Examples with ISimpleChemObjectReader org.openscience.cdk.io.ISimpleChemObjectReader used on opensource projects

Example 1 with ISimpleChemObjectReader

use of org.openscience.cdk.io.ISimpleChemObjectReader in project ambit-mirror by ideaconsult.

the class CdkJmolAdapter method openBufferedReader.

/* **************************************************************
	 * the file related methods
	 * **************************************************************/
public Object openBufferedReader(String name, BufferedReader bufferedReader) {
    IChemFile chemFile = null;
    try {
        ISimpleChemObjectReader chemObjectReader = null;
        try {
            chemObjectReader = new ReaderFactory().createReader(bufferedReader);
        } catch (IOException ex) {
            return "Jmol: Error determining input format: " + ex;
        }
        if (chemObjectReader == null) {
            return "Jmol: unrecognized input format";
        }
        chemFile = (IChemFile) chemObjectReader.read(new org.openscience.cdk.ChemFile());
    } catch (CDKException ex) {
        return "Error reading input:" + ex;
    }
    if (chemFile == null)
        return "unknown error reading file";
    try {
        AtomTypeFactory factory = AtomTypeFactory.getInstance("pdb_atomtypes.txt", chemFile.getBuilder());
        // IAtomContainer atomContainer = (IAtomContainer)ChemFileManipulator.getAllInOneContainer(chemFile);
        Iterator<IChemSequence> seq = chemFile.chemSequences().iterator();
        while (seq.hasNext()) {
            Iterator<IChemModel> model = seq.next().chemModels().iterator();
            while (model.hasNext()) {
                Iterator<IAtomContainer> c = model.next().getMoleculeSet().atomContainers().iterator();
                while (c.hasNext()) {
                    Iterator<IAtom> it = c.next().atoms().iterator();
                    while (it.hasNext()) {
                        IAtom atom = it.next();
                        try {
                            factory.configure(atom);
                        } catch (CDKException exception) {
                            bcLogger.severe("Could not configure atom: " + atom);
                            bcLogger.log(Level.SEVERE, "  because: " + exception.getMessage(), exception);
                        }
                    }
                }
            }
        }
        return chemFile;
    } catch (Exception x) {
        return "Error configuring atoms input:" + x;
    }
}

Example 2 with ISimpleChemObjectReader

use of org.openscience.cdk.io.ISimpleChemObjectReader in project cdk by cdk.

the class GraphOnlyFingerprinterTest method createMolecule.

private static IAtomContainer createMolecule(String molecule) throws IOException, CDKException {
    IAtomContainer structure = null;
    if (molecule != null) {
        ISimpleChemObjectReader reader = new MDLV2000Reader(new StringReader(molecule));
        Assert.assertNotNull("Could not create reader", reader);
        if (reader.accepts(AtomContainer.class)) {
            structure = reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class));
        }
    }
    return structure;
}

Example 3 with ISimpleChemObjectReader

use of org.openscience.cdk.io.ISimpleChemObjectReader in project cdk by cdk.

the class ZagrebIndexDescriptorTest method test2Dvs3D.

@Test
public void test2Dvs3D() throws Exception {
    SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
    IAtomContainer mol = sp.parseSmiles("O1C2C34C(C(C1O)CCCc1cc(cc(c1)C(F)(F)F)C(F)(F)F)CCC(C3CCC(O2)(OO4)C)C");
    addExplicitHydrogens(mol);
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
    Aromaticity.cdkLegacy().apply(mol);
    double value2D = ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue();
    String filename = "cpsa-uncharged.sdf";
    InputStream ins = this.getClass().getResourceAsStream(filename);
    ISimpleChemObjectReader reader = new MDLV2000Reader(ins);
    ChemFile content = (ChemFile) reader.read((ChemObject) new ChemFile());
    List cList = ChemFileManipulator.getAllAtomContainers(content);
    mol = (IAtomContainer) cList.get(0);
    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
    Aromaticity.cdkLegacy().apply(mol);
    double value3D = ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue();
    Assert.assertEquals(value2D, value3D, 0.001);
}

Example 4 with ISimpleChemObjectReader

use of org.openscience.cdk.io.ISimpleChemObjectReader in project cdk by cdk.

the class MomentOfInertiaDescriptorTest method testMomentOfInertia2.

@Test
public void testMomentOfInertia2() throws java.lang.Exception {
    String filename = "momi2.hin";
    InputStream ins = this.getClass().getResourceAsStream(filename);
    ISimpleChemObjectReader reader = new HINReader(ins);
    ChemFile content = (ChemFile) reader.read((ChemObject) new ChemFile());
    List cList = ChemFileManipulator.getAllAtomContainers(content);
    IAtomContainer ac = (IAtomContainer) cList.get(0);
    DoubleArrayResult retval = (DoubleArrayResult) descriptor.calculate(ac).getValue();
    Assert.assertEquals(10068.419360, retval.get(0), 0.00001);
    Assert.assertEquals(9731.078356, retval.get(1), 0.00001);
    Assert.assertEquals(773.612799, retval.get(2), 0.00001);
    Assert.assertEquals(1.034666, retval.get(3), 0.00001);
    Assert.assertEquals(13.014804, retval.get(4), 0.00001);
    Assert.assertEquals(12.578745, retval.get(5), 0.00001);
    Assert.assertEquals(8.2966226, retval.get(6), 0.00001);
}

Example 5 with ISimpleChemObjectReader

use of org.openscience.cdk.io.ISimpleChemObjectReader in project cdk by cdk.

the class PetitjeanShapeIndexDescriptorTest method testPetitjeanShapeIndexDescriptor.

@Test
public void testPetitjeanShapeIndexDescriptor() throws Exception {
    // first molecule is nbutane, second is naphthalene
    String filename = "petitejean.sdf";
    InputStream ins = this.getClass().getResourceAsStream(filename);
    ISimpleChemObjectReader reader = new MDLV2000Reader(ins);
    ChemFile content = (ChemFile) reader.read((ChemObject) new ChemFile());
    List cList = ChemFileManipulator.getAllAtomContainers(content);
    IAtomContainer ac = (IAtomContainer) cList.get(0);
    DescriptorValue result = descriptor.calculate(ac);
    DoubleArrayResult dar = (DoubleArrayResult) result.getValue();
    Assert.assertEquals(0.5, dar.get(0), 0.00001);
    Assert.assertEquals(0.606477, dar.get(1), 0.000001);
    ac = (IAtomContainer) cList.get(1);
    result = descriptor.calculate(ac);
    dar = (DoubleArrayResult) result.getValue();
    Assert.assertEquals(0.666666, dar.get(0), 0.000001);
    Assert.assertEquals(0.845452, dar.get(1), 0.000001);
}