mdlv2000readertest.java

化学图形处理软件

        assertNotNull(chemFile);
        List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
        assertEquals(1, containersList.size());
        assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0);
        assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0);
    }
    
    public void testReserpine() throws Exception {
        String filename = "data/mdl/reserpine.mol";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLV2000Reader reader = new MDLV2000Reader(ins);
        ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
        assertNotNull(chemFile);
        List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
        assertEquals(1, containersList.size());
        assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0);
        assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0);
    }    


    public void testSixRing() throws Exception {
        String filename = "data/mdl/six-ring-4x4.mol";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLV2000Reader reader = new MDLV2000Reader(ins);
        ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
        assertNotNull(chemFile);
        List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
        assertEquals(1, containersList.size());
        assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0);
        assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0);
    }


    public void testSuperspiro() throws Exception {
        String filename = "data/mdl/superspiro.mol";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLV2000Reader reader = new MDLV2000Reader(ins);
        ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
        assertNotNull(chemFile);
        List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
        assertEquals(1, containersList.size());
        assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0);
        assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0);
    }

    public void testGhemicalOutput() throws Exception {
        String filename = "data/mdl/butanoic_acid.mol";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLV2000Reader reader = new MDLV2000Reader(ins);
        ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
        assertNotNull(chemFile);
        List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
        assertEquals(1, containersList.size());
        assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0);
        assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0);
    }

    public void testUsesGivenMolecule() throws Exception {
        String filename = "data/mdl/superspiro.mol"; // just a random file
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLV2000Reader reader = new MDLV2000Reader(ins);
        Molecule superspiro = new Molecule();
        superspiro.setID("superspiro");
        Molecule result = (Molecule)reader.read(superspiro);
        assertEquals(superspiro.getID(), result.getID());
    }

    /** 
     * @cdk.bug 835571
     */
    public void testReadFromStringReader () throws Exception {
        String mdl =
                "cyclopropane.mol\n" +
                "\n" +
                "\n" +
                "  9  9  0  0  0                 1 V2000\n" +
                "   -0.0073   -0.5272    0.9655 C   0  0  0  0  0\n" +
                "   -0.6776   -0.7930   -0.3498 C   0  0  0  0  0\n" +
                "    0.2103    0.4053   -0.1891 C   0  0  0  0  0\n" +
                "    0.8019   -1.1711    1.2970 H   0  0  0  0  0\n" +
                "   -0.6000   -0.2021    1.8155 H   0  0  0  0  0\n" +
                "   -1.7511   -0.6586   -0.4435 H   0  0  0  0  0\n" +
                "   -0.3492   -1.6277   -0.9620 H   0  0  0  0  0\n" +
                "    1.1755    0.4303   -0.6860 H   0  0  0  0  0\n" +
                "   -0.2264    1.3994   -0.1675 H   0  0  0  0  0\n" +
                "  1  2  1  6  0  0\n" +
                "  1  3  1  6  0  0\n" +
                "  1  4  1  0  0  0\n" +
                "  1  5  1  1  0  0\n" +
                "  2  3  1  0  0  0\n" +
                "  2  6  1  0  0  0\n" +
                "  2  7  1  6  0  0\n" +
                "  3  8  1  6  0  0\n" +
                "  3  9  1  0  0  0\n" +
                "M  END\n";
        MDLV2000Reader reader = new MDLV2000Reader(new StringReader(mdl));
        ChemFile chemFile = (ChemFile) reader.read(new ChemFile());
        assertNotNull(chemFile);
        assertEquals(1, chemFile.getChemSequenceCount());
        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);

        org.openscience.cdk.interfaces.IMoleculeSet som = model.getMoleculeSet();
        assertNotNull(som);
        assertEquals(1, som.getMoleculeCount());
        org.openscience.cdk.interfaces.IMolecule m = som.getMolecule(0);
        assertNotNull(m);
        assertEquals(9, m.getAtomCount());
        assertEquals(9, m.getBondCount());
    }
    
    public void testRGroup() throws Exception {
        String filename = "data/mdl/SARGROUPTEST.sdf";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLV2000Reader reader = new MDLV2000Reader(ins);
        Molecule mol = (Molecule)reader.read(new Molecule());
        assertEquals("R2",((PseudoAtom)mol.getAtom(19)).getLabel());
    }

    public void testAliasPropertyGroup() throws Exception {
        String filename = "data/mdl/AliasPropertyRGroup.sdf";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLV2000Reader reader = new MDLV2000Reader(ins);
        Molecule mol = (Molecule)reader.read(new Molecule());
        IAtom atom = mol.getAtom(3);
        assertTrue(atom instanceof PseudoAtom);
        assertEquals("R1", ((PseudoAtom)atom).getLabel());
    }

    /**
     * @cdk.bug 1587283
     */
    public void testBug1587283() throws Exception {
        String filename = "data/mdl/bug1587283.mol";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLV2000Reader reader = new MDLV2000Reader(ins);
        ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
        assertNotNull(chemFile);
        List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
        assertEquals(1, containersList.size());
        assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0);
        assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0);
    }
    
    public void testReadProton() throws Exception {
    	String mdl =
            "proton.mol\n" +
            "\n" +
            "\n" +
            "  1  0  0  0  0                 1 V2000\n" +
            "   -0.0073   -0.5272    0.9655 H   0  0  0  0  0\n" +
            "M  CHG  1   1   1\n" +
            "M  END\n";
    	MDLV2000Reader reader = new MDLV2000Reader(new StringReader(mdl));
    	Molecule mol = (Molecule)reader.read(new Molecule());
    	assertNotNull(mol);
    	assertEquals(1, mol.getAtomCount());
    	assertEquals(0, mol.getBondCount());
    	assertEquals(1, AtomContainerManipulator.getTotalFormalCharge(mol));
    	IAtom atom = mol.getAtom(0);
    	assertEquals(1, atom.getFormalCharge());
    }

    public void testReadingCharges() throws CDKException {
    	String filename = "data/mdl/withcharges.mol";
    	logger.info("Testing: " + filename);
    	InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
    	MDLV2000Reader reader = new MDLV2000Reader(ins);
    	IChemFile chemFile = (IChemFile) reader.read((IChemObject) new org.openscience.cdk.ChemFile());
    	assertEquals(1,chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0).getAtom(6).getFormalCharge());
    	assertEquals(-1,chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0).getAtom(8).getFormalCharge());
    }

}