package org.biojava.bio.structure; import java.io.IOException; import java.io.InputStream; import java.util.List; import java.util.Map; import junit.framework.TestCase; import org.biojava.bio.structure.io.PDBFileParser; import org.biojava.bio.structure.jama.Matrix; /** * * @author Andreas Prlic * @since 1.5 */ public class StructureTest extends TestCase { Structure structure; protected void setUp() { InputStream inStream = this.getClass().getResourceAsStream("/files/5pti_old.pdb"); assertNotNull(inStream); PDBFileParser pdbpars = new PDBFileParser(); try { structure = pdbpars.parsePDBFile(inStream) ; } catch (IOException e) { e.printStackTrace(); } assertNotNull(structure); assertEquals("structure does not contain one chain ", 2 ,structure.size()); } public void testSeqResParsing() { // System.out.println(structure); List chains = structure.getChains(0); assertEquals(" nr of found chains not correct!",2,chains.size()); Chain c = chains.get(0); //System.out.println(c); List seqResGroups = c.getSeqResGroups(); assertEquals("nr of SEQRES groups not correct!",58,seqResGroups.size()); List atomGroups = c.getAtomGroups(); Group g3 = seqResGroups.get(2); int indexAtom = atomGroups.indexOf(g3); //System.out.println(" index in atomlist: " + indexAtom); assertEquals("the SEQRES group can not be found in the ATOM list",2,indexAtom); Group g5 = atomGroups.get(5); assertEquals("The ATOM group can not be fond in the SEQRES list", 5,seqResGroups.indexOf(g5)); Chain c2 = chains.get(1); ListatomGroups2 = c2.getAtomGroups(); Group g58 = atomGroups2.get(0); assertEquals("The group is not PO4","PO4", g58.getPDBName()); assertEquals("The group P04 should not be in the SEQRES list", -1 , seqResGroups.indexOf(g58)); } /** test if a PDB file can be parsed * @throws Exception */ public void testReadPDBFile() throws Exception { assertEquals("pdb code not set!","5PTI",structure.getPDBCode()); Chain c = structure.getChain(0); assertEquals("did not find the expected 58 amino acids!",58,c.getAtomGroups("amino").size()); assertTrue(c.getAtomGroups("hetatm").size() == 0); Chain c2 = structure.getChain(1); assertTrue(c2.getAtomGroups("hetatm").size() == 65); assertTrue(c2.getAtomGroups("nucleotide").size() == 0 ); List compounds= structure.getCompounds(); assertTrue(compounds.size() == 1); Compound mol = compounds.get(0); assertTrue(mol.getMolName().startsWith("TRYPSIN INHIBITOR")); } public void testSSBondParsing() throws Exception { assertNotNull(structure); List ssbonds = structure.getSSBonds(); assertEquals("did not find the correct nr of SSBonds ",3,ssbonds.size()); String pdb1 = "SSBOND 1 CYS A 5 CYS A 55"; String pdb2 = "SSBOND 2 CYS A 14 CYS A 38"; SSBond bond1 = ssbonds.get(0); String b1 = bond1.toPDB(); assertTrue("PDB representation incorrect",pdb1.equals(b1.trim())); assertTrue("not right resnum1 " , bond1.getResnum1().equals("5")); assertTrue("not right resnum2 " , bond1.getResnum2().equals("55")); SSBond bond2 = ssbonds.get(1); String b2 = bond2.toPDB(); assertTrue("not right resnum1 " , bond2.getResnum1().equals("14")); assertTrue("not right resnum2 " , bond2.getResnum2().equals("38")); assertTrue("PDB representation incorrect",pdb2.equals(b2.trim())); } /** Tests that standard amino acids are working properly * @throws Exception */ public void testStandardAmino() throws Exception { AminoAcid arg = StandardAminoAcid.getAminoAcid("ARG"); assertTrue(arg.size() == 11 ); AminoAcid gly = StandardAminoAcid.getAminoAcid("G"); assertTrue(gly.size() == 4); } public void testHeader() { Map m = structure.getHeader(); assertNotNull(m); String classification = (String)m.get("classification"); assertTrue(classification.equals("PROTEINASE INHIBITOR (TRYPSIN)")); String idCode = (String)m.get("idCode"); assertEquals("the idCode in the Header is " + idCode + " and not 5PTI, as expected","5PTI",idCode); Float resolution = (Float) m.get("resolution"); assertEquals("the resolution in the Header is " + resolution + " and not 1.0, as expected",new Float(1.0),resolution); String technique = (String) m.get("technique"); String techShould = "X-RAY DIFFRACTION "; assertEquals("the technique in the Header is " + technique, techShould,technique); List compounds = structure.getCompounds(); assertEquals("did not find the right number of compounds! ", 1, compounds.size()); Compound comp = compounds.get(0); assertEquals("did not get the right compounds info",true,comp.getMolName().startsWith("TRYPSIN INHIBITOR")); List chainIds = comp.getChainId(); List chains = comp.getChains(); assertEquals("the number of chain ids and chains did not match!",chainIds.size(),chains.size()); assertEquals("the chain ID did not match", chainIds.get(0),chains.get(0).getName()); } public void testPDBHeader(){ Map m = structure.getHeader(); PDBHeader header = structure.getPDBHeader(); String classification = (String)m.get("classification"); assertTrue(classification.equals(header.getClassification())); String idCode = (String)m.get("idCode"); assertTrue(idCode.equals(header.getIdCode())); Float resolution = (Float) m.get("resolution"); assertTrue(resolution.floatValue() == header.getResolution()); String technique = (String) m.get("technique"); assertTrue(technique.equals(header.getTechnique())); } public void testCreateVirtualCBAtom(){ Group g1 = structure.getChain(0).getAtomGroup(11); if ( g1.getPDBName().equals("GLY")){ if ( g1 instanceof AminoAcid){ try { Atom cb = Calc.createVirtualCBAtom((AminoAcid)g1); g1.addAtom(cb); } catch (StructureException e){ fail ("createVirtualCBAtom failed with " + e.getMessage()); } } } else { fail("the group at position 11 is not a GLY!"); } } public void testMutation() throws Exception { Group g1 = (Group)structure.getChain(0).getAtomGroup(21).clone(); assertTrue(g1 != null); Group g2 = (Group)structure.getChain(0).getAtomGroup(53).clone(); assertTrue(g2 != null); assertEquals("The group at position 22 is not a PHE","PHE", g1.getPDBName()); assertEquals("The group position is not number 22","22", g1.getPDBCode()); assertEquals("The group at position 54 is not a THR","THR", g2.getPDBName()); assertEquals("The group position is not number 54","54", g2.getPDBCode()); Atom[] atoms1 = new Atom[3]; Atom[] atoms2 = new Atom[3]; atoms1[0] = g1.getAtom("N"); atoms1[1] = g1.getAtom("CA"); atoms1[2] = g1.getAtom("CB"); atoms2[0] = g2.getAtom("N"); atoms2[1] = g2.getAtom("CA"); atoms2[2] = g2.getAtom("CB"); SVDSuperimposer svds = new SVDSuperimposer(atoms1,atoms2); Matrix rotMatrix = svds.getRotation(); Atom tran = svds.getTranslation(); Group newGroup = (Group)g2.clone(); Calc.rotate(newGroup,rotMatrix); Calc.shift(newGroup,tran); Atom ca1 = g1.getAtom("CA"); Atom oldca2 = g2.getAtom("CA"); Atom newca2 = newGroup.getAtom("CA"); // this also tests the cloning ... double olddistance = Calc.getDistance(ca1,oldca2); assertTrue( olddistance > 10 ); // final test check that the distance between the CA atoms is small ; double newdistance = Calc.getDistance(ca1,newca2); assertTrue( newdistance < 0.1); } }