xlogpdescriptortest.java

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    }

    public void testno937() throws ClassNotFoundException, CDKException, java.lang.Exception {
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("ClCC(O)C[nH0]1c([nH0]cc1[N+](=O)[O-])C"); // xlogp training set molecule no937
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no937:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(0.66, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void testno990() throws ClassNotFoundException, CDKException, java.lang.Exception {
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("FC(F)(F)c1ccc(cc1)C(=O)N"); // xlogp training set molecule no990
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no990:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(1.834, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void testno1000() throws ClassNotFoundException, CDKException, java.lang.Exception {
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("Clc1cccc(c1)/C=C/[N+](=O)[O-]"); // xlogp training set molecule no1000
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no10000:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(2.809, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void testApirinBug1296383() throws ClassNotFoundException, CDKException, java.lang.Exception {
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("CC(=O)OC1=CC=CC=C1C(=O)O"); // aspirin
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("Aspirin:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(1.422, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void testno1429() throws ClassNotFoundException, CDKException, java.lang.Exception {
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("O=C(OC)CNC(=O)c1ccc(N)cc1"); // xlogp training set molecule no1429
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no1429:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(0.31, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void testno1274() throws ClassNotFoundException, CDKException, java.lang.Exception {
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("O=[N+]([O-])c1ccc(cc1)CC(N)C(=O)O"); // xlogp training set molecule no1274
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no1274:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(-1.487, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void testno454() throws ClassNotFoundException, CDKException, java.lang.Exception {
        //xlogp program gives a result of -0.89, because one N is classified as in ring and not as amid
        //if one takes a 5 or 7 ring than the program assignes amid ... strange
        //sometimes amid is O=C-N-C=O sometimes not...
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("O=C1NC(=O)C=CN1C1OC(CO)C(O)C1O"); // xlogp training set molecule no454
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no454:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(-2.11, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void testno498() throws ClassNotFoundException, CDKException, java.lang.Exception {
        //even here the amid assignment is very strange
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("O=C1N(C)C=CC(=O)N1C"); // xlogp training set molecule no498
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no498:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(-0.59, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void testAprindine() throws ClassNotFoundException, CDKException, java.lang.Exception {
        //even here the amid assignment is very strange
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("CCN(CC)CCCN(C2Cc1ccccc1C2)c3ccccc3"); // xlogp training set molecule Aprindine
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("Aprindine:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(5.03, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void test1844() throws ClassNotFoundException, CDKException, java.lang.Exception {
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("Brc1cc(Cl)c(O[P+]([S-])(OC)OC)cc1Cl"); // xlogp training set molecule 1844
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no1844:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(5.22, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void test1810() throws ClassNotFoundException, CDKException, java.lang.Exception {
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("Clc1ccc2Sc3ccccc3N(CCCN3CCN(C)CC3)c2c1"); // xlogp training set molecule 1810
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no1810:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(4.56, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void test1822() throws ClassNotFoundException, CDKException, java.lang.Exception {
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("[S+]([O-])(CCC1C(=O)N(N(c2ccccc2)C1=O)c1ccccc1)c1ccccc1"); // xlogp training set molecule 1822
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no1822:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(2.36, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }
}