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

Example 1 with InvalidSmilesException

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

the class LoadersTests method addaTest.

@Test
public void addaTest() {
    String smiles = "CC(C=C(C)C=CC(C(C)C(=O)O)N)C(CC1=CC=CC=C1)OC";
    try {
        smiles = SmilesConverter.conv.toCanonicalSmiles(smiles);
    } catch (InvalidSmilesException e) {
        System.err.println("Impossible to parse " + smiles);
    }
    Monomer adda = new Monomer("Adda", "Adda", smiles);
    IMolecule mol = adda.getMolecule();
    Assert.assertTrue("O=C(O)C(C)C(N)C=CC(=CC(C)C(OC)Cc1ccccc1)C".equals(SmilesConverter.conv.mol2Smiles(mol)));
}

Example 2 with InvalidSmilesException

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

the class TreeWidthTests method test.

@Test
public void test() {
    MolTreeWidth mtw = new MolTreeWidth();
    Polymer pep = null;
    try {
        pep = this.pepDB.getObject("250");
    } catch (NullPointerException e) {
        e.printStackTrace();
    }
    try {
        assertEquals(2, mtw.calculateTreeWidth(SmilesConverter.conv.transform(pep.getSmiles())));
    } catch (InvalidSmilesException e) {
        System.err.println("Impossible to parse smiles");
    }
}

Example 3 with InvalidSmilesException

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

the class OverlapData method main.

public static void main(String[] args) {
    // Norine Loading
    MonomersJsonLoader monosLoader = new MonomersJsonLoader();
    MonomersDB norMonos = monosLoader.loadFile("data/monomers.json");
    PolymersJsonLoader loader = new PolymersJsonLoader(norMonos);
    PolymersDB norine = loader.loadFile("data/peptides_clean.json");
    // CCD Loading
    MonomersDB ccdMonos = monosLoader.loadFile("data/pdbe_monos_min.json");
    loader = new PolymersJsonLoader(ccdMonos);
    PolymersDB ccd = loader.loadFile("data/pdbe_polys_clean.json");
    // Norine smiles generation
    HashMap<String, Polymer> polymers = new HashMap<>();
    for (Polymer poly : norine.getObjects()) {
        String smiles = null;
        try {
            smiles = SmilesConverter.conv.toCanonicalSmiles(poly.getSmiles());
        } catch (InvalidSmilesException e) {
            e.printStackTrace();
            continue;
        }
        polymers.put(smiles, poly);
    }
    // Test overlapping peptides
    int overlap = 0;
    for (Polymer poly : ccd.getObjects()) {
        String smiles = null;
        try {
            smiles = SmilesConverter.conv.toCanonicalSmiles(poly.getSmiles());
        } catch (InvalidSmilesException e) {
            e.printStackTrace();
            continue;
        }
        if (polymers.containsKey(smiles)) {
            System.out.println(polymers.get(smiles).getName());
            overlap++;
        }
    }
    System.out.println("Total peptides overlapping : " + overlap);
    // Norine smiles generation
    HashMap<String, Monomer> monomers = new HashMap<>();
    for (Monomer mono : norMonos.getObjects()) {
        String smiles = null;
        try {
            smiles = SmilesConverter.conv.toCanonicalSmiles(mono.getSmiles());
        } catch (InvalidSmilesException e) {
            e.printStackTrace();
            continue;
        }
        monomers.put(smiles, mono);
    }
    // Test overlapping peptides
    overlap = 0;
    for (Monomer mono : ccdMonos.getObjects()) {
        String smiles = null;
        try {
            smiles = SmilesConverter.conv.toCanonicalSmiles(mono.getSmiles());
        } catch (InvalidSmilesException e) {
            e.printStackTrace();
            continue;
        }
        if (monomers.containsKey(smiles)) {
            System.out.println(monomers.get(smiles).getName());
            overlap++;
        }
    }
    System.out.println("Total monomers overlapping : " + overlap + "/" + ccdMonos.size());
}

Example 4 with InvalidSmilesException

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

the class AbstractChemicalObject method getMol.

private Molecule getMol() {
    if (this.mol == null) {
        try {
            boolean generateCoordinates = this.generateCoordinate == null ? false : this.generateCoordinate;
            boolean explicite = this.explicitHydrogens == null ? false : this.explicitHydrogens;
            if (this.generateH != null && this.generateH.equals(new Boolean(true)))
                this.mol = SmilesConverter.conv.transform(this.smiles, false, generateCoordinates, explicite);
            else
                this.mol = SmilesConverter.conv.transform(this.smiles, true, generateCoordinates, explicite);
        } catch (InvalidSmilesException e) {
            System.err.println("Impossible to parse \"" + this.smiles + "\"");
            Molecule mol = new Molecule();
            return mol;
        }
    }
    return this.mol;
}

Example 5 with InvalidSmilesException

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

the class ResidueCreator method getResiduesWithRule.

/*
	 * Search Residues for one monomer and one rule.
	 */
private Set<Residue> getResiduesWithRule(Residue res, Rule rule) {
    Set<Residue> residues = new HashSet<>();
    IMolecule ruleMol = null;
    try {
        ruleMol = SmilesConverter.conv.transform(rule.getFormula(), false, false, true);
    } catch (InvalidSmilesException e) {
        System.err.println("Impossible to parse " + rule.getName() + " rule");
        return residues;
    }
    boolean status = false;
    try {
        status = UniversalIsomorphismTester.isSubgraph(res.getMolecule(), ruleMol);
    } catch (CDKException e) {
        e.printStackTrace();
    }
    // If rule is found
    if (status) {
        List<List<RMap>> matches = null;
        try {
            matches = UniversalIsomorphismTester.getSubgraphAtomsMaps(res.getMolecule(), ruleMol);
        } catch (CDKException e) {
            e.printStackTrace();
        }
        if (!"".equals(rule.getExclusion()))
            for (String exclusion : rule.getExclusion()) this.removeExclusions(matches, exclusion, res.getMolecule());
        for (List<RMap> match : matches) {
            Set<Residue> residuesByMatch = this.createResidue(match, rule, res);
            residues.addAll(residuesByMatch);
        }
    }
    return residues;
}