Examples with SMILESReader org.openscience.cdk.io.SMILESReader used on opensource projects

Example 1 with SMILESReader

use of org.openscience.cdk.io.SMILESReader in project cdk by cdk.

the class CrossoverMachineTest method testdoCrossover_IAtomContainer.

@Test
public void testdoCrossover_IAtomContainer() throws Exception {
    String filename = "c10h16isomers.smi";
    InputStream ins = this.getClass().getResourceAsStream(filename);
    SMILESReader reader = new SMILESReader(ins);
    IAtomContainerSet som = reader.read(new AtomContainerSet());
    Assert.assertEquals("We must have read 99 structures", 99, som.getAtomContainerCount());
    CrossoverMachine cm = new CrossoverMachine();
    String correctFormula = "C10H16";
    int errorcount = 0;
    for (int i = 0; i < som.getAtomContainerCount(); i++) {
        int[] hydrogencount1 = new int[4];
        for (IAtom atom : som.getAtomContainer(i).atoms()) {
            hydrogencount1[atom.getImplicitHydrogenCount()]++;
        }
        for (int k = i + 1; k < som.getAtomContainerCount(); k++) {
            try {
                List<IAtomContainer> result = cm.doCrossover(som.getAtomContainer(i), som.getAtomContainer(k));
                int[] hydrogencount2 = new int[4];
                for (IAtom atom : som.getAtomContainer(k).atoms()) {
                    hydrogencount2[atom.getImplicitHydrogenCount()]++;
                }
                Assert.assertEquals("Result size must be 2", 2, result.size());
                for (int l = 0; l < 2; l++) {
                    IAtomContainer ac = result.get(l);
                    Assert.assertTrue("Result must be connected", ConnectivityChecker.isConnected(ac));
                    Assert.assertEquals("Molecular formula must be the same as" + "of the input", MolecularFormulaManipulator.getString(MolecularFormulaManipulator.getMolecularFormula(ac)), correctFormula);
                    int[] hydrogencountresult = new int[4];
                    int hcounttotal = 0;
                    for (IAtom atom : result.get(l).atoms()) {
                        hydrogencountresult[atom.getImplicitHydrogenCount()]++;
                        hcounttotal += atom.getImplicitHydrogenCount();
                    }
                    if (hydrogencount1[0] == hydrogencount2[0])
                        Assert.assertEquals("Hydrogen count of the result must" + " be same as of input", hydrogencount1[0], hydrogencountresult[0]);
                    if (hydrogencount1[1] == hydrogencount2[1])
                        Assert.assertEquals("Hydrogen count of the result must" + " be same as of input", hydrogencount1[1], hydrogencountresult[1]);
                    if (hydrogencount1[2] == hydrogencount2[2])
                        Assert.assertEquals("Hydrogen count of the result must" + " be same as of input", hydrogencount1[2], hydrogencountresult[2]);
                    if (hydrogencount1[3] == hydrogencount2[3])
                        Assert.assertEquals("Hydrogen count of the result must" + " be same as of input", hydrogencount1[3], hydrogencountresult[3]);
                    Assert.assertEquals(16, hcounttotal);
                }
            } catch (CDKException ex) {
                errorcount++;
            }
        }
    }
    Assert.assertTrue("We tolerate up to 300 errors", errorcount < 300);
}