pdbreadertest.java

化学图形处理软件

	    assertNotNull(reader);

	    IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
	    assertNotNull(chemFile);
	    assertEquals(1, chemFile.getChemSequenceCount());

	    org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
	    assertNotNull(seq);
	    assertEquals(1, seq.getChemModelCount());

	    IChemModel model = seq.getChemModel(0);
	    assertNotNull(model);
	    assertEquals(1, model.getMoleculeSet().getMoleculeCount());

	    IAtomContainer container = model.getMoleculeSet().getMolecule(0);
	    assertTrue(container instanceof IBioPolymer);
	    IBioPolymer polymer = (IBioPolymer)container;

	    // chemical validation
	    assertEquals(4770, ChemFileManipulator.getAtomCount(chemFile));
	    assertEquals(4, polymer.getStrandCount());
	    assertEquals(574, polymer.getMonomerCount());

	    assertTrue(polymer instanceof PDBPolymer);
	    PDBPolymer pdb = (PDBPolymer)polymer;

	    // PDB validation
	    assertEquals(35, pdb.getStructures().size());
	      
    }


    public void test1BOQ() throws Exception {
	    String filename = "data/pdb/1BOQ.pdb";
	    InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);

	    IChemObjectReader reader = new PDBReader(ins);
	    assertNotNull(reader);

	    IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
	    assertNotNull(chemFile);
	    assertEquals(1, chemFile.getChemSequenceCount());

	    org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
	    assertNotNull(seq);
	    assertEquals(1, seq.getChemModelCount());

	    IChemModel model = seq.getChemModel(0);
	    assertNotNull(model);
	    assertEquals(1, model.getMoleculeSet().getMoleculeCount());

	    IAtomContainer container = model.getMoleculeSet().getMolecule(0);
	    assertTrue(container instanceof IBioPolymer);
	    IBioPolymer polymer = (IBioPolymer)container;

	    // chemical validation
	    assertEquals(1538, ChemFileManipulator.getAtomCount(chemFile));
	    assertEquals(1, polymer.getStrandCount());
	    assertEquals(198, polymer.getMonomerCount());

	    assertTrue(polymer instanceof PDBPolymer);
	    PDBPolymer pdb = (PDBPolymer)polymer;

	    // PDB validation
	    assertEquals(21, pdb.getStructures().size());
	      
    }

    public void test1TOH() throws Exception {
	    String filename = "data/pdb/1TOH.pdb";
	    InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);

	    IChemObjectReader reader = new PDBReader(ins);
	    assertNotNull(reader);

	    IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
	    assertNotNull(chemFile);
	    assertEquals(1, chemFile.getChemSequenceCount());

	    org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
	    assertNotNull(seq);
	    assertEquals(1, seq.getChemModelCount());

	    IChemModel model = seq.getChemModel(0);
	    assertNotNull(model);
	    assertEquals(1, model.getMoleculeSet().getMoleculeCount());

	    IAtomContainer container = model.getMoleculeSet().getMolecule(0);
	    assertTrue(container instanceof IBioPolymer);
	    IBioPolymer polymer = (IBioPolymer)container;

	    // chemical validation
	    assertEquals(2804, ChemFileManipulator.getAtomCount(chemFile));
	    assertEquals(1, polymer.getStrandCount());
	    assertEquals(325, polymer.getMonomerCount());

	    assertTrue(polymer instanceof PDBPolymer);
	    PDBPolymer pdb = (PDBPolymer)polymer;

	    // PDB validation
	    assertEquals(23, pdb.getStructures().size());
    }
    
    public void test1CKV() throws Exception {
	    String filename = "data/pdb/1CKV.pdb";
	    InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);

	    IChemObjectReader reader = new PDBReader(ins);
	    assertNotNull(reader);

	    IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
	    assertNotNull(chemFile);
	    assertEquals(1, chemFile.getChemSequenceCount());

	    org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
	    assertNotNull(seq);
	    assertEquals(14, seq.getChemModelCount());

	    IChemModel model = seq.getChemModel(0);
	    assertNotNull(model);
	    assertEquals(1, model.getMoleculeSet().getMoleculeCount());

	    IAtomContainer container = model.getMoleculeSet().getMolecule(0);
	    assertTrue(container instanceof IBioPolymer);
	    IBioPolymer polymer = (IBioPolymer)container;

	    // chemical validation
	    assertEquals(31066, ChemFileManipulator.getAtomCount(chemFile));
	    assertEquals(1, polymer.getStrandCount());
	    assertEquals(141, polymer.getMonomerCount());

	    assertTrue(polymer instanceof PDBPolymer);
	    PDBPolymer pdb = (PDBPolymer)polymer;

	    // PDB validation
	    assertEquals(9, pdb.getStructures().size());
    }
    
    public void test1D66() throws Exception {
	    String filename = "data/pdb/1D66.pdb";
	    InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);

	    IChemObjectReader reader = new PDBReader(ins);
	    assertNotNull(reader);

	    IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
	    assertNotNull(chemFile);
	    assertEquals(1, chemFile.getChemSequenceCount());

	    org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
	    assertNotNull(seq);
	    assertEquals(1, seq.getChemModelCount());

	    IChemModel model = seq.getChemModel(0);
	    assertNotNull(model);
	    assertEquals(1, model.getMoleculeSet().getMoleculeCount());

	    IAtomContainer container = model.getMoleculeSet().getMolecule(0);
	    assertTrue(container instanceof IBioPolymer);
	    IBioPolymer polymer = (IBioPolymer)container;

	    assertTrue(polymer instanceof PDBPolymer);
	    PDBPolymer pdb = (PDBPolymer)polymer;
	    assertEquals(4, pdb.getStrandCount());

	    assertTrue(polymer.getStrandNames().contains("D"));
	    assertTrue(
	    	"Strand D is not a PDBStrand",
	    	polymer.getStrand("D") instanceof PDBStrand
	    );
	    assertTrue(polymer.getStrandNames().contains("E"));
	    assertTrue(
		    	"Strand E is not a PDBStrand",
		    	polymer.getStrand("E") instanceof PDBStrand
		    );
	    assertTrue(polymer.getStrandNames().contains("A"));
	    assertTrue(
		    	"Strand A is not a PDBStrand",
		    	polymer.getStrand("A") instanceof PDBStrand
		    );
	    assertTrue(polymer.getStrandNames().contains("B"));
	    assertTrue(
		    	"Strand B is not a PDBStrand",
		    	polymer.getStrand("B") instanceof PDBStrand
		    );

	    //Check to pick up all 4 strands
	    assertEquals(polymer.getStrands().size(),4);

	    //The following check is to see that the first monomers in a strand
	    //can be accessed consecutively
	    //i.e. their resSeq numbering follows that in the File

	    //Strand A
	    PDBStrand strandA=(PDBStrand)polymer.getStrand("A");
	    List lst=(List)strandA.getMonomerNamesInSequentialOrder();
	    
	    //Should be 57 monomers in strand A
	    assertEquals(57, lst.size());
	    
	    String monomer1=(String)lst.get(0);
	    IMonomer mono1=strandA.getMonomer(monomer1);
	    assertNotNull(mono1);
	    assertNotNull(mono1.getMonomerName());
	    assertTrue(
		    	"Monomer is not a PDBMonomer",
		    	mono1 instanceof PDBMonomer
		    	);
	    PDBMonomer pdbMonomer=(PDBMonomer)mono1;
	    assertEquals("A", pdbMonomer.getChainID());
	    assertEquals("8", pdbMonomer.getResSeq());

	    monomer1=(String)lst.get(1);
	    mono1=strandA.getMonomer(monomer1);
	    pdbMonomer=(PDBMonomer)mono1;
	    assertEquals("A", pdbMonomer.getChainID());
	    assertEquals("9", pdbMonomer.getResSeq());

	    monomer1=(String)lst.get(2);
	    mono1=strandA.getMonomer(monomer1);
	    pdbMonomer =(PDBMonomer)mono1;
	    assertEquals("A", pdbMonomer.getChainID());
	    assertEquals("10",pdbMonomer.getResSeq());

	    //Strand B
	    PDBStrand strandB=(PDBStrand)polymer.getStrand("B");
	    lst=(List)strandB.getMonomerNamesInSequentialOrder();
	    
	    //Should be 57 monomers in strand B
	    assertEquals(57, lst.size());
	    
	    monomer1=(String)lst.get(0);
	    mono1=strandB.getMonomer(monomer1);
	    assertNotNull(mono1);
	    assertNotNull(mono1.getMonomerName());
	    assertTrue(
		    	"Monomer is not a PDBMonomer",
		    	mono1 instanceof PDBMonomer
		    	);
	    pdbMonomer=(PDBMonomer)mono1;
	    assertEquals("B", pdbMonomer.getChainID());
	    assertEquals("8", pdbMonomer.getResSeq());

	    monomer1=(String)lst.get(1);
	    mono1=strandB.getMonomer(monomer1);
	    pdbMonomer=(PDBMonomer)mono1;
	    assertEquals("B", pdbMonomer.getChainID());
	    assertEquals("9", pdbMonomer.getResSeq());

	    monomer1=(String)lst.get(2);
	    mono1=strandB.getMonomer(monomer1);
	    pdbMonomer =(PDBMonomer)mono1;
	    assertEquals("B", pdbMonomer.getChainID());
	    assertEquals("10",pdbMonomer.getResSeq());


	    //Strand E
	    PDBStrand strandE=(PDBStrand)polymer.getStrand("E");
	    lst=(List)strandE.getMonomerNamesInSequentialOrder();
	    
	    //Should be 19 monomers in strand E
	    assertEquals(19, lst.size());
	    
	    monomer1=(String)lst.get(0);
	    mono1=strandE.getMonomer(monomer1);
	    assertNotNull(mono1);
	    assertNotNull(mono1.getMonomerName());
	    assertTrue(
		    	"Monomer is not a PDBMonomer",
		    	mono1 instanceof PDBMonomer
		    	);
	    pdbMonomer=(PDBMonomer)mono1;
	    assertEquals("E", pdbMonomer.getChainID());
	    assertEquals("20", pdbMonomer.getResSeq());

	    monomer1=(String)lst.get(1);
	    mono1=strandE.getMonomer(monomer1);
	    pdbMonomer=(PDBMonomer)mono1;
	    assertEquals("E", pdbMonomer.getChainID());
	    assertEquals("21", pdbMonomer.getResSeq());

	    monomer1=(String)lst.get(2);
	    mono1=strandE.getMonomer(monomer1);
	    pdbMonomer =(PDBMonomer)mono1;
	    assertEquals("E", pdbMonomer.getChainID());
	    assertEquals("22",pdbMonomer.getResSeq());


	    
	    //Chain D should be 1,2,3...19
	    PDBStrand strandD=(PDBStrand)polymer.getStrand("D");
	    lst=(List)strandD.getMonomerNamesInSequentialOrder();

	    //Should be 19 monomers in strand D
	    assertEquals(19, lst.size());
	    
	    monomer1=(String)lst.get(0);
	    mono1=strandD.getMonomer(monomer1);
	    assertNotNull(mono1);
	    assertNotNull(mono1.getMonomerName());
	    assertTrue(
		    	"Monomer is not a PDBMonomer",
		    	mono1 instanceof PDBMonomer
		    	);
	    pdbMonomer=(PDBMonomer)mono1;
	    assertEquals("D", pdbMonomer.getChainID());
	    assertEquals("1", pdbMonomer.getResSeq());

	    monomer1=(String)lst.get(1);
	    mono1=strandD.getMonomer(monomer1);
	    pdbMonomer=(PDBMonomer)mono1;
	    assertEquals("D", pdbMonomer.getChainID());
	    assertEquals("2", pdbMonomer.getResSeq());

	    monomer1=(String)lst.get(2);
	    mono1=strandD.getMonomer(monomer1);
	    pdbMonomer=(PDBMonomer)mono1;
	    assertEquals("D", pdbMonomer.getChainID());
	    assertEquals("3",pdbMonomer.getResSeq());

	    // PDB Structures validation
	    //Should have 6 helices
	    assertEquals(6, pdb.getStructures().size());
	      
    }
  
    
}