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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 org.biojava.nbio.structure;
import static org.junit.Assert.*;
import java.io.IOException;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.io.StructureFiletype;
import org.junit.Ignore;
import org.junit.Test;
/**
* Created by andreas on 9/16/15.
*/
public class Test2JA5 {
@Ignore("The test requires the network")
@Test
public void test2JA5() throws IOException, StructureException {
FileParsingParameters fileParsingParameters = new FileParsingParameters();
fileParsingParameters.setAlignSeqRes(true); // Need to align seqres to match chains.
fileParsingParameters.setHeaderOnly(false); // Need header only off to have chains to match.
AtomCache cache = new AtomCache();
cache.setFiletype(StructureFiletype.PDB);
cache.setFileParsingParams(fileParsingParameters);
StructureIO.setAtomCache(cache);
Structure s1 = StructureIO.getStructure("2ja5");
// This is not applicable anymore, we need to parse atoms to have chains to match.
// assertTrue(StructureTools.getNrAtoms(s1) == 0);
// SeqRes contains 14 chains, but since we cannot align Chain N to AtomGroups => 14.
// 2ja5 has been remediated on March 2017, now it has 14 chains in seqres matching the 14 chains in atoms (chain N has been removed)
assertEquals(14, s1.getPolyChains().size());
Chain nChain = s1.getPolyChain("N");
assertNotNull(nChain);
Chain chain = s1.getPolyChainByPDB("N");
assertNull(chain);
}
@Ignore("The test requires the network")
@Test
public void test2JA5noHeader() throws IOException, StructureException {
FileParsingParameters fileParsingParameters = new FileParsingParameters();
fileParsingParameters.setHeaderOnly(true);
AtomCache cache = new AtomCache();
cache.setFiletype(StructureFiletype.PDB);
cache.setFileParsingParams(fileParsingParameters);
StructureIO.setAtomCache(cache);
Structure s1 = StructureIO.getStructure("2ja5");
// This is not applicable anymore, we need to parse atoms to have chains to match.
assertEquals(0, StructureTools.getNrAtoms(s1));
// 2ja5 has been remediated on March 2017, now it has 14 chains in seqres matching the 14 chains in atoms (chain N has been removed)
assertEquals(14, s1.getPolyChains().size());
Chain nChain = s1.getPolyChainByPDB("N");
assertNull(nChain);
}
}
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