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<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"> */</span>
<span class="source-line-no">021</span><span id="line-21">package demo;</span>
<span class="source-line-no">022</span><span id="line-22"></span>
<span class="source-line-no">023</span><span id="line-23">import org.biojava.nbio.structure.ResidueNumber;</span>
<span class="source-line-no">024</span><span id="line-24">import org.biojava.nbio.structure.Structure;</span>
<span class="source-line-no">025</span><span id="line-25">import org.biojava.nbio.structure.StructureException;</span>
<span class="source-line-no">026</span><span id="line-26">import org.biojava.nbio.structure.align.util.AtomCache;</span>
<span class="source-line-no">027</span><span id="line-27">import org.biojava.nbio.structure.gui.BiojavaJmol;</span>
<span class="source-line-no">028</span><span id="line-28">import org.biojava.nbio.structure.io.FastaStructureParser;</span>
<span class="source-line-no">029</span><span id="line-29">import org.biojava.nbio.core.sequence.ProteinSequence;</span>
<span class="source-line-no">030</span><span id="line-30">import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;</span>
<span class="source-line-no">031</span><span id="line-31">import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;</span>
<span class="source-line-no">032</span><span id="line-32">import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;</span>
<span class="source-line-no">033</span><span id="line-33">import org.biojava.nbio.core.sequence.io.ProteinSequenceCreator;</span>
<span class="source-line-no">034</span><span id="line-34">import org.biojava.nbio.core.sequence.io.template.SequenceCreatorInterface;</span>
<span class="source-line-no">035</span><span id="line-35">import org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface;</span>
<span class="source-line-no">036</span><span id="line-36"></span>
<span class="source-line-no">037</span><span id="line-37">import java.io.ByteArrayInputStream;</span>
<span class="source-line-no">038</span><span id="line-38">import java.io.IOException;</span>
<span class="source-line-no">039</span><span id="line-39">import java.io.InputStream;</span>
<span class="source-line-no">040</span><span id="line-40">import java.io.UnsupportedEncodingException;</span>
<span class="source-line-no">041</span><span id="line-41"></span>
<span class="source-line-no">042</span><span id="line-42">/**</span>
<span class="source-line-no">043</span><span id="line-43"> * Demo of how to use the {@link FastaStructureParser} class to read protein</span>
<span class="source-line-no">044</span><span id="line-44"> * structures from a FASTA file.</span>
<span class="source-line-no">045</span><span id="line-45"> *</span>
<span class="source-line-no">046</span><span id="line-46"> * @author Spencer Bliven</span>
<span class="source-line-no">047</span><span id="line-47"> *</span>
<span class="source-line-no">048</span><span id="line-48"> */</span>
<span class="source-line-no">049</span><span id="line-49">public class DemoStructureFromFasta {</span>
<span class="source-line-no">050</span><span id="line-50"></span>
<span class="source-line-no">051</span><span id="line-51"> @SuppressWarnings("unused")</span>
<span class="source-line-no">052</span><span id="line-52"> public static void getStructureFromFasta() {</span>
<span class="source-line-no">053</span><span id="line-53"></span>
<span class="source-line-no">054</span><span id="line-54"> // Load a test sequence</span>
<span class="source-line-no">055</span><span id="line-55"> // Normally this would come from a file, eg</span>
<span class="source-line-no">056</span><span id="line-56"> // File fasta = new File("/path/to/file.fa");</span>
<span class="source-line-no">057</span><span id="line-57"> String fastaStr =</span>
<span class="source-line-no">058</span><span id="line-58"> "> 4HHB\n" +</span>
<span class="source-line-no">059</span><span id="line-59"> "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK\n" +</span>
<span class="source-line-no">060</span><span id="line-60"> "KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA\n" +</span>
<span class="source-line-no">061</span><span id="line-61"> "VHASLDKFLASVSTVLTSKYR\n";</span>
<span class="source-line-no">062</span><span id="line-62"> InputStream fasta;</span>
<span class="source-line-no">063</span><span id="line-63"> try {</span>
<span class="source-line-no">064</span><span id="line-64"> fasta = new ByteArrayInputStream(fastaStr.getBytes("UTF-8"));</span>
<span class="source-line-no">065</span><span id="line-65"> } catch (UnsupportedEncodingException e) {</span>
<span class="source-line-no">066</span><span id="line-66"> e.printStackTrace();</span>
<span class="source-line-no">067</span><span id="line-67"> return;</span>
<span class="source-line-no">068</span><span id="line-68"> }</span>
<span class="source-line-no">069</span><span id="line-69"></span>
<span class="source-line-no">070</span><span id="line-70"> // Create a header parser to parse the header lines into valid structure accessions.</span>
<span class="source-line-no">071</span><span id="line-71"> // The resulting accession can be anything interpretable by AtomCache.getStructure.</span>
<span class="source-line-no">072</span><span id="line-72"> // Possible Examples: "4HHB" (whole structure), "d4hhba_" (SCOP domain),</span>
<span class="source-line-no">073</span><span id="line-73"> // "4HHB.A:1-15" (residue range)</span>
<span class="source-line-no">074</span><span id="line-74"> // For this example, the built-in fasta parser will extract the correct accession.</span>
<span class="source-line-no">075</span><span id="line-75"> SequenceHeaderParserInterface<ProteinSequence, AminoAcidCompound> headerParser;</span>
<span class="source-line-no">076</span><span id="line-76"> headerParser = new GenericFastaHeaderParser<>();</span>
<span class="source-line-no">077</span><span id="line-77"></span>
<span class="source-line-no">078</span><span id="line-78"> // Create AtomCache to fetch structures from the PDB</span>
<span class="source-line-no">079</span><span id="line-79"> AtomCache cache = new AtomCache();</span>
<span class="source-line-no">080</span><span id="line-80"></span>
<span class="source-line-no">081</span><span id="line-81"> // Create SequenceCreator. This converts a String to a ProteinSequence</span>
<span class="source-line-no">082</span><span id="line-82"> AminoAcidCompoundSet aaSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();</span>
<span class="source-line-no">083</span><span id="line-83"> SequenceCreatorInterface<AminoAcidCompound> creator;</span>
<span class="source-line-no">084</span><span id="line-84"> creator = new ProteinSequenceCreator(aaSet);</span>
<span class="source-line-no">085</span><span id="line-85"></span>
<span class="source-line-no">086</span><span id="line-86"> // parse file</span>
<span class="source-line-no">087</span><span id="line-87"> FastaStructureParser parser = new FastaStructureParser(</span>
<span class="source-line-no">088</span><span id="line-88"> fasta, headerParser, creator, cache);</span>
<span class="source-line-no">089</span><span id="line-89"> try {</span>
<span class="source-line-no">090</span><span id="line-90"> parser.process();</span>
<span class="source-line-no">091</span><span id="line-91"> } catch (IOException e) {</span>
<span class="source-line-no">092</span><span id="line-92"> e.printStackTrace();</span>
<span class="source-line-no">093</span><span id="line-93"> return;</span>
<span class="source-line-no">094</span><span id="line-94"> } catch (StructureException e) {</span>
<span class="source-line-no">095</span><span id="line-95"> e.printStackTrace();</span>
<span class="source-line-no">096</span><span id="line-96"> return;</span>
<span class="source-line-no">097</span><span id="line-97"> }</span>
<span class="source-line-no">098</span><span id="line-98"></span>
<span class="source-line-no">099</span><span id="line-99"> // Get info from the parser</span>
<span class="source-line-no">100</span><span id="line-100"> ResidueNumber[][] residues = parser.getResidues();</span>
<span class="source-line-no">101</span><span id="line-101"> ProteinSequence[] sequences = parser.getSequences();</span>
<span class="source-line-no">102</span><span id="line-102"> Structure[] structures = parser.getStructures();</span>
<span class="source-line-no">103</span><span id="line-103"> String[] accessions = parser.getAccessions();</span>
<span class="source-line-no">104</span><span id="line-104"></span>
<span class="source-line-no">105</span><span id="line-105"> // Use it! For example:</span>
<span class="source-line-no">106</span><span id="line-106"> // Display the structure, highlighting the sequence</span>
<span class="source-line-no">107</span><span id="line-107"> displayStructure( structures[0], residues[0]);</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>
<span class="source-line-no">111</span><span id="line-111"> /**</span>
<span class="source-line-no">112</span><span id="line-112"> * Displays the given structure and highlights the given residues.</span>
<span class="source-line-no">113</span><span id="line-113"> *</span>
<span class="source-line-no">114</span><span id="line-114"> * @param structure The structure to display</span>
<span class="source-line-no">115</span><span id="line-115"> * @param residues A list of residues to highlight</span>
<span class="source-line-no">116</span><span id="line-116"> */</span>
<span class="source-line-no">117</span><span id="line-117"> private static void displayStructure(Structure structure,</span>
<span class="source-line-no">118</span><span id="line-118"> ResidueNumber[] residues) {</span>
<span class="source-line-no">119</span><span id="line-119"> //Display each structure</span>
<span class="source-line-no">120</span><span id="line-120"> BiojavaJmol jmol = new BiojavaJmol();</span>
<span class="source-line-no">121</span><span id="line-121"> jmol.setStructure(structure);</span>
<span class="source-line-no">122</span><span id="line-122"></span>
<span class="source-line-no">123</span><span id="line-123"> //Highlight non-null atoms</span>
<span class="source-line-no">124</span><span id="line-124"> jmol.evalString("select *; spacefill off; wireframe off; color chain; backbone 0.4; ");</span>
<span class="source-line-no">125</span><span id="line-125"> String selectionCmd = buildJmolSelection(residues);</span>
<span class="source-line-no">126</span><span id="line-126"> jmol.evalString(selectionCmd);</span>
<span class="source-line-no">127</span><span id="line-127"> jmol.evalString("backbone 1.0; select none;");</span>
<span class="source-line-no">128</span><span id="line-128"> }</span>
<span class="source-line-no">129</span><span id="line-129"></span>
<span class="source-line-no">130</span><span id="line-130"></span>
<span class="source-line-no">131</span><span id="line-131"></span>
<span class="source-line-no">132</span><span id="line-132"> /**</span>
<span class="source-line-no">133</span><span id="line-133"> * Converts an array of ResidueNumbers into a jMol selection.</span>
<span class="source-line-no">134</span><span id="line-134"> *</span>
<span class="source-line-no">135</span><span id="line-135"> * <p>For example, "select 11^ :A.CA or 12^ :A.CA;" would select the</span>
<span class="source-line-no">136</span><span id="line-136"> * CA atoms of residues 11-12 on chain A.</span>
<span class="source-line-no">137</span><span id="line-137"> * @param residues Residues to include in the selection. Nulls are ignored.</span>
<span class="source-line-no">138</span><span id="line-138"> * @return</span>
<span class="source-line-no">139</span><span id="line-139"> */</span>
<span class="source-line-no">140</span><span id="line-140"> private static String buildJmolSelection(ResidueNumber[] residues) {</span>
<span class="source-line-no">141</span><span id="line-141"> StringBuilder cmd = new StringBuilder("select ");</span>
<span class="source-line-no">142</span><span id="line-142"> for(ResidueNumber res : residues) {</span>
<span class="source-line-no">143</span><span id="line-143"> if(res != null) {</span>
<span class="source-line-no">144</span><span id="line-144"> cmd.append(String.format("%d^%s:%s.CA or ", res.getSeqNum(),</span>
<span class="source-line-no">145</span><span id="line-145"> res.getInsCode()==null?" ":res.getInsCode(),</span>
<span class="source-line-no">146</span><span id="line-146"> res.getChainName()));</span>
<span class="source-line-no">147</span><span id="line-147"> }</span>
<span class="source-line-no">148</span><span id="line-148"> }</span>
<span class="source-line-no">149</span><span id="line-149"> cmd.append("none;");//easier than removing the railing 'or'</span>
<span class="source-line-no">150</span><span id="line-150"> return cmd.toString();</span>
<span class="source-line-no">151</span><span id="line-151"> }</span>
<span class="source-line-no">152</span><span id="line-152"></span>
<span class="source-line-no">153</span><span id="line-153"></span>
<span class="source-line-no">154</span><span id="line-154"></span>
<span class="source-line-no">155</span><span id="line-155"> public static void main(String[] args) {</span>
<span class="source-line-no">156</span><span id="line-156"> getStructureFromFasta();</span>
<span class="source-line-no">157</span><span id="line-157"> }</span>
<span class="source-line-no">158</span><span id="line-158">}</span>
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