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DemoQsAlign.java
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67 lines (58 loc) · 2 KB
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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package demo;
import java.io.IOException;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIO;
import org.biojava.nbio.structure.align.quaternary.QsAlign;
import org.biojava.nbio.structure.align.quaternary.QsAlignParameters;
import org.biojava.nbio.structure.align.quaternary.QsAlignResult;
import org.biojava.nbio.structure.cluster.SubunitClustererParameters;
/**
* Demo on how to use programatically {@link QsAlign} for the alignment of
* quaternary structures.
* <p>
* Small oligomers: proliferating cell nuclear antigens (1PLR, 3HI8, 3IFV),
* photosynthetic reaction centers (2JIY, 1DXR)
* <p>
* Big oligomers: cytochrome bc1 complexes (1bcc, 1kb9, 1qcr), phycocyanin
* (2VML, 2BV8), bacterial ribosome (1FJG, 4V54).
*
*
* @author Aleix Lafita
* @since 5.0.0
*
*/
public class DemoQsAlign {
public static void main(String[] args) throws IOException,
StructureException {
// Align two trimeric DNA clamps
Structure s1 = StructureIO.getStructure("1bcc");
Structure s2 = StructureIO.getStructure("1kb9");
// Select the parameters for clustering and alignment
SubunitClustererParameters clusterParams = new SubunitClustererParameters();
QsAlignParameters alignParams = new QsAlignParameters();
QsAlignResult result = QsAlign
.align(s1, s2, clusterParams, alignParams);
System.out.println(result);
}
}