Examples with InvalidSmilesException org.openscience.cdk.exception.InvalidSmilesException used on opensource projects

Example 11 with InvalidSmilesException

use of org.openscience.cdk.exception.InvalidSmilesException in project Smiles2Monomers by yoann-dufresne.

the class MySmilesTests method oxydoAromaticTest.

@Test
public void oxydoAromaticTest() {
    String smiles = "c1ccccc1O";
    String result = "O(c(c(c(c(c[1]))))(c[1]))";
    IMolecule mol = null;
    try {
        mol = SmilesConverter.conv.transform(smiles);
    } catch (InvalidSmilesException e) {
        e.printStackTrace();
    }
    Assert.assertEquals(result, this.ms.convert(mol, false));
}

Example 12 with InvalidSmilesException

use of org.openscience.cdk.exception.InvalidSmilesException in project Smiles2Monomers by yoann-dufresne.

the class MySmilesTests method doubleLinkTest.

@Test
public void doubleLinkTest() {
    String smiles = "CC(=O)O";
    String result = "C(=O)(C)(O)";
    IMolecule mol = null;
    try {
        mol = SmilesConverter.conv.transform(smiles);
    } catch (InvalidSmilesException e) {
        e.printStackTrace();
    }
    Assert.assertEquals(result, this.ms.convert(mol, false));
}

Example 13 with InvalidSmilesException

use of org.openscience.cdk.exception.InvalidSmilesException in project Smiles2Monomers by yoann-dufresne.

the class CDKMoleculesTests method setUp.

@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();
    }
}

Example 14 with InvalidSmilesException

use of org.openscience.cdk.exception.InvalidSmilesException in project Smiles2Monomers by yoann-dufresne.

the class ResidueCreator method removeExclusions.

/*
	 * Remove results corresponding to an exclusion in rule
	 */
private void removeExclusions(List<List<RMap>> matches, String ex, IMolecule mol) {
    // Verifying exclusions
    boolean areExclusion = false;
    IMolecule exclusionMol = null;
    try {
        exclusionMol = SmilesConverter.conv.transform(ex, false, false, true);
    } catch (InvalidSmilesException e) {
        System.err.println("Impossible to parse " + ex);
        return;
    }
    try {
        areExclusion = UniversalIsomorphismTester.isSubgraph(mol, exclusionMol);
    } catch (CDKException e) {
        e.printStackTrace();
    }
    if (areExclusion) {
        List<RMap> toExclude = null;
        boolean flag = false;
        List<List<RMap>> exclusions = null;
        try {
            exclusions = UniversalIsomorphismTester.getSubgraphAtomsMaps(mol, exclusionMol);
        } catch (CDKException e) {
            e.printStackTrace();
        }
        for (List<RMap> exclusion : exclusions) {
            for (List<RMap> match : matches) {
                for (RMap rmMatch : match) {
                    for (RMap exId : exclusion) {
                        if (rmMatch.getId1() == exId.getId1()) {
                            flag = true;
                            break;
                        }
                    }
                    if (flag)
                        break;
                }
                if (flag) {
                    toExclude = match;
                    break;
                }
            }
            if (flag) {
                matches.remove(toExclude);
                toExclude = null;
                flag = false;
            }
        }
    }
/**/
}