Java SilentChemObjectBuilder类代码示例

import org.openscience.cdk.silent.SilentChemObjectBuilder; //导入依赖的package包/类
private static void highlightSmartsPattern(IAtomContainer container, Color highlightColor, String smarts) {
    if (smarts == null)
        return;
    try {
        Pattern ptrn = SmartsPattern.create(smarts,
                                            SilentChemObjectBuilder.getInstance());
        Mappings mappings = ptrn.matchAll(container);

        int[] p = mappings.first();
        for (int x : p) {
            container.getAtom(x).setProperty(HIGHLIGHT_COLOR,
                                             highlightColor);
        }
        for (IBond bond : container.bonds()) {
            if (bond.getAtom(0).getProperty(HIGHLIGHT_COLOR) != null && bond.getAtom(1).getProperty(HIGHLIGHT_COLOR) != null)
                bond.setProperty(HIGHLIGHT_COLOR,
                                 highlightColor);
        }
    } catch (IOException e) {
        System.err.println(e.getMessage());
    }
}
 

import org.openscience.cdk.silent.SilentChemObjectBuilder; //导入依赖的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; //导入依赖的package包/类
public static void main(String[] args) throws CDKException, IOException {
    
    final Font font = new Font("Verdana",
                               Font.PLAIN,
                               24);
    final DepictionGenerator generator = new DepictionGenerator(Arrays.asList(new BasicSceneGenerator(),
                                                                              new StandardGenerator(font)));

    IAtomContainer container = new SmilesParser(SilentChemObjectBuilder.getInstance()).parseSmiles("[nH]1cccc1.c1ccccc1.[Na+].[Cl-]");
    
    IAtomContainerSet acSet = ConnectivityChecker.partitionIntoMolecules(container);

    StructureDiagramGenerator sdg = new StructureDiagramGenerator();
    sdg.setUseTemplates(false);
    for (IAtomContainer ac : acSet.atomContainers()) {
        sdg.setMolecule(ac, false);
        sdg.generateCoordinates();
    }
    
    SetDepiction depiction = generator.generate(acSet);
    depiction.setLayout(SetDepiction.Layout.Vertical);
    
    FileWriter fw = new FileWriter("/Users/johnmay/Desktop/fragments.svg");
    fw.write(depiction.toSvg());
    fw.close();
    fw = new FileWriter("/Users/johnmay/Desktop/fragments_x2.svg");
    fw.write(depiction.toSvg(2));
    fw.close();
    fw = new FileWriter("/Users/johnmay/Desktop/fragments_x4.svg");
    fw.write(depiction.toSvg(4));
    fw.close();

    ImageIO.write(depiction.toBufferedImage(2), "png", new File("/Users/johnmay/Desktop/fragments_vert.png"));
    depiction.setLayout(SetDepiction.Layout.Horizontal);
    ImageIO.write(depiction.toBufferedImage(2), "png", new File("/Users/johnmay/Desktop/fragments_horz.png"));
    
    
}
 

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

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

        if (args.length < 2) {
            System.err.println("usage: ./fpsscan {input.fps} 'SMILES' ['t']");
            return;
        }

        final String fpsPath = args[0];
        final String smi = args[1];
        final double lim = args.length > 2 ? Double.parseDouble(args[2]) : DEFAULT_THRESHOLD;

        final int len = 1024;
        final long[] words = new long[len / 64];

        // generate query fp (TODO make choosable)
        CircularFingerprinter fpr = new CircularFingerprinter(CircularFingerprinter.CLASS_ECFP4);
        IAtomContainer container = new SmilesParser(SilentChemObjectBuilder.getInstance()).parseSmiles(smi);
        BinaryFingerprint qFp = BinaryFingerprint.valueOf(fpr.getBitFingerprint(container).asBitSet().toLongArray(), len);

        int cnt = 0;
        BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out));
        long t0 = System.nanoTime();

        FileChannel in = new FileInputStream(fpsPath).getChannel();
        ByteBuffer buffer = in.map(FileChannel.MapMode.READ_ONLY, 0, new File(fpsPath).length());

        StringBuilder idStrBldr = new StringBuilder();

        while (buffer.hasRemaining()) {

            // reset
            idStrBldr.setLength(0);

            FpsFmt.readHex(buffer, len, words); // hex bit set
            buffer.get(); // tab
            readToEnd(buffer, idStrBldr); // id

            BinaryFingerprint dFp = BinaryFingerprint.valueOf(words, len);
            double t = qFp.similarity(dFp, Similarity.Tanimoto);
            boolean display = t >= lim;

            if (display) {
                bw.write(idStrBldr.toString());
                bw.write(SEPARATOR);
                bw.write(String.format("%.2f", t));
                bw.newLine();
            }
        }
        long t1 = System.nanoTime();
        in.close();
        bw.close();
        System.err.printf("\rScanned in %.2fs \n", (t1 - t0) / 1e9);
    }
 

import org.openscience.cdk.silent.SilentChemObjectBuilder; //导入依赖的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);

}