Java SilentChemObjectBuilder.getInstance方法代码示例

import org.openscience.cdk.silent.SilentChemObjectBuilder; //导入方法依赖的package包/类
public static IAtomContainer parseSmiles(String smiles) {
	SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
	IAtomContainer precursorMolecule = null;
	try {
		precursorMolecule = sp.parseSmiles(smiles);
	} catch (InvalidSmilesException e) {
		e.printStackTrace();
	}
	prepareAtomContainer(precursorMolecule, true);
	return precursorMolecule;
}
 

import org.openscience.cdk.silent.SilentChemObjectBuilder; //导入方法依赖的package包/类
/**
 * 
 * @param smiles
 * @return
 */
public static IAtomContainer parseSmilesImplicitHydrogen(String smiles) {
	SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
	IAtomContainer precursorMolecule = null;
	try {
		precursorMolecule = sp.parseSmiles(smiles);
	} catch (InvalidSmilesException e) {
		e.printStackTrace();
	}
	MoleculeFunctions.prepareAtomContainer(precursorMolecule, true);
	MoleculeFunctions.convertExplicitToImplicitHydrogens(precursorMolecule);
	return precursorMolecule;
}
 

import org.openscience.cdk.silent.SilentChemObjectBuilder; //导入方法依赖的package包/类
public Structure2DComponent(String structure) throws CDKException,
    IOException {

// Create a silend CDK builder
IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();

// Create a new molecule instance
molecule = builder.newInstance(IAtomContainer.class);

// Load the structure into the molecule
MDLV2000Reader molReader = new MDLV2000Reader(new StringReader(
	structure));
molReader.read(molecule);
molReader.close();

// Suppress the hydrogens
AtomContainerManipulator.suppressHydrogens(molecule);

// If the model has no coordinates, let's generate them
if (!GeometryUtil.has2DCoordinates(molecule)) {
    StructureDiagramGenerator sdg = new StructureDiagramGenerator();
    sdg.setMolecule(molecule, false);
    sdg.generateCoordinates();
}

// Generators make the image elements
Font font = new Font("Verdana", Font.PLAIN, 14);
List<IGenerator<IAtomContainer>> generators = new ArrayList<IGenerator<IAtomContainer>>();
generators.add(new BasicSceneGenerator());
generators.add(new StandardGenerator(font));

// Renderer needs to have a toolkit-specific font manager
renderer = new AtomContainerRenderer(generators, new AWTFontManager());

// Set default atom colors for the renderer
RendererModel rendererModel = renderer.getRenderer2DModel();
rendererModel.set(StandardGenerator.AtomColor.class,
	new CDK2DAtomColors());

   }
 

import org.openscience.cdk.silent.SilentChemObjectBuilder; //导入方法依赖的package包/类
static
public IAtomContainer parseAtomContainer(String structure){
	SmilesParser parser = new SmilesParser(SilentChemObjectBuilder.getInstance());

	try {
		return prepareAtomContainer(parser.parseSmiles(structure));
	} catch(CDKException ce){
		throw new EvaluationException(ce.toString());
	}
}
 

import org.openscience.cdk.silent.SilentChemObjectBuilder; //导入方法依赖的package包/类
public static void main(String[] args) throws IOException, CDKException {

    if (args.length < 1 || !args[0].endsWith(".sdf")) {
        System.err.println("Expected input SDF as argument.");
        return;
    }
    
    if (args[0].startsWith("~"))
        args[0] = System.getProperty("user.home") + args[0].substring(1);
    
    String sdfInPath  = args[0];
    String sdfOutPath = sdfInPath.substring(0, sdfInPath.length() - 4) + "-templates.sdf";
    
    System.out.println("Extracting ring templates to '" + sdfOutPath + "'");
    System.out.println(" - input SDfile: '" + sdfInPath + "'");

    RingTemplateExtractor extractor = new RingTemplateExtractor();

    IteratingSDFReader sdfReader = new IteratingSDFReader(new FileReader(sdfInPath),
                                                          SilentChemObjectBuilder.getInstance());
    SDfile:
    while (sdfReader.hasNext()) {

        IAtomContainer container = sdfReader.next();            
        
        if (container instanceof IQueryAtomContainer)
            continue;

        for (IAtom atom : container.atoms()) {
            if (atom.getImplicitHydrogenCount() == null)
                continue SDfile;
            if (atom.getPoint2d() == null)
                continue SDfile;
        }

        extractor.add(container);
    }
    
    extractor.writeSDfile(new File(sdfOutPath));
}
 

import org.openscience.cdk.silent.SilentChemObjectBuilder; //导入方法依赖的package包/类
public void initSmilesParser() {
	this.sp  = new SmilesParser(SilentChemObjectBuilder.getInstance());
}
 

import org.openscience.cdk.silent.SilentChemObjectBuilder; //导入方法依赖的package包/类
/**
 * @see java.lang.Runnable#run()
 */
public void run() {

    setStatus(TaskStatus.PROCESSING);

    resultWindow = new ResultWindow(
            "Searching for " + MZmineCore.getConfiguration().getMZFormat()
                    .format(searchedMass),
            peakListRow, searchedMass, charge, this);
    resultWindow.setVisible(true);

    logger.finest("Starting search for formulas for " + massRange + " Da");

    IsotopePattern detectedPattern = peakListRow.getBestIsotopePattern();
    if ((checkIsotopes) && (detectedPattern == null)) {
        final String msg = "Cannot calculate isotope pattern scores, because selected"
                + " peak does not have any isotopes. Have you run the isotope peak grouper?";
        MZmineCore.getDesktop().displayMessage(resultWindow, msg);
    }

    IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();

    generator = new MolecularFormulaGenerator(builder,
            massRange.lowerEndpoint(), massRange.upperEndpoint(),
            elementCounts);

    IMolecularFormula cdkFormula;
    while ((cdkFormula = generator.getNextFormula()) != null) {

        if (isCanceled())
            return;

        // Mass is ok, so test other constraints
        checkConstraints(cdkFormula);

    }

    if (isCanceled())
        return;

    logger.finest("Finished formula search for " + massRange
            + " m/z, found " + foundFormulas + " formulas");

    SwingUtilities.invokeLater(new Runnable() {
        public void run() {
            resultWindow.setTitle("Finished searching for "
                    + MZmineCore.getConfiguration().getMZFormat()
                            .format(searchedMass)
                    + " amu, " + foundFormulas + " formulas found");

        }
    });

    setStatus(TaskStatus.FINISHED);

}
 

import org.openscience.cdk.silent.SilentChemObjectBuilder; //导入方法依赖的package包/类
public static void main(String[] args) throws IOException, InvalidSmilesException {

        if (args.length < 1) {
            System.err.println("Usage ./smi2fps {input.smi} [{output.smi}]");
            return;
        }

        final String path = args[0];
        final BufferedWriter bw = args.length > 1
                            ? new BufferedWriter(new FileWriter(args[1])) :
                              new BufferedWriter(new OutputStreamWriter(System.out));

        final BufferedReader rdr    = new BufferedReader(new FileReader(path));
        final SmilesParser   smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());

        // TODO choose fingerprint
        IFingerprinter fpr = new CircularFingerprinter(CircularFingerprinter.CLASS_ECFP4);
        final int len = fpr.getSize();

        int cnt = 0;

        long t0 = System.nanoTime();
        String line;
        while ((line = rdr.readLine()) != null) {
            try {

                final IAtomContainer container = smipar.parseSmiles(line);
                final String         id        = suffixedId(line);
                final BitSet         bitSet    = fpr.getBitFingerprint(container).asBitSet();

                StringBuilder sb = new StringBuilder();
                FpsFmt.writeHex(sb, len, bitSet.toLongArray());

                bw.write(sb.toString());
                bw.write("\t");
                bw.write(id);
                bw.newLine();

                if (++cnt % TIME_STAMP_INTERVAL == 0)
                    System.err.print("\r[RUN] processed " + cnt+ " compounds, elapsed time " + elapsedTime(t0, System.nanoTime()));

            } catch (Exception e) {
                System.err.println("[INFO] Skipping " + line + " " + e.getMessage());
            }
        }
        long t1 = System.nanoTime();

        System.err.println("\r[FINISHED] processed " + cnt+ " compounds, elapsed time " + elapsedTime(t0, t1));

        rdr.close();
        bw.close();
    }
 

import org.openscience.cdk.silent.SilentChemObjectBuilder; //导入方法依赖的package包/类
public static IsotopePattern calculateIsotopePattern(
    String molecularFormula, double minAbundance, int charge,
    PolarityType polarity) {

IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();

IMolecularFormula cdkFormula = MolecularFormulaManipulator
	.getMolecularFormula(molecularFormula, builder);

return calculateIsotopePattern(cdkFormula, minAbundance, charge,
	polarity);

   }
 

import org.openscience.cdk.silent.SilentChemObjectBuilder; //导入方法依赖的package包/类
/**
 * @see java.lang.Runnable#run()
 */
public void run() {

    setStatus(TaskStatus.PROCESSING);

    totalRows = peakList.getNumberOfRows();

    for (PeakListRow row : peakList.getRows()) {

        if (row.getPeakIdentities().length > 0) {
            continue;
        }

        this.ResultingFormulas = new ArrayList<ResultFormula>();

        this.searchedMass = (row.getAverageMZ() - ionType.getAddedMass())
                * charge;

        message = "Formula prediction for " + MZmineCore.getConfiguration()
                .getMZFormat().format(searchedMass);

        massRange = mzTolerance.getToleranceRange(searchedMass);

        IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
        generator = new MolecularFormulaGenerator(builder,
                massRange.lowerEndpoint(), massRange.upperEndpoint(),
                elementCounts);

        IMolecularFormula cdkFormula;
        while ((cdkFormula = generator.getNextFormula()) != null) {
            // Mass is ok, so test other constraints
            checkConstraints(cdkFormula, row);

        }

        if (isCanceled())
            return;

        for (ResultFormula f : this.ResultingFormulas) {
            SimplePeakIdentity newIdentity = new SimplePeakIdentity(
                    f.getFormulaAsString());
            row.addPeakIdentity(newIdentity, false);
        }

        finishedRows++;

    }

    if (isCanceled())
        return;

    logger.finest("Finished formula search for all the peaks");

    setStatus(TaskStatus.FINISHED);

}