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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 org.biojava.nbio.structure.chem.ChemComp;
import org.biojava.nbio.structure.chem.ChemCompGroupFactory;
import org.biojava.nbio.structure.chem.ChemCompProvider;
import org.biojava.nbio.structure.chem.DownloadChemCompProvider;
import org.biojava.nbio.structure.chem.PolymerType;
import org.biojava.nbio.structure.chem.ReducedChemCompProvider;
import org.biojava.nbio.structure.chem.ResidueType;
import org.junit.Ignore;
import org.junit.Test;
import static org.junit.Assert.*;
public class ChemCompTest {
@Test
public void testALA(){
String chemID = "ALA";
ChemComp cc = ChemCompGroupFactory.getChemComp(chemID);
assertNotNull(cc.getPolymerType());
assertEquals(cc.getPolymerType(), PolymerType.peptide);
assertNotNull("residue type has not been set!", cc.getResidueType());
assertTrue (" is not amino ", cc.getResidueType().equals(ResidueType.lPeptideLinking));
}
@Ignore("The test requires the network")
@Test
public void testMEA(){
String chemID = "MEA";
// also test replacing providers...
ChemCompProvider oldProvider = ChemCompGroupFactory.getChemCompProvider();
DownloadChemCompProvider all = new DownloadChemCompProvider();
ChemCompGroupFactory.setChemCompProvider(all);
ChemComp cc = ChemCompGroupFactory.getChemComp(chemID);
assertNotNull(cc);
assertTrue(" is not mea" , cc.getId().equals(chemID));
assertEquals(" one letter code is not correct", "F", cc.getOneLetterCode());
assertEquals("MEA",cc.getThreeLetterCode());
assertNotNull(cc.getPolymerType());
assertEquals( PolymerType.peptide, cc.getPolymerType());
assertNotNull("residue type has not been set!", cc.getResidueType());
assertTrue (" is not amino ", cc.getResidueType().equals(ResidueType.lPeptideLinking));
Group g = ChemCompGroupFactory.getGroupFromChemCompDictionary(chemID);
assertTrue( g.getType().equals(GroupType.AMINOACID));
ChemCompGroupFactory.setChemCompProvider(oldProvider);
}
@Ignore("The test requires the network")
@Test
public void testPRR(){
ChemCompProvider oldProvider = ChemCompGroupFactory.getChemCompProvider();
DownloadChemCompProvider all = new DownloadChemCompProvider();
ChemCompGroupFactory.setChemCompProvider(all);
String chemID = "PRR";
Group g = ChemCompGroupFactory.getGroupFromChemCompDictionary(chemID);
assertTrue("Got back group of wrong type! " + g.getClass().getName(), g instanceof AminoAcid);
AminoAcid aa = (AminoAcid) g;
assertNotNull(aa.getAminoType());
assertTrue(aa.getAminoType().equals('X'));
ChemCompGroupFactory.setChemCompProvider(oldProvider);
}
@Ignore("The test requires the network")
@Test
public void testChangingProviders(){
// test for issue #145
String chemID = "MEA";
// first we test with reduced chem comp provider
ChemCompGroupFactory.setChemCompProvider(new ReducedChemCompProvider());
ChemComp cc = ChemCompGroupFactory.getChemComp(chemID);
assertNotNull(cc);
assertTrue(" is not mea" , cc.getId().equals(chemID));
assertTrue(cc.isEmpty());
// now we change to download chem comp provider
ChemCompGroupFactory.setChemCompProvider(new DownloadChemCompProvider());
cc = ChemCompGroupFactory.getChemComp(chemID);
assertNotNull(cc);
assertTrue(" is not mea" , cc.getId().equals(chemID));
assertEquals("MEA",cc.getThreeLetterCode());
// now testing in opposite order
// first we test with download chem comp provider
ChemCompGroupFactory.setChemCompProvider(new DownloadChemCompProvider());
cc = ChemCompGroupFactory.getChemComp(chemID);
assertNotNull(cc);
assertTrue(" is not mea" , cc.getId().equals(chemID));
assertEquals("MEA",cc.getThreeLetterCode());
// now we change to reduced chem comp provider
ChemCompGroupFactory.setChemCompProvider(new ReducedChemCompProvider());
cc = ChemCompGroupFactory.getChemComp(chemID);
assertNotNull(cc);
assertTrue(" is not mea" , cc.getId().equals(chemID));
//the cached description contains all information even with the ReducedProvider
assertNotNull(cc.getThreeLetterCode());
}
}
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