Java SmilesParser.parseSmiles方法代码示例

import org.openscience.cdk.smiles.SmilesParser; //导入方法依赖的package包/类
@Before
public void setUp() throws Exception {
	this.testFile = new File("data_tests/pictureTest.png");
	if (this.testFile.exists())
		this.testFile.delete();
	
	this.smiles = "c1ccccc1";
	
	SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
	this.imol = null;
	try {
		this.imol = sp.parseSmiles(this.smiles);
	} catch (InvalidSmilesException e) {
		e.printStackTrace();
	}
}
 

import org.openscience.cdk.smiles.SmilesParser; //导入方法依赖的package包/类
/**
 * Checks if the given structures are isomorph.
 * 
 * @param candidate1 the candidate1
 * @param candidate2 the candidate2
 * 
 * @return true, if is isomorph
 * 
 * @throws CDKException the CDK exception
 */
public boolean isIsomorph(String candidate1, String candidate2) throws CDKException
{
	IAtomContainer cand1 = null;
	IAtomContainer cand2 = null;
	
	if(hasAtomContainer)
	{
		cand1 = this.candidateToStructure.get(candidate1);
		cand2 = this.candidateToStructure.get(candidate2);
	}
	else
	{
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		cand1 = sp.parseSmiles(candidatesToSmiles.get(candidate1));
		cand2 = sp.parseSmiles(candidatesToSmiles.get(candidate2));
	}
	
	return UniversalIsomorphismTester.isIsomorph(cand1, cand2);
}
 

import org.openscience.cdk.smiles.SmilesParser; //导入方法依赖的package包/类
/**
 * Gets the mol from smiles.
 * 
 * @param smiles the smiles
 * 
 * @return the mol from smiles
 */
public IAtomContainer getMolFromSmiles(String smiles) {
	if (smiles == null || smiles.isEmpty())
		return null;

	IAtomContainer container = null;
	try {
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		IMolecule m = sp.parseSmiles(smiles);
		container = m;
		
		// hydrogen handling
		container = hydrogenHandling(container);
	} catch (InvalidSmilesException ise) {
		return null;
	}
	return container;
}
 

import org.openscience.cdk.smiles.SmilesParser; //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.smiles.SmilesParser; //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.smiles.SmilesParser; //导入方法依赖的package包/类
public static ChemicalCompound createFromSmiles(String name, String smilesString)
        throws CDKException
{
    SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
    IMolecule cdkMolecule = smilesParser.parseSmiles(smilesString);
    return new ChemicalCompound(name, cdkMolecule);
}
 

import org.openscience.cdk.smiles.SmilesParser; //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();
    }