Examples with IteratingDelimitedFileReader ambit2.core.io.IteratingDelimitedFileReader used on opensource projects

Example 1 with IteratingDelimitedFileReader

use of ambit2.core.io.IteratingDelimitedFileReader in project ambit-mirror by ideaconsult.

the class ListenerTest method testListenerCSV.

@Test
public void testListenerCSV() throws Exception {
    String[] labels = { "Code", "Compound", "SMILES", "MolWeigth", "CasRN", "log_P", "eLumo", "eHomo", "IL", "Dev.", "Pred", "abs dev", "Obs" };
    IIteratingChemObjectReader reader = new IteratingDelimitedFileReader(getClass().getClassLoader().getResourceAsStream("Debnath_smiles.csv"));
    readFile(reader, labels);
}

Example 2 with IteratingDelimitedFileReader

use of ambit2.core.io.IteratingDelimitedFileReader in project ambit-mirror by ideaconsult.

the class RawIteratingWrapperTest method test.

@Test
public void test() throws Exception {
    IIteratingChemObjectReader reader = FileInputState.getReader(RawIteratingWrapperTest.class.getClassLoader().getResourceAsStream("ambit2/core/data/io/test.txt"), "test.txt");
    Assert.assertTrue(reader != null);
    // Assert.assertTrue(reader instanceof IteratingDelimitedFileReader);
    RawIteratingWrapper wrapper = new RawIteratingWrapper(reader);
    int count = 0;
    while (wrapper.hasNext()) {
        IStructureRecord record = (IStructureRecord) wrapper.next();
        count++;
    }
    Assert.assertEquals(11, count);
    wrapper.close();
}

Example 3 with IteratingDelimitedFileReader

use of ambit2.core.io.IteratingDelimitedFileReader in project ambit-mirror by ideaconsult.

the class PKASmartsDescriptorTest method testPredictions.

@Test
public void testPredictions() throws Exception {
    File file = File.createTempFile("ambit_results", ".csv");
    file.deleteOnExit();
    // System.out.println(file.getAbsolutePath());
    DelimitedFileWriter writer = new DelimitedFileWriter(new FileOutputStream(file));
    HydrogenAdderProcessor ha = new HydrogenAdderProcessor();
    ha.setAddEexplicitHydrogens(true);
    Preferences.setProperty(Preferences.STOP_AT_UNKNOWNATOMTYPES, "true");
    InputStream in = PKASmartsDescriptor.class.getClassLoader().getResourceAsStream("ambit2/descriptors/pka/benchmark_new.csv");
    IteratingDelimitedFileReader reader = new IteratingDelimitedFileReader(in);
    while (reader.hasNext()) {
        Object o = reader.next();
        Assert.assertTrue(o instanceof IAtomContainer);
        IAtomContainer a = null;
        try {
            a = ha.process((IAtomContainer) o);
            // AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(a);
            CDKHueckelAromaticityDetector.detectAromaticity(a);
            DescriptorValue value = pka.calculate(a);
            VerboseDescriptorResult<String, DoubleResult> result = (VerboseDescriptorResult<String, DoubleResult>) value.getValue();
            a.setProperty(value.getNames()[0], result.getResult().doubleValue());
            a.setProperty(value.getNames()[0] + "-trace", result.getExplanation());
            Double d = Double.valueOf(a.getProperty("pKa-SMARTS").toString());
            if (!d.equals(result.getResult().doubleValue())) {
            }
            writer.write(a);
        } catch (CDKException x) {
            continue;
        } catch (AmbitException x) {
            continue;
        } catch (Exception x) {
            x.printStackTrace();
            continue;
        }
    }
    in.close();
    writer.close();
}

Example 4 with IteratingDelimitedFileReader

use of ambit2.core.io.IteratingDelimitedFileReader in project ambit-mirror by ideaconsult.

the class DragonShell method parseOutput.

@Override
protected synchronized IAtomContainer parseOutput(String path, IAtomContainer mol) throws ShellException {
    // mol.getProperties().clear();
    MoleculeTools.clearProperties(mol);
    for (int i = 0; i < outFile.length; i++) {
        String fname = path + "/" + outFile[i];
        File f = new File(fname);
        if (!f.exists())
            continue;
        logger.fine("<outfile name=\"" + fname + "\">");
        try {
            IteratingDelimitedFileReader re = new IteratingDelimitedFileReader(new InputStreamReader(new FileInputStream(f)), new DelimitedFileFormat("\t", '"'));
            while (re.hasNext()) {
                IAtomContainer m = (IAtomContainer) re.next();
                mol.setProperties(m.getProperties());
                break;
            }
            re.close();
        // f.delete();
        } catch (Exception x) {
            logger.fine("<error name=\"" + x.getMessage() + "\"/>");
            logger.fine("</outfile>");
            throw new ShellException(this, x);
        } finally {
        }
        logger.fine("</outfile>");
    }
    return mol;
}

Example 5 with IteratingDelimitedFileReader

use of ambit2.core.io.IteratingDelimitedFileReader in project ambit-mirror by ideaconsult.

the class VegaShell method parseOutput.

@Override
protected IAtomContainer parseOutput(String path, IAtomContainer mol) throws ShellException {
    // mol.getProperties().clear();
    MoleculeTools.clearProperties(mol);
    for (int i = 0; i < outFile.length; i++) {
        String fname = path + "/" + outFile[i];
        File f = new File(fname);
        if (!f.exists())
            continue;
        logger.fine("<outfile name=\"" + fname + "\">");
        try {
            IteratingDelimitedFileReader re = new IteratingDelimitedFileReader(new InputStreamReader(new FileInputStream(f)), new DelimitedFileFormat("\t", '"')) {

                @Override
                public void setReader(Reader reader) throws CDKException {
                    super.setReader(reader);
                    try {
                        // skipLines(35); //for all models
                        skipLines(13);
                    } catch (Exception x) {
                        logger.log(Level.WARNING, x.getMessage());
                    }
                }
            };
            while (re.hasNext()) {
                IAtomContainer m = (IAtomContainer) re.next();
                for (Entry<Object, Object> e : m.getProperties().entrySet()) {
                    if ("-".equals(e.getValue()))
                        continue;
                    Property p = properties.get(e.getKey().toString().replaceAll("\"", ""));
                    if (p == null)
                        continue;
                    mol.setProperty(p, e.getValue());
                }
                break;
            }
            re.close();
        // f.delete();
        } catch (Exception x) {
            logger.fine("<error name=\"" + x.getMessage() + "\"/>");
            logger.fine("</outfile>");
            throw new ShellException(this, x);
        } finally {
        }
        logger.fine("</outfile>");
    }
    return mol;
}