Examples with Polymer model.Polymer used on opensource projects

Example 1 with Polymer

use of model.Polymer in project Smiles2Monomers by yoann-dufresne.

the class IsomorphismTests method notMatchingAromaticTest.

@Test
public void notMatchingAromaticTest() {
    Polymer pep = new Polymer(0, "", "SC1CCCCC1", null);
    List<MappedChain> mbs = Isomorphism.searchAChain(this.bloc, pep, MatchingType.STRONG);
    Assert.assertFalse(mbs.size() > 0);
}

Example 2 with Polymer

use of model.Polymer in project Smiles2Monomers by yoann-dufresne.

the class IsomorphismTests method lightMatchingAromaticTest.

@Test
public void lightMatchingAromaticTest() {
    Polymer pep = new Polymer(0, "", "SC1CCCCC1", null);
    List<MappedChain> mbs = Isomorphism.searchAChain(this.bloc, pep, MatchingType.LIGHT);
    Assert.assertTrue(mbs.size() > 0);
}

Example 3 with Polymer

use of model.Polymer in project Smiles2Monomers by yoann-dufresne.

the class IsomorphismTests method setUp.

@Before
public void setUp() throws Exception {
    // Database
    Monomer[] monos = new Monomer[1];
    Polymer pepTest = new Polymer(0, "malformin A1", "O=C1NC2C(=O)NC(C(=O)NC(C(=O)NC(C(=O)NC1CSSC2)C(C)CC)CC(C)C)C(C)C", monos);
    // Extensions
    IAtom a = new Atom("C");
    IBond b1 = new Bond(new Atom("S"), a, Order.SINGLE);
    this.ext1 = new Extension(b1);
    a = new Atom("C");
    IAtom a2 = new Atom("C");
    IBond b2 = new Bond(a, a2, Order.SINGLE);
    this.ext2 = new Extension(b2);
    // Mapped blocs
    this.mb0 = new MappedChain(pepTest, null, new ArrayList<Integer>(), new ArrayList<Integer>(), new ArrayList<MatchingType>(), new HashMap<Integer, Integer>());
    // For blocs Tests
    this.bloc = new Chain("S,0,c,0,0,-1,-1;c,0,c,0,0,-1,1");
}

Example 4 with Polymer

use of model.Polymer in project Smiles2Monomers by yoann-dufresne.

the class IsomorphismTests method matchingAromaticTest.

@Test
public void matchingAromaticTest() {
    Polymer pep = new Polymer(0, "", "Sc1ccccc1", null);
    List<MappedChain> mbs = Isomorphism.searchAChain(this.bloc, pep, MatchingType.STRONG);
    Assert.assertTrue(mbs.size() > 0);
}

Example 5 with Polymer

use of model.Polymer 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");
    }
}