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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/
*
* Created on Jun 8, 2007
*
*/
package org.biojava.bio.structure;
import java.io.IOException;
import java.io.InputStream;
import org.biojava.bio.structure.align.StructurePairAligner;
import org.biojava.bio.structure.align.pairwise.AlternativeAlignment;
import org.biojava.bio.structure.io.PDBFileParser;
import junit.framework.TestCase;
public class StructurePairAlignerTest extends TestCase {
Structure structure1;
Structure structure2;
protected void setUp()
{
InputStream inStream = this.getClass().getResourceAsStream("/files/5pti.pdb");
assertNotNull(inStream);
InputStream inStream2 = this.getClass().getResourceAsStream("/files/1tap.pdb");
assertNotNull(inStream2);
PDBFileParser pdbpars = new PDBFileParser();
try {
structure1 = pdbpars.parsePDBFile(inStream) ;
structure2 = pdbpars.parsePDBFile(inStream2);
} catch (IOException e) {
e.printStackTrace();
}
assertNotNull(structure1);
assertNotNull(structure2);
assertEquals("structure does not contain one chain ", 1 ,structure1.size());
}
public void testAlignStructureStructure() {
StructurePairAligner aligner = new StructurePairAligner();
boolean allFine = true;
String msg = "";
try {
aligner.align(structure1,structure2);
AlternativeAlignment[] aligs = aligner.getAlignments();
assertEquals("the number of obtained alternative alignments is not correct",20, aligs.length);
AlternativeAlignment a = aligs[0];
assertEquals("the expected nr of eq. residues is not correct.",48,a.getEqr());
// they are v. close, but not identical
assertTrue(a.getRmsd() < 3);
assertTrue(a.getRmsd() > 2);
assertTrue(a.getPercId() > 9);
assertTrue(a.getScore() > 150);
} catch (Exception e){
msg = e.getMessage();
allFine = false;
}
assertTrue(allFine);
assertEquals("an error occured","" ,msg);
}
}
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