Examples with Extension algorithms.isomorphism.chains.Extension used on opensource projects

Example 6 with Extension

use of algorithms.isomorphism.chains.Extension 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 7 with Extension

use of algorithms.isomorphism.chains.Extension in project Smiles2Monomers by yoann-dufresne.

the class BonbMatchingTests method perfectMatching.

@Test
public void perfectMatching() {
    Extension ext = new Extension("c,1,N,0,1");
    List<BondMapping> matchs = ext.match(this.bond1, MatchingType.EXACT);
    Assert.assertTrue(matchs.size() == 1);
}

Example 8 with Extension

use of algorithms.isomorphism.chains.Extension in project Smiles2Monomers by yoann-dufresne.

the class BonbMatchingTests method noPerfectMatching.

@Test
public void noPerfectMatching() {
    Extension ext = new Extension("c,1,N,0,0");
    List<BondMapping> matchs = ext.match(this.bond1, MatchingType.EXACT);
    Assert.assertTrue(matchs.size() == 0);
}

Example 9 with Extension

use of algorithms.isomorphism.chains.Extension in project Smiles2Monomers by yoann-dufresne.

the class BonbMatchingTests method hydrogenNoMatching.

@Test
public void hydrogenNoMatching() {
    Extension ext = new Extension("c,1,N,1,1");
    List<BondMapping> matchs = ext.match(this.bond1, MatchingType.STRONG);
    Assert.assertTrue(matchs.size() == 0);
}

Example 10 with Extension

use of algorithms.isomorphism.chains.Extension in project Smiles2Monomers by yoann-dufresne.

the class BonbMatchingTests method strongMatching2.

@Test
public void strongMatching2() {
    Extension ext = new Extension("c,1,N,0,0");
    List<BondMapping> matchs = ext.match(this.bond1, MatchingType.STRONG);
    Assert.assertTrue(matchs.size() == 1);
}