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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 Apr 5, 2008
*/
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 SourceCompoundTest extends TestCase{
private Structure getStructure(String fileName){
InputStream inStream = this.getClass().getResourceAsStream(fileName);
assertNotNull(inStream);
PDBFileParser pdbpars = new PDBFileParser();
Structure structure = null;
try {
structure = pdbpars.parsePDBFile(inStream) ;
} catch (IOException e) {
e.printStackTrace();
}
return structure;
}
public void testCompoundSourceStructure(){
Structure s2 = getStructure("/files/2gox.pdb");
assertEquals(2, s2.getCompounds().size());
for (Compound compound : s2.getCompounds()){
if (compound.getMolId().equals("1")) {
assertEquals("COMPLEMENT C3", compound.getMolName());
assertEquals("[A, C]", compound.getChainId().toString());
assertEquals("FRAGMENT OF ALPHA CHAIN: RESIDUES 996-1287", compound.getFragment());
assertEquals("YES", compound.getEngineered());
assertEquals("YES", compound.getMutation());
assertEquals("HOMO SAPIENS", compound.getOrganismScientific());
assertEquals("HUMAN", compound.getOrganismCommon());
assertEquals("C3", compound.getGene());
assertEquals("ESCHERICHIA COLI", compound.getExpressionSystem());
assertEquals("BL21(DE3)", compound.getExpressionSystemStrain());
assertEquals("PLASMID", compound.getExpressionSystemVectorType());
assertEquals("PT7-", compound.getExpressionSystemPlasmid());
}
if (compound.getMolId().equals("2")) {
assertEquals("FIBRINOGEN-BINDING PROTEIN", compound.getMolName());
assertEquals("[B, D]", compound.getChainId().toString());
assertEquals("C-TERMINAL DOMAIN: RESIDUES 101-165", compound.getFragment());
assertEquals("YES", compound.getEngineered());
assertEquals("STAPHYLOCOCCUS AUREUS", compound.getOrganismScientific());
assertEquals("BACTERIA", compound.getOrganismCommon());
assertEquals("MU50 / ATCC 700699", compound.getStrain());
assertEquals("EFB", compound.getGene());
assertEquals("ESCHERICHIA COLI", compound.getExpressionSystem());
assertEquals("BL21(DE3)", compound.getExpressionSystemStrain());
assertEquals("PLASMID", compound.getExpressionSystemVectorType());
assertEquals("PT7HMT", compound.getExpressionSystemPlasmid());
}
}
}
public void testCOMPNDsectionFRAGMENT(){
Structure s2 = getStructure("/files/2gox.pdb");
Structure s4 = getStructure("/files/3cfy.pdb");
// this file has a CHAIN: string in the value for the FRAGMENT: filed which breaks the version 1.4 parser
for (Compound compound : s2.getCompounds()) {
if (compound.getMolId().equals("1")) {
assertEquals("FRAGMENT OF ALPHA CHAIN: RESIDUES 996-1287", compound.getFragment());
}
}
for (Compound compound : s4.getCompounds()) {
if (compound.getMolId().equals("1")) {
assertEquals("SIGNAL RECEIVER DOMAIN: RESIDUES 2-128", compound.getFragment());
}
}
}
public void testCOMPNDsectionCHAINS(){
Structure s3 = getStructure("/files/2pos.pdb");
assertEquals(1, s3.getCompounds().size());
for (Compound compound : s3.getCompounds()){
/*System.out.println(compound.getMolId());
System.out.println(compound.getMolName());
System.out.println(compound.getChainId().toString());
System.out.println(compound.getOrganismScientific());
System.out.println(compound.getStrain());
*/
assertEquals("1", compound.getMolId());
assertEquals("SYLVATICIN", compound.getMolName());
assertEquals("[A, B, C, D]", compound.getChainId().toString());
assertEquals("PYTHIUM SYLVATICUM", compound.getOrganismScientific());
assertEquals("STRAIN 37", compound.getStrain());
}
}
public void testSOURCEsectionSTRAIN(){
Structure s4 = getStructure("/files/3cfy.pdb");
for (Compound compound : s4.getCompounds()){
if (compound.getMolId().equals("1")) {
/*System.out.println(compound.getMolId());
System.out.println(compound.getMolName());
System.out.println(compound.getChainId().toString());
System.out.println(compound.getFragment());
System.out.println(compound.getEngineered());
System.out.println(compound.getOrganismScientific());
System.out.println(compound.getOrganismCommon());
System.out.println(compound.getStrain());
System.out.println(compound.getGene());
System.out.println(compound.getExpressionSystem());
System.out.println(compound.getExpressionSystemVectorType());
System.out.println(compound.getExpressionSystemVector());
System.out.println(compound.getExpressionSystemPlasmid());
*/
assertEquals("1", compound.getMolId());
assertEquals("PUTATIVE LUXO REPRESSOR PROTEIN", compound.getMolName());
assertEquals("[A]", compound.getChainId().toString());
assertEquals("SIGNAL RECEIVER DOMAIN: RESIDUES 2-128", compound.getFragment());
assertEquals("YES", compound.getEngineered());
assertEquals("VIBRIO PARAHAEMOLYTICUS RIMD 2210633", compound.getOrganismScientific());
assertEquals("BACTERIA", compound.getOrganismCommon());
assertEquals("RIMD 2210633 / SEROTYPE O3:K6", compound.getStrain());
assertEquals("VP1469", compound.getGene());
assertEquals("ESCHERICHIA COLI", compound.getExpressionSystem());
assertEquals("PLASMID", compound.getExpressionSystemVectorType());
assertEquals("PET", compound.getExpressionSystemVector());
assertEquals("BC-PSGX3(BC)", compound.getExpressionSystemPlasmid());
}
}
}
public void testSOURCEsectionORGSCI(){
Structure s5 = getStructure("/files/3cdl.pdb");
for (Compound compound : s5.getCompounds()){
if (compound.getMolId().equals("1")) {
//System.out.println(compound.getOrganismScientific());
assertEquals("PSEUDOMONAS SYRINGAE PV. TOMATO STR. DC3000", compound.getOrganismScientific());
}
}
}
/**
* There is a file format change in v3.2 of the PDB file format, adding the
* tax id.
* This test makes sure that the tax id for the organism and expression
* systems is set correctly.
*/
public void testSourceTaxIdVersion32File(){
Structure structure = getStructure("/files/3dl7_v32.pdb");
Compound comp = structure.getCompoundById("1");
comp.showSource();
assertEquals("10090", comp.getOrganismTaxId());
assertEquals("9606", comp.getExpressionSystemTaxId());
}
/**
* 3.2 format includes PMID and DOI in the JRNL section.
*/
public void testJournalRefs(){
// JRNL AUTH M.HAMMEL,G.SFYROERA,D.RICKLIN,P.MAGOTTI,
// JRNL AUTH 2 J.D.LAMBRIS,B.V.GEISBRECHT
// JRNL TITL A STRUCTURAL BASIS FOR COMPLEMENT INHIBITION BY
// JRNL TITL 2 STAPHYLOCOCCUS AUREUS.
// JRNL REF NAT.IMMUNOL. V. 8 430 2007
// JRNL REFN ISSN 1529-2908
// JRNL PMID 17351618
// JRNL DOI 10.1038/NI1450
Structure structure = getStructure("/files/2gox_v315.pdb");
//check that there really is an publication
assertTrue(structure.hasJournalArticle());
if (structure.hasJournalArticle()) {
JournalArticle journal = structure.getJournalArticle();
List<Author> authorList = journal.getAuthorList();
Author firstAuthor = authorList.get(0);
//check the authors
assertEquals(6, authorList.size());
assertEquals("HAMMEL", firstAuthor.getSurname());
assertEquals("M.", firstAuthor.getInitials());
//check the other publication details
assertEquals("A STRUCTURAL BASIS FOR COMPLEMENT INHIBITION BY STAPHYLOCOCCUS AUREUS.", journal.getTitle());
assertEquals("NAT.IMMUNOL.", journal.getJournalName());
assertEquals(2007, journal.getPublicationDate());
assertEquals("8", journal.getVolume());
assertEquals("430", journal.getStartPage());
assertEquals("ISSN 1529-2908", journal.getRefn());
assertEquals("17351618", journal.getPmid());
assertEquals("10.1038/NI1450", journal.getDoi());
}
}
}
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