Examples with SmilesParserWrapper ambit2.core.smiles.SmilesParserWrapper used on opensource projects

Example 1 with SmilesParserWrapper

use of ambit2.core.smiles.SmilesParserWrapper in project ambit-mirror by ideaconsult.

the class MoleculeTools method getFingerPrint.

public static BitSet getFingerPrint(String smiles, int fpLength) throws Exception {
    SmilesParserWrapper sp = SmilesParserWrapper.getInstance();
    IAtomContainer mol = sp.parseSmiles(smiles);
    if (fingerprinter == null)
        fingerprinter = new Fingerprinter(fpLength);
    return fingerprinter.getBitFingerprint(mol).asBitSet();
}

Example 2 with SmilesParserWrapper

use of ambit2.core.smiles.SmilesParserWrapper in project ambit-mirror by ideaconsult.

the class AtomEnvironmentHammingDistanceTest method testGetDistance.

/**
 * Test method for {@link ambit2.similarity.AtomEnvironmentHammingDistance#getDistance(ambit2.data.descriptors.AtomEnvironmentList, ambit2.data.descriptors.AtomEnvironmentList)}.
 */
@Test
public void testGetDistance() throws Exception {
    IAtomContainer mol = MoleculeFactory.makeAlkane(3);
    IAtomContainer mol1 = MoleculeFactory.makeAlkane(3);
    SmilesParserWrapper p = SmilesParserWrapper.getInstance();
    IAtomContainer mol2 = p.parseSmiles("CCCC");
    AtomEnvironmentGenerator g = new AtomEnvironmentGenerator();
    g.setUseHydrogens(true);
    g.setMaxLevels(3);
    AtomEnvironmentList ae = g.generateProperty(mol);
    AtomEnvironmentList ae1 = g.generateProperty(mol1);
    AtomEnvironmentList ae2 = g.generateProperty(mol2);
    AtomEnvironmentsDistance hd = new AtomEnvironmentsDistance();
    Assert.assertEquals(1.0, hd.getDistance(ae, ae1), 1E-10);
    Assert.assertEquals(hd.getDistance(ae1, ae), hd.getDistance(ae, ae1), 1E-10);
    System.out.println(ae);
    System.out.println(ae2);
    float d = hd.getDistance(ae, ae2);
    // System.out.println(d);
    Assert.assertTrue(d < 1.0);
    Assert.assertEquals(hd.getDistance(ae2, ae), hd.getDistance(ae1, ae2), 1E-10);
}

Example 3 with SmilesParserWrapper

use of ambit2.core.smiles.SmilesParserWrapper in project ambit-mirror by ideaconsult.

the class Mopac7WriterTest method testReader2009.

@Test
public void testReader2009() throws Exception {
    InputStream in = Mopac7Writer.class.getClassLoader().getResourceAsStream("ambit2/mopac/mopac2009.out");
    Mopac7Reader r = new Mopac7Reader(in);
    SmilesParserWrapper p = SmilesParserWrapper.getInstance(SMILES_PARSER.CDK);
    String smiles = "C=C";
    IChemObject m = p.parseSmiles(smiles);
    m = r.read(m);
    in.close();
    Object e = m.getProperty("TOTAL ENERGY");
    Assert.assertEquals("-1223.60097", e.toString());
    /*
            this fails - todo check why
            Assert.assertEquals(-9.925,
            		Double.parseDouble(m.getProperty(DescriptorMopacShell.EHOMO).toString()),
            		1E-3);
            Assert.assertEquals(1.007,
            		Double.parseDouble(m.getProperty(DescriptorMopacShell.ELUMO).toString()),
            		1E-3);   
            		*/
    for (int i = 0; i < ((IAtomContainer) m).getAtomCount(); i++) {
        Assert.assertNotNull(((IAtomContainer) m).getAtom(i).getPoint3d());
    }
}

Example 4 with SmilesParserWrapper

use of ambit2.core.smiles.SmilesParserWrapper in project ambit-mirror by ideaconsult.

the class StructureEditorProcessor method process.

@Override
public String process(IStructureRecord record) throws AmbitException {
    try {
        MOL_TYPE mtype = MOL_TYPE.valueOf(record.getFormat());
        IAtomContainer mol = null;
        switch(mtype) {
            case SDF:
                {
                    MoleculeReader reader = new MoleculeReader();
                    mol = reader.process(record);
                    AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
                    reader = null;
                    break;
                }
            case CSV:
                {
                    // smiles
                    SmilesParserWrapper p = SmilesParserWrapper.getInstance(SMILES_PARSER.CDK);
                    mol = p.parseSmiles(record.getContent());
                    break;
                }
            default:
                throw new AmbitException("Unsupported format");
        }
        // actions
        if (mol != null && mol.getAtomCount() > 0)
            switch(command) {
                case layout:
                    {
                        IAtomContainerSet molecules = new AtomContainerSet();
                        CompoundImageTools cit = new CompoundImageTools();
                        cit.generate2D(mol, true, molecules);
                        mol = MoleculeTools.newAtomContainer(mol.getBuilder());
                        for (IAtomContainer m : molecules.atomContainers()) {
                            mol.add(m);
                        }
                        break;
                    }
                case aromatize:
                    if (mol != null)
                        CDKHueckelAromaticityDetector.detectAromaticity(mol);
                    break;
                case dearomatize:
                    if (mol != null) {
                        Kekulization.kekulize(mol);
                        for (IBond bond : mol.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
                    }
                    break;
                default:
                    throw new AmbitException("Unknown command");
            }
        StringWriter w = new StringWriter();
        SDFWriter writer = new SDFWriter(w);
        writer.write(mol);
        writer.close();
        return w.toString();
    } catch (AmbitException x) {
        throw x;
    } catch (Exception x) {
        throw new AmbitException(x);
    }
}

Example 5 with SmilesParserWrapper

use of ambit2.core.smiles.SmilesParserWrapper in project ambit-mirror by ideaconsult.

the class RendererTest method testFullerene.

@Test
public void testFullerene() throws Exception {
    // String smiles =
    // "O=C(O)C(N)CCCCNC%31%26C%29C5C3=C%25C=%23C%17=C4C=2c%16c1c%15c%14C%12=C1C=%10C=2C=9C(=C34)C5=C8c%30c7c6c%28C%22=C%21C6=C%13C=%11C7=C8C=9C=%10C=%11C%12=C%13C=%20c%14c%19c%18c%15c(c%16%17)C%24=C%18C=%27C(=C%19C=%20%21)C%22=C(C=%27C(C=%23%24)C%25%26)C%31c%28c%29%30";
    // String smiles =
    // "NC(=O)C%32=C(N)C(N1C=CC=CC1)=C(C(N)=O)C%31%35C3=C%30C=2c%29c%10C=9C=2C=%26C3=C%34C%27=C8c7c%33c6c(c%28C=5C%31C%30=C4c%29c%11C%12=C4C=5C=%13c%28c%14c6c%15c7C%16=C8C%17=C(C=9C%18C%20c%10c%11C%19C%24=C%12C=%13C=%23C%14=C%15C%25=C%16C(=C%17%18)C%21(C(C(N)=O)=C(C(N)=C(C(N)=O)C%19%20%21)N%22C=CC=CC%22)C%25C=%23%24)C=%26%27)C%32%35C%33%34";
    String smiles = "c1ccccc1";
    SmilesParserWrapper w = SmilesParserWrapper.getInstance(SMILES_PARSER.CDK);
    IAtomContainer a = w.parseSmiles(smiles);
    for (int i = 0; i < a.getAtomCount(); i++) {
        a.getAtom(i).setID(Integer.toString(i + 1));
    }
    int[][] aMatrix = PathTools.computeFloydAPSP(AdjacencyMatrix.getMatrix(a));
    /*
		 * System.out.println("%%MatrixMarket matrix coordinate real general"); System
		 * .out.println(String.format("%d %d %d",a.getAtomCount(),a.getAtomCount
		 * (),a.getBondCount()));
		 */
    int count = 0;
    double max = 0;
    for (int i = 0; i < aMatrix.length; i++) for (int j = i + 1; j < aMatrix[i].length; j++) {
        double v = getVal(aMatrix[i][j]);
        if (v > max)
            max = v;
        if (v > 0)
            count++;
    }
    Logger.getGlobal().log(java.util.logging.Level.FINEST, "%%MatrixMarket matrix coordinate real general");
    Logger.getGlobal().log(java.util.logging.Level.FINEST, String.format("%d %d %d", aMatrix.length, aMatrix.length, count));
    for (int i = 0; i < aMatrix.length; i++) for (int j = i + 1; j < aMatrix[i].length; j++) if (aMatrix[i][j] > 0) {
        double v = getVal(aMatrix[i][j]);
        Logger.getGlobal().log(java.util.logging.Level.FINEST, String.format("%s %s %f", i + 1, j + 1, v));
    }
}