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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 at Aug 12, 2013
* Author: ap3
*/
package org.biojava.nbio.structure.io;
import org.biojava.nbio.structure.EntityInfo;
import org.biojava.nbio.structure.EntityType;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIO;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.junit.BeforeClass;
import org.junit.Ignore;
import org.junit.Test;
import java.io.IOException;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
public class TestMMcifOrganismParsing {
@BeforeClass
public static void setUp() throws Exception {
AtomCache cache = new AtomCache();
cache.setFiletype(StructureFiletype.CIF);
StructureIO.setAtomCache(cache);
}
@Ignore("The test requires the network")
@Test
public void test1STP() throws IOException, StructureException{
String pdbId = "1stp";
checkPDB(pdbId, "1895");
}
// removed this test, since entity 3 of 1a4w has no organism tax_id
public void test1a4w() throws IOException, StructureException{
String pdbId = "1a4w";
checkPDB(pdbId, "9606");
}
@Ignore("The test requires the network")
@Test
public void test4hhb() throws IOException, StructureException{
String pdbId = "4hhb";
checkPDB(pdbId, "9606");
}
@Ignore("The test requires the network")
@Test
public void test3ZD6() throws IOException, StructureException {
// a PDB ID that contains a synthetic entity
String pdbId = "3zd6";
checkPDB(pdbId, "9606");
}
private void checkPDB(String pdbId, String organismTaxId) throws IOException, StructureException {
Structure s = StructureIO.getStructure(pdbId);
assertNotNull(s.getEntityInfos());
assertTrue(s.getEntityInfos().size() > 0);
for ( EntityInfo c : s.getEntityInfos()) {
if(EntityType.POLYMER.equals(c.getType())) {
assertNotNull(c.getOrganismTaxId());
if(pdbId.equals("3zd6")){
if(c.getMolId()==2) {
assertEquals(c.getOrganismTaxId(), "32630");
continue;
}
}
assertEquals(c.getOrganismTaxId(), organismTaxId);
}
}
}
}
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