Examples with Atom org.openscience.cdk.silent.Atom used on opensource projects

Example 1 with Atom

use of org.openscience.cdk.silent.Atom 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 Atom

use of org.openscience.cdk.silent.Atom 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");
}