cml2test.java

化学图形处理软件

        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getMoleculeSet().getMoleculeCount(), 1);

        // test the molecule
        org.openscience.cdk.interfaces.IMolecule mol = model.getMoleculeSet().getMolecule(0);
        assertNotNull(mol);
        assertEquals(15, mol.getAtomCount());
        assertEquals(14, mol.getBondCount());
        assertFalse(GeometryToolsInternalCoordinates.has3DCoordinates(mol));
        assertTrue(GeometryToolsInternalCoordinates.has2DCoordinates(mol));
    }

    public void testCMLOK9() throws Exception {
        String filename = "data/cml/nsc3dmol.1.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getMoleculeSet().getMoleculeCount(), 1);

        // test the molecule
        org.openscience.cdk.interfaces.IMolecule mol = model.getMoleculeSet().getMolecule(0);
        assertNotNull(mol);
        assertEquals(15, mol.getAtomCount());
        assertEquals(15, mol.getBondCount());
        assertTrue(GeometryToolsInternalCoordinates.has3DCoordinates(mol));
        assertFalse(GeometryToolsInternalCoordinates.has2DCoordinates(mol));
    }

    public void testCMLOK10() throws Exception {
        String filename = "data/cml/nsc3dmol.2.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getMoleculeSet().getMoleculeCount(), 1);

        // test the molecule
        org.openscience.cdk.interfaces.IMolecule mol = model.getMoleculeSet().getMolecule(0);
        assertNotNull(mol);
        assertEquals(15, mol.getAtomCount());
        assertEquals(15, mol.getBondCount());
        assertTrue(GeometryToolsInternalCoordinates.has3DCoordinates(mol));
        assertFalse(GeometryToolsInternalCoordinates.has2DCoordinates(mol));
    }

    public void testCMLOK11() throws Exception {
        String filename = "data/cml/nsc3dmol.a1.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getMoleculeSet().getMoleculeCount(), 1);

        // test the molecule
        org.openscience.cdk.interfaces.IMolecule mol = model.getMoleculeSet().getMolecule(0);
        assertNotNull(mol);
        assertEquals(15, mol.getAtomCount());
        assertEquals(15, mol.getBondCount());
        assertTrue(GeometryToolsInternalCoordinates.has3DCoordinates(mol));
        assertFalse(GeometryToolsInternalCoordinates.has2DCoordinates(mol));
    }

    public void testCMLOK12() throws Exception {
        String filename = "data/cml/nsc3dmol.a2.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getMoleculeSet().getMoleculeCount(), 1);

        // test the molecule
        org.openscience.cdk.interfaces.IMolecule mol = model.getMoleculeSet().getMolecule(0);
        assertNotNull(mol);
        assertEquals(15, mol.getAtomCount());
        assertEquals(15, mol.getBondCount());
        assertTrue(GeometryToolsInternalCoordinates.has3DCoordinates(mol));
        assertFalse(GeometryToolsInternalCoordinates.has2DCoordinates(mol));
    }

    /**
     * This test tests wether the CMLReader is able to ignore the CMLSpect part
     * of a CML file, while extracting the molecule.
     */
    public void testCMLSpectMolExtraction() throws Exception {
        String filename = "data/cml/molAndspect.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getMoleculeSet().getMoleculeCount(), 1);

        // test the molecule
        org.openscience.cdk.interfaces.IMolecule mol = model.getMoleculeSet().getMolecule(0);
        assertNotNull(mol);
        assertEquals(17, mol.getAtomCount());
        assertEquals(18, mol.getBondCount());
        assertFalse(GeometryToolsInternalCoordinates.has3DCoordinates(mol));
        assertTrue(GeometryToolsInternalCoordinates.has2DCoordinates(mol));
    }

    /**
     * This test tests wether the CMLReader is able to ignore the CMLReaction part
     * of a CML file, while extracting the reaction.
     */
    public void testCMLReaction() throws Exception {
        String filename = "data/cml/reaction.2.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getReactionSet().getReactionCount(), 1);

        // test the reaction
        IReaction reaction = model.getReactionSet().getReaction(0);
        assertNotNull(reaction);
        assertEquals("react",reaction.getReactants().getAtomContainer(0).getID());
        assertEquals("product",reaction.getProducts().getAtomContainer(0).getID());
        assertEquals("a14293164",reaction.getReactants().getAtomContainer(0).getAtom(0).getID());
        assertEquals(6, reaction.getProducts().getAtomContainer(0).getAtomCount());
        assertEquals(6, reaction.getReactants().getAtomContainer(0).getAtomCount());
    }

    /**
     * This test tests wether the CMLReader is able to ignore the CMLReaction part
     * of a CML file, while extracting the reaction.
     */
    public void testCMLReactionWithAgents() throws Exception {
        String filename = "data/cml/reaction.1.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getReactionSet().getReactionCount(), 1);

        // test the reaction
        IReaction reaction = model.getReactionSet().getReaction(0);
        assertNotNull(reaction);
        assertEquals("react",reaction.getReactants().getAtomContainer(0).getID());
        assertEquals("product",reaction.getProducts().getAtomContainer(0).getID());
        assertEquals("water",reaction.getAgents().getAtomContainer(0).getID());
        assertEquals("H+",reaction.getAgents().getAtomContainer(1).getID());
        assertEquals(6, reaction.getProducts().getAtomContainer(0).getAtomCount());
        assertEquals(6, reaction.getReactants().getAtomContainer(0).getAtomCount());
    }
    /**
     * This test tests wether the CMLReader is able to ignore the CMLReaction part
     * of a CML file, while extracting the reaction.
     */
    public void testCMLReactionList() throws Exception {
        String filename = "data/cml/reactionList.1.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(1,seq.getChemModelCount());
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(2,model.getReactionSet().getReactionCount());
        assertEquals("1.3.2",model.getReactionSet().getReaction(0).getID());

        // test the reaction
        IReaction reaction = model.getReactionSet().getReaction(0);
        assertNotNull(reaction);
        assertEquals("actey",reaction.getReactants().getAtomContainer(0).getID());
        assertEquals("a14293164",reaction.getReactants().getAtomContainer(0).getAtom(0).getID());
        assertEquals(6, reaction.getProducts().getAtomContainer(0).getAtomCount());
        assertEquals(6, reaction.getReactants().getAtomContainer(0).getAtomCount());
    }

    /**
     * @cdk.bug 1560486
     */
    public void testCMLWithFormula() throws Exception {
        String filename = "data/cml/cmlWithFormula.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);

        IMolecule mol = model.getMoleculeSet().getMolecule(0);
        assertNotNull(mol);
        assertEquals("a",mol.getID());
        assertEquals("a1",mol.getAtom(0).getID());
        assertEquals(27, mol.getAtomCount());
        assertEquals(32, mol.getBondCount());
    }

    /**
	 * @cdk.bug 1085912
	 */
	public void testSFBug1085912_1() throws Exception {
		if (!runSlowTests()) { fail("Not running this slow test"); }
		
		String filename_pdb = "data/pdb/1CKV.pdb";
		String filename_cml = "data/cml/1CKV_1.cml";
	    InputStream ins1 = this.getClass().getClassLoader().getResourceAsStream(filename_pdb);
	    InputStream ins2 = this.getClass().getClassLoader().getResourceAsStream(filename_cml);
	    
	    /*1*/
	    IChemObjectReader reader = new PDBReader(ins1);
	    IChemFile chemFile1 = (IChemFile) reader.read(new NNChemFile());
	    IChemSequence seq1 = chemFile1.getChemSequence(0);
	    IChemModel model1 = seq1.getChemModel(0);
	    IAtomContainer container = model1.getMoleculeSet().getMolecule(0);
	    IBioPolymer polymer1 = (IBioPolymer)container;
	    int countchemFile1 = chemFile1.getChemSequenceCount();
	    int countseq1 = seq1.getChemModelCount();
	    int countmodel1 = model1.getMoleculeSet().getAtomContainerCount();
	    int countpolymer1 = polymer1.getAtomCount();


	    StringWriter writer = new StringWriter();
	    CMLWriter cmlWriter = new CMLWriter(writer);
	    cmlWriter.write(polymer1);
	    String cmlContent1 = writer.toString();


	    /*2*/
	    CMLReader reader2 = new CMLReader(new ByteArrayInputStream(cmlContent1.getBytes()));
	    IChemFile chemFil2 = (IChemFile)reader2.read(new NNChemFile());
	    IChemSequence seq2 = chemFil2.getChemSequence(0);
	    IChemModel model2 = seq2.getChemModel(0);
	    PDBPolymer polymer2 =  (PDBPolymer) model2.getMoleculeSet().getAtomContainer(0);


	    int countchemFile2 = chemFil2.getChemSequenceCount();
	    int countseq2 = seq2.getChemModelCount();
	    int countmodel2 = model2.getMoleculeSet().getAtomContainerCount();
	    int countpolymer2 = polymer2.getAtomCount();

	    assertEquals(countchemFile1, countchemFile2);
//	    assertEquals(countseq1,countseq2); /*not the same because the pdb file has more models*/
	    assertEquals(countmodel1,countmodel2);
	    assertEquals(countpolymer1,countpolymer2);


	    writer = new StringWriter();
	    cmlWriter = new CMLWriter(writer);
	    cmlWriter.write(polymer2);
	    String cmlContent2 = writer.toString();

	    String conte1 = cmlContent1.substring(0, 1000);
	    String conte2 = cmlContent2.substring(0, 1000);
	    assertEquals(conte1,conte2);
    }
    
}