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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 Jul 26, 2007
*
*/
package org.biojava.bio.structure;
import java.io.IOException;
import java.io.InputStream;
import java.util.List;
import org.biojava.bio.structure.io.PDBFileParser;
import junit.framework.TestCase;
public class PdbFileFormat30Test extends TestCase {
protected void setUp(){
}
/** there is a file format change in v3.0 of the PDB file format
* this test makes sure that the atom name changes are being processed correctly
*
*
*/
public void testRead30File(){
Structure s = getStructure("/files/388d_v30.pdb");
int nrNuc = getNrNucleotides(s);
// there are 4 nucleotides less in the new version
// some chemically modified nucleotides residues have been declared to be HETATOMS
int shouldNr = 20;
assertEquals("structure does not contain the right number of nucleotides ", shouldNr ,nrNuc);
Structure s2 = getStructure("/files/104D_v30.pdb");
int nrNuc2 = getNrNucleotides(s2);
int shouldNr2 = 24;
assertEquals("structure does not contain the right number of nucleotides ", shouldNr2 , nrNuc2);
List<Compound> compounds= s.getCompounds();
assertTrue(compounds.size() == 1);
Compound mol = compounds.get(0);
assertTrue(mol.getMolName().startsWith("DNA"));
}
public void testRead23File(){
Structure s = getStructure("/files/388d_v23.pdb");
int nrNuc = getNrNucleotides(s);
int shouldNr = 24;
assertEquals("structure does not contain the right number of nucleotides ", shouldNr , nrNuc);
Structure s2 = getStructure("/files/104D_v23.pdb");
int nrNuc2 = getNrNucleotides(s2);
int shouldNr2 = 24;
assertEquals("structure does not contain the right number of nucleotides ", shouldNr2 , nrNuc2);
List<Compound> compounds= s.getCompounds();
assertTrue(compounds.size() == 1);
Compound mol = compounds.get(0);
assertTrue(mol.getMolName().startsWith("DNA"));
}
private Structure getStructure(String fileName){
InputStream inStream = this.getClass().getResourceAsStream(fileName);
assertNotNull(inStream);
PDBFileParser pdbpars = new PDBFileParser();
pdbpars.setAlignSeqRes(false);
Structure structure = null;
try {
structure = pdbpars.parsePDBFile(inStream) ;
} catch (IOException e) {
e.printStackTrace();
}
return structure;
}
private int getNrNucleotides(Structure s){
GroupIterator iter = new GroupIterator(s);
int nr = 0;
while(iter.hasNext()){
Group g = (Group) iter.next();
if (g.getType().equals("nucleotide")){
nr ++;
} else {
//System.out.println(g.getType() + g.getPDBName());
}
}
return nr;
}
}
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