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

Example 1 with Extension

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

the class BlocsTests method setUp.

@Before
public void setUp() throws Exception {
    this.sc = SmilesConverter.conv;
    // String smiles = "C(C(=O)O)C(=O)N";
    IAtom a1;
    IAtom a2;
    a1 = new Atom("C");
    a1.setFlag(CDKConstants.ISAROMATIC, true);
    a2 = new Atom("N");
    a2.setFlag(CDKConstants.ISAROMATIC, true);
    // NC
    this.ext1 = new Extension(new Bond(a1, a2, Order.SINGLE));
    a2 = new Atom("O");
    // NC=O
    this.ext2 = new Extension(new Bond(a1, a2, Order.DOUBLE));
    a2 = new Atom("C");
    a2.setFlag(CDKConstants.ISAROMATIC, true);
    // NC(C)=O
    this.ext3 = new Extension(new Bond(a1, a2, Order.SINGLE));
    a1 = new Atom("C");
    a1.setFlag(CDKConstants.ISAROMATIC, true);
    // NC(CC)=O
    this.ext4 = new Extension(new Bond(a1, a2, Order.SINGLE));
    a2 = new Atom("C");
    a2.setFlag(CDKConstants.ISAROMATIC, true);
    // NC(CCC)=O
    this.ext5 = new Extension(new Bond(a1, a2, Order.SINGLE));
    a1 = new Atom("C");
    a1.setFlag(CDKConstants.ISAROMATIC, true);
    a2 = new Atom("N");
    a2.setFlag(CDKConstants.ISAROMATIC, true);
    // N1C(CCC1)=O
    this.ext6 = new Extension(new Bond(a1, a2, Order.SINGLE));
    // NC
    this.blc1 = new Chain(null, ext1, -1, -1);
    // NC=O
    this.blc2 = new Chain(blc1, ext2, -1, 0);
    // NC(C)=O
    this.blc3 = new Chain(blc2, ext3, 0, -1);
    // NC(CC)=O
    this.blc4 = new Chain(blc3, ext4, 3, -1);
    // NC(CCC)=O
    this.blc5 = new Chain(blc4, ext5, 4, -1);
    // N1C(CC1)=O
    this.blc6 = new Chain(blc5, ext6, 5, 1);
}

Example 2 with Extension

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

the class BonbMatchingTests method lightMatching.

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

Example 3 with Extension

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

the class BonbMatchingTests method strongMatching.

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

Example 4 with Extension

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

the class BonbMatchingTests method noHydrogenMatching.

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

Example 5 with Extension

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

the class BonbMatchingTests method aromaticNoMatching.

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