class="source-line-no">040</span><span id="line-40"></span>
<span class="source-line-no">041</span><span id="line-41"></span>
<span class="source-line-no">042</span><span id="line-42">public class CookBook</span>
<span class="source-line-no">043</span><span id="line-43">{</span>
<span class="source-line-no">044</span><span id="line-44"></span>
<span class="source-line-no">045</span><span id="line-45"></span>
<span class="source-line-no">046</span><span id="line-46"> public static void main(String[] args){</span>
<span class="source-line-no">047</span><span id="line-47"></span>
<span class="source-line-no">048</span><span id="line-48"> String name1="1HNG.B";</span>
<span class="source-line-no">049</span><span id="line-49"> String name2="1A64.A";</span>
<span class="source-line-no">050</span><span id="line-50"></span>
<span class="source-line-no">051</span><span id="line-51"></span>
<span class="source-line-no">052</span><span id="line-52"> try {</span>
<span class="source-line-no">053</span><span id="line-53"></span>
<span class="source-line-no">054</span><span id="line-54"> // for this example we are going to use the jFatCat-rigid algorithm</span>
<span class="source-line-no">055</span><span id="line-55"> StructureAlignment algorithm = StructureAlignmentFactory.getAlgorithm(FatCatFlexible.algorithmName);</span>
<span class="source-line-no">056</span><span id="line-56"></span>
<span class="source-line-no">057</span><span id="line-57"> // the cache takes care of loading the structures</span>
<span class="source-line-no">058</span><span id="line-58"> // Downloads files to a temp dir by default</span>
<span class="source-line-no">059</span><span id="line-59"> AtomCache cache = new AtomCache();</span>
<span class="source-line-no">060</span><span id="line-60"></span>
<span class="source-line-no">061</span><span id="line-61"></span>
<span class="source-line-no">062</span><span id="line-62"> //////////////////////////////</span>
<span class="source-line-no">063</span><span id="line-63"> // no need to change anything below this line</span>
<span class="source-line-no">064</span><span id="line-64"> // ////////////////////////////</span>
<span class="source-line-no">065</span><span id="line-65"></span>
<span class="source-line-no">066</span><span id="line-66"> // load the structures</span>
<span class="source-line-no">067</span><span id="line-67"> Structure structure1 = cache.getStructure(name1);</span>
<span class="source-line-no">068</span><span id="line-68"> Structure structure2 = cache.getStructure(name2);</span>
<span class="source-line-no">069</span><span id="line-69"></span>
<span class="source-line-no">070</span><span id="line-70"> // we are only using the CA atoms in the structure for the alignment</span>
<span class="source-line-no">071</span><span id="line-71"> Atom[] ca1 = StructureTools.getAtomCAArray(structure1);</span>
<span class="source-line-no">072</span><span id="line-72"> Atom[] ca2 = StructureTools.getAtomCAArray(structure2);</span>
<span class="source-line-no">073</span><span id="line-73"></span>
<span class="source-line-no">074</span><span id="line-74"> // do the actual alignment</span>
<span class="source-line-no">075</span><span id="line-75"> AFPChain afpChain = algorithm.align(ca1,ca2);</span>
<span class="source-line-no">076</span><span id="line-76"></span>
<span class="source-line-no">077</span><span id="line-77"> // just name the two molecules</span>
<span class="source-line-no">078</span><span id="line-78"> afpChain.setName1(name1);</span>
<span class="source-line-no">079</span><span id="line-79"> afpChain.setName2(name2);</span>
<span class="source-line-no">080</span><span id="line-80"></span>
<span class="source-line-no">081</span><span id="line-81"> // print and display results:</span>
<span class="source-line-no">082</span><span id="line-82"></span>
<span class="source-line-no">083</span><span id="line-83"></span>
<span class="source-line-no">084</span><span id="line-84"> // flexible original results:</span>
<span class="source-line-no">085</span><span id="line-85"> System.out.println(afpChain.toFatcat(ca1,ca2));</span>
<span class="source-line-no">086</span><span id="line-86"></span>
<span class="source-line-no">087</span><span id="line-87"> // show the alignment in 3D in jmol</span>
<span class="source-line-no">088</span><span id="line-88"> StructureAlignmentJmol jmol= StructureAlignmentDisplay.display(afpChain, ca1, ca2);</span>
<span class="source-line-no">089</span><span id="line-89"></span>
<span class="source-line-no">090</span><span id="line-90"> // set the display title for the frame</span>
<span class="source-line-no">091</span><span id="line-91"> jmol.setTitle(algorithm.getAlgorithmName() + " : " + name1 + " vs. " + name2);</span>
<span class="source-line-no">092</span><span id="line-92"></span>
<span class="source-line-no">093</span><span id="line-93"> // here we open up the alignment - text panel that can interact with the 3D jmol display.</span>
<span class="source-line-no">094</span><span id="line-94"> DisplayAFP.showAlignmentPanel(afpChain, ca1,ca2,jmol);</span>
<span class="source-line-no">095</span><span id="line-95"></span>
<span class="source-line-no">096</span><span id="line-96"> // we can print an XML version</span>
<span class="source-line-no">097</span><span id="line-97"> //System.out.println(AFPChainXMLConverter.toXML(afpChain, ca1, ca2));</span>
<span class="source-line-no">098</span><span id="line-98"></span>
<span class="source-line-no">099</span><span id="line-99"> // or print the same output as original FATCAT</span>
<span class="source-line-no">100</span><span id="line-100"> System.out.println(AfpChainWriter.toFatCat(afpChain, ca1, ca2));</span>
<span class="source-line-no">101</span><span id="line-101"></span>
<span class="source-line-no">102</span><span id="line-102"></span>
<span class="source-line-no">103</span><span id="line-103"></span>
<span class="source-line-no">104</span><span id="line-104"></span>
<span class="source-line-no">105</span><span id="line-105"></span>
<span class="source-line-no">106</span><span id="line-106"> } catch (Exception e){</span>
<span class="source-line-no">107</span><span id="line-107"> e.printStackTrace();</span>
<span class="source-line-no">108</span><span id="line-108"> }</span>
<span class="source-line-no">109</span><span id="line-109"> }</span>
<span class="source-line-no">110</span><span id="line-110">}</span>
</pre>
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