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286 lines (212 loc) · 7.75 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/
*
* Created on Mar 1, 2010
* Author: Andreas Prlic
*
*/
package org.biojava.nbio.structure;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.io.LocalPDBDirectory;
import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
import org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior;
import org.biojava.nbio.structure.io.MMCIFFileReader;
import org.biojava.nbio.structure.io.PDBFileReader;
import org.junit.Before;
import org.junit.Test;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import static org.junit.Assert.*;
// TODO dmyersturnbull: we should merge TestAtomCache and AtomCacheTest
public class TestAtomCache {
public static final String lineSplit = System.getProperty("file.separator");
private AtomCache cache;
@Before
public void setUp() {
cache = new AtomCache();
// Delete files which were cached in previous tests
String[] uncacheIDs = new String[] {
"1cmw", "1hhb","4hhb"
};
List<LocalPDBDirectory> readers = new ArrayList<LocalPDBDirectory>();
readers.add(new MMCIFFileReader(cache.getPath()) );
readers.add(new PDBFileReader(cache.getPath()) );
for(LocalPDBDirectory reader : readers) {
reader.setFetchBehavior(cache.getFetchBehavior());
reader.setObsoleteBehavior(cache.getObsoleteBehavior());
for(String pdbId : uncacheIDs) {
reader.deleteStructure(pdbId);
}
}
}
// TODO dmyersturnbull: Which of these syntaxes do we support? We should re-enable after
@Test
public void testAtomCacheNameParsing() throws IOException, StructureException {
String name1= "4hhb";
Structure s = cache.getStructure(name1);
assertNotNull(s);
assertEquals(4,s.getPolyChains().size());
String name2 = "4hhb.C";
String chainId2 = "C";
s = cache.getStructure(name2);
assertEquals(1,s.getPolyChains().size());
// Chain name 'C' corresponds to three IDs: C (141 res), I (1 HEM), and M (59 water)
assertEquals(3,s.getChains().size());
Chain c = s.getPolyChainByPDB(chainId2);
assertEquals(chainId2,c.getName());
// Number of groups: Polymer + water + ligand
assertEquals(141,c.getAtomLength());
assertEquals(141, s.getChainByIndex(0).getAtomLength());
assertEquals(1, s.getChainByIndex(1).getAtomLength());
assertEquals(59, s.getChainByIndex(2).getAtomLength());
// Colon separators removed in BioJava 4.1.0
String name2b = "4hhb:A";
try {
s = cache.getStructure(name2b);
fail("Invalid structure format");
} catch(StructureException e) {
}
// Numeric chain IDs are allowed but deprecated.
String name3 = "4hhb.1";
String chainId3 = "B";
s = cache.getStructure(name3);
assertNotNull(s);
assertEquals(1,s.getPolyChains().size());
c = s.getPolyChainByPDB(chainId3);
assertEquals(chainId3,c.getName());
String name4 = "4hhb.A:10-20,B:10-20,C:10-20";
s = cache.getStructure(name4);
assertNotNull(s);
assertEquals(3,s.getPolyChains().size());
assertEquals(3,s.getChains().size());
c = s.getPolyChainByPDB("B");
assertEquals(11,c.getAtomLength());
String name5 = "4hhb.(A:10-20,A:30-40)";
s =cache.getStructure(name5);
assertNotNull(s);
assertEquals(1,s.getPolyChains().size() );
// two chains: A (22 res), and G (1 HEM)
assertEquals(2,s.getChains().size() );
c = s.getPolyChainByPDB("A");
assertEquals(22,c.getAtomLength());
try {
// This syntax used to work, since the first paren is treated as a separator
String name6 = "4hhb(A:10-20,A:30-40)";
s =cache.getStructure(name6);
fail("A chain separator is required after the ID since 4.2.0");
} catch(StructureException e) {}
// Works since we detect a separator
String name8 = "4hhb.(C)";
s = cache.getStructure(name8);
assertEquals(1,s.getPolyChains().size());
c = s.getPolyChainByPDB(chainId2);
assertEquals(chainId2,c.getName());
}
@Test(expected=IOException.class)
public void testObsoleteId() throws StructureException, IOException {
cache.setFetchBehavior(FetchBehavior.FETCH_FILES);
cache.setObsoleteBehavior(ObsoleteBehavior.THROW_EXCEPTION);
// OBSOLETE PDB; should throw an exception
cache.setUseMmCif(false);
cache.getStructure("1HHB");
}
// note: we expect an IOException because 1CMW is obsolete and hasn't got a replacement
@Test
public void testFetchCurrent1CMW() throws IOException, StructureException {
cache.setFetchBehavior(FetchBehavior.FETCH_FILES);
cache.setObsoleteBehavior(ObsoleteBehavior.FETCH_CURRENT);
// OBSOLETE PDB; should throw an exception
cache.setUseMmCif(false);
try {
cache.getStructure("1CMW");
fail("Obsolete structure should throw exception");
} catch(IOException e) {}
cache.setUseMmCif(true);
try {
cache.getStructure("1CMW");
fail("Obsolete structure should throw exception");
} catch(IOException e) {}
}
// 1HHB is obsolete with a replacement
@Test
public void testFetchCurrent1HHB() throws IOException, StructureException {
cache.setFetchBehavior(FetchBehavior.FETCH_FILES);
cache.setObsoleteBehavior(ObsoleteBehavior.FETCH_CURRENT);
cache.setUseMmCif(false);
Structure s = cache.getStructure("1HHB");
assertEquals("Failed to get the current ID for 1HHB.","4HHB",s.getPDBCode());
cache.setUseMmCif(true);
s = cache.getStructure("1HHB");
assertEquals("Failed to get the current ID for 1HHB.","4HHB",s.getPDBCode());
}
// Fetching obsolete directly
@Test
public void testFetchObsolete() throws IOException, StructureException {
cache.setFetchBehavior(FetchBehavior.FETCH_FILES);
cache.setObsoleteBehavior(ObsoleteBehavior.FETCH_OBSOLETE);
Structure s;
cache.setUseMmtf(false);
cache.setUseMmCif(false);
s = cache.getStructure("1CMW");
assertEquals("Failed to get OBSOLETE file 1CMW.","1CMW", s.getPDBCode());
s = cache.getStructure("1HHB");
assertEquals("Failed to get OBSOLETE file 1HHB.","1HHB", s.getPDBCode());
cache.setUseMmCif(true);
s = cache.getStructure("1CMW");
assertEquals("Failed to get OBSOLETE file 1CMW.","1CMW", s.getPDBCode());
s = cache.getStructure("1HHB");
assertEquals("Failed to get OBSOLETE file 1HHB.","1HHB", s.getPDBCode());
}
@Test
public void testSettingFileParsingType(){
AtomCache cache = new AtomCache();
//test defaults
// by default we either use mmtf or mmcif, but not both.
assertNotEquals(cache.isUseMmtf(), cache.isUseMmCif());
// first is mmtf, second is mmcif
testFlags(cache,true,false);
// now change the values
cache.setUseMmCif(true);
testFlags(cache,false,true);
cache.setUseMmtf(true);
testFlags(cache,true,false);
// this sets to use PDB!
cache.setUseMmCif(false);
testFlags(cache,false,false);
// back to defaults
cache.setUseMmtf(true);
testFlags(cache,true,false);
// back to parsing PDB
cache.setUseMmtf(false);
testFlags(cache,false,false);
}
/** test the flags for parsing in the atom cache
*
* @param cache
* @param useMmTf
* @param useMmCif
*/
private void testFlags(AtomCache cache ,boolean useMmTf, boolean useMmCif) {
assertEquals("flag for parsing mmtf is set to " + cache.isUseMmtf() + " but should be " + useMmTf,
cache.isUseMmtf(), useMmTf);
assertEquals("flag for parsing mmcif is set to " + cache.isUseMmCif() + " but should be set to " + useMmCif,
cache.isUseMmCif(), useMmCif);
}
}