cml23fragmentstest.java

化学图形处理软件

        
        IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);
        
        assertEquals(2, mol.getAtomCount());
        assertNull(mol.getAtom(0).getPoint3d());
        assertNull(mol.getAtom(1).getPoint3d());
        assertNotNull(mol.getAtom(0).getFractionalPoint3d());
        assertNotNull(mol.getAtom(1).getFractionalPoint3d());
    }
    
    public void testMissing2DCoordinates() throws Exception {
        String cmlString = 
          "<molecule id='m1'><atomArray><atom id='a1' xy2='0.0 0.1'/><atom id='a2'/><atom id='a3' xy2='0.1 0.0'/></atomArray></molecule>";
          
        IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);
        
        assertEquals(3, mol.getAtomCount());
        IAtom atom1 = mol.getAtom(0);
        IAtom atom2 = mol.getAtom(1);
        IAtom atom3 = mol.getAtom(2);
        
        assertNotNull(atom1.getPoint2d());
        assertNull   (atom2.getPoint2d());
        assertNotNull(atom3.getPoint2d());
    }

    public void testMissing3DCoordinates() throws Exception {
        String cmlString = 
          "<molecule id='m1'><atomArray><atom id='a1' xyz3='0.0 0.1 0.2'/><atom id='a2'/><atom id='a3' xyz3='0.1 0.0 0.2'/></atomArray></molecule>";
          
        IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);
        
        assertEquals(3, mol.getAtomCount());
        IAtom atom1 = mol.getAtom(0);
        IAtom atom2 = mol.getAtom(1);
        IAtom atom3 = mol.getAtom(2);
        
        assertNotNull(atom1.getPoint3d());
        assertNull   (atom2.getPoint3d());
        assertNotNull(atom3.getPoint3d());
    }
    
    public void testMoleculeId() throws Exception {
        String cmlString = "<molecule id='m1'><atomArray><atom id='a1'/></atomArray></molecule>";
        
        IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);

        assertEquals("m1", mol.getID());
    }
    
    public void testName() throws Exception {
        String cmlString = "<molecule id='m1'><name>acetic acid</name><atomArray atomID='a1 a2 a3'/></molecule>";
        
        IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);
        
        assertEquals("acetic acid", mol.getProperty(CDKConstants.TITLE));
    }
    
    public void testInChI() throws Exception {
        String cmlString = "<molecule id='m1'><identifier convention='iupac:inchi' value='InChI=1/CH2O2/c2-1-3/h1H,(H,2,3)'/><atomArray atomID='a1 a2 a3'/></molecule>";
        
        IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);
        
        assertEquals("InChI=1/CH2O2/c2-1-3/h1H,(H,2,3)", mol.getProperty(CDKConstants.INCHI));
    }
    
    public void testDictRef() throws Exception {
    	String cmlString = "<molecule id=\"alanine\" dictRef=\"pdb:aminoAcid\"><name>alanine</name><name dictRef=\"pdb:residueName\">Ala</name><name dictRef=\"pdb:oneLetterCode\">A</name><scalar dictRef=\"pdb:id\">3</scalar><atomArray><atom id=\"a1\" elementType=\"C\" x2=\"265.0\" y2=\"989.0\"/><atom id=\"a2\" elementType=\"N\" x2=\"234.0\" y2=\"972.0\" dictRef=\"pdb:nTerminus\"/><atom id=\"a3\" elementType=\"C\" x2=\"265.0\" y2=\"1025.0\"/><atom id=\"a4\" elementType=\"C\" x2=\"296.0\" y2=\"971.0\" dictRef=\"pdb:cTerminus\"/><atom id=\"a5\" elementType=\"O\" x2=\"296.0\" y2=\"935.0\"/><atom id=\"a6\" elementType=\"O\" x2=\"327.0\" y2=\"988.0\"/></atomArray><bondArray><bond id=\"b1\" atomRefs2=\"a2 a1\" order=\"S\"/><bond id=\"b2\" atomRefs2=\"a1 a3\" order=\"S\"/><bond id=\"b3\" atomRefs2=\"a1 a4\" order=\"S\"/><bond id=\"b4\" atomRefs2=\"a4 a5\" order=\"D\"/><bond id=\"b5\" atomRefs2=\"a4 a6\" order=\"S\"/></bondArray></molecule>";
    	
    	IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);
        
        Enumeration props = mol.getProperties().keys();
        boolean foundDictRefs = false;
		while (props.hasMoreElements()) {
			Object next = props.nextElement();
			if (next instanceof DictRef) foundDictRefs = true;
		}
		assertTrue(foundDictRefs);
    }
    
    public void testQSAROutput() throws Exception {
    	String specificationReference = "qsar:weight";
    	String implementationTitle = "org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor";
    	String implementationIdentifier = "$Id: CML23FragmentsTest.java 8301 2007-05-05 12:00:36 +0000 (Sa, 05 Mai 2007) egonw $";
    	String implementationVendor = "The Chemistry Development Kit";
    	
    	String cmlString = "<molecule xmlns=\"http://www.xml-cml.org/schema\"><atomArray><atom id=\"a5256233\" " +
    	    "elementType=\"C\" formalCharge=\"0\" hydrogenCount=\"0\" /><atom id=\"a26250401\" elementType=\"C\" " +
    	    "formalCharge=\"0\" hydrogenCount=\"0\" /><atom id=\"a16821027\" elementType=\"C\" formalCharge=\"0\" " +
    	    "hydrogenCount=\"0\" /><atom id=\"a14923925\" elementType=\"C\" formalCharge=\"0\" hydrogenCount=\"0\" />" +
    	    "<atom id=\"a7043360\" elementType=\"C\" formalCharge=\"0\" hydrogenCount=\"0\" /><atom id=\"a31278839\" " +
    	    "elementType=\"C\" formalCharge=\"0\" hydrogenCount=\"0\" /></atomArray><bondArray><bond id=\"b6175092\" " +
    	    "atomRefs2=\"a5256233 a26250401\" order=\"S\" /><bond id=\"b914691\" atomRefs2=\"a26250401 a16821027\" " +
    	    "order=\"D\" /><bond id=\"b5298332\" atomRefs2=\"a16821027 a14923925\" order=\"S\" /><bond id=\"b29167060\" " +
    	    "atomRefs2=\"a14923925 a7043360\" order=\"D\" /><bond id=\"b14093690\" atomRefs2=\"a7043360 a31278839\" " +
    	    "order=\"S\" /><bond id=\"b11924794\" atomRefs2=\"a31278839 a5256233\" order=\"D\" /></bondArray>" +
    	    "<propertyList><property xmlns:qsar=\"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/\" " +
    	    "convention=\"qsar:DescriptorValue\"><metadataList><metadata dictRef=\"qsar:specificationReference\" " +
    	    "content=\"" + specificationReference + "\" /><metadata dictRef=\"qsar:implementationTitle\" content=\"" +
    	    implementationTitle + "\" /><metadata dictRef=\"qsar:implementationIdentifier\" " +
    	    "content=\"" + implementationIdentifier + "\" /><metadata dictRef=\"" +
    	    "qsar:implementationVendor\" content=\"" + implementationVendor + "\" /><metadataList title=\"qsar:" +
    	    "descriptorParameters\"><metadata title=\"elementSymbol\" content=\"*\" /></metadataList></metadataList>" +
    	    "<scalar dataType=\"xsd:double\" dictRef=\"qsar:weight\">72.0</scalar></property></propertyList></molecule>";

    	IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);
        
        assertNotNull(mol);
        assertEquals(1, mol.getProperties().size());
        Object key = mol.getProperties().keySet().toArray()[0];
        assertNotNull(key);
        assertTrue(key instanceof DescriptorSpecification);
        DescriptorSpecification spec = (DescriptorSpecification)key;
        assertEquals(specificationReference, spec.getSpecificationReference());
        assertEquals(implementationTitle, spec.getImplementationTitle());
        assertEquals(implementationIdentifier, spec.getImplementationIdentifier());
        assertEquals(implementationVendor, spec.getImplementationVendor());
        
        assertNotNull(mol.getProperty(key));
        assertTrue(mol.getProperty(key) instanceof DescriptorValue);
        DescriptorValue value = (DescriptorValue)mol.getProperty(key);
        IDescriptorResult result = value.getValue();
        assertNotNull(result);
        assertTrue(result instanceof DoubleResult);
        assertEquals(72.0, ((DoubleResult)result).doubleValue(), 0.001);
    }
    
    private IChemFile parseCMLString(String cmlString) throws Exception {
        IChemFile chemFile = null;
        CMLReader reader = new CMLReader(new ByteArrayInputStream(cmlString.getBytes()));
        chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());
        return chemFile;
    }

    /**
     * Tests wether the file is indeed a single molecule file
     */
    private IMolecule checkForSingleMoleculeFile(IChemFile chemFile) {
        return checkForXMoleculeFile(chemFile, 1);
    }
    
    private IMolecule checkForXMoleculeFile(IChemFile chemFile, int numberOfMolecules) {
        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);
        
        org.openscience.cdk.interfaces.IMoleculeSet moleculeSet = model.getMoleculeSet();
        assertNotNull(moleculeSet);
        
        assertEquals(moleculeSet.getMoleculeCount(), numberOfMolecules);
        IMolecule mol = null;
        for (int i=0; i<numberOfMolecules; i++) {
            mol = moleculeSet.getMolecule(i);
            assertNotNull(mol);
        }
        return mol;
    }

//    private ICrystal checkForCrystalFile(IChemFile chemFile) {
//        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);
//        
//        org.openscience.cdk.interfaces.ICrystal crystal = model.getCrystal();
//        assertNotNull(crystal);
//        
//        return crystal;
//    }
    
    public void testReaction() throws Exception {
        String cmlString = "<reaction>"+
        "<reactantList><reactant><molecule id='react'/></reactant></reactantList>"+
		"<productList><product><molecule id='product'/></product></productList>"+
        "<substanceList><substance><molecule id='water'/></substance></substanceList>"+
        "</reaction>";
        
        IChemFile chemFile = parseCMLString(cmlString);
        IReaction reaction = checkForSingleReactionFile(chemFile);

        assertEquals(1, reaction.getReactantCount());
        assertEquals(1, reaction.getProductCount());
        assertEquals(1, reaction.getAgents().getMoleculeCount());
        assertEquals("react", reaction.getReactants().getMolecule(0).getID());
        assertEquals("product", reaction.getProducts().getMolecule(0).getID());
        assertEquals("water", reaction.getAgents().getMolecule(0).getID());
    }
    
    /**
     * Tests wether the file is indeed a single reaction file
     */
    private IReaction checkForSingleReactionFile(IChemFile chemFile) {
        return checkForXReactionFile(chemFile, 1);
    }
    
    private IReaction checkForXReactionFile(IChemFile chemFile, int numberOfReactions) {
        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);
        
        IReactionSet reactionSet = model.getReactionSet();
        assertNotNull(reactionSet);
        
        assertEquals(reactionSet.getReactionCount(), numberOfReactions);
        IReaction reaction = null;
        for (int i=0; i<numberOfReactions; i++) {
            reaction = reactionSet.getReaction(i);
            assertNotNull(reaction);
        }
        return reaction;
    }

}