Examples with Bond org.openscience.cdk.Bond used on opensource projects

Example 1 with Bond

use of org.openscience.cdk.Bond 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 Bond

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

the class BonbMatchingTests method setUp.

@Before
public void setUp() throws Exception {
    // cNH
    IAtom a2 = new Atom("C");
    a2.setImplicitHydrogenCount(0);
    a2.setFlag(CDKConstants.ISAROMATIC, true);
    IAtom a1 = new Atom("N");
    a1.setImplicitHydrogenCount(1);
    this.bond1 = new Bond(a1, a2, Order.DOUBLE);
}

Example 3 with Bond

use of org.openscience.cdk.Bond 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 Bond

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

the class Extension method createBond.

private void createBond(String name0, int h0, boolean arom0, String name1, int h1, boolean arom1, Order ord) {
    if (arom0)
        name0 = name0.toLowerCase();
    if (arom1)
        name1 = name1.toLowerCase();
    List<String> names = new ArrayList<>();
    names.add(name0 + ":" + h0);
    names.add(name1 + ":" + h1);
    Collections.sort(names);
    // this.inverted = !names.get(0).equals(name0 + ":" + h0);
    IAtom c0 = null;
    String n0 = names.get(0);
    if (Extension.savedAtoms.containsKey(n0))
        c0 = Extension.savedAtoms.get(n0);
    else {
        String[] split = n0.split(":");
        char first = Character.toUpperCase(split[0].charAt(0));
        String name = first + split[0].substring(1);
        c0 = new Atom(name);
        c0.setFlag(CDKConstants.ISAROMATIC, Character.isLowerCase(split[0].charAt(0)));
        c0.setImplicitHydrogenCount(new Integer(split[1]));
        Extension.savedAtoms.put(n0, c0);
    }
    IAtom c1 = null;
    String n1 = names.get(1);
    if (Extension.savedAtoms.containsKey(n1))
        c1 = Extension.savedAtoms.get(n1);
    else {
        String[] split = n1.split(":");
        char first = Character.toUpperCase(split[0].charAt(0));
        String name = first + split[0].substring(1);
        c1 = new Atom(name);
        c1.setFlag(CDKConstants.ISAROMATIC, Character.isLowerCase(split[0].charAt(0)));
        c1.setImplicitHydrogenCount(new Integer(split[1]));
        Extension.savedAtoms.put(n1, c1);
    }
    String key = names.get(0) + ord + names.get(1);
    if (Extension.savedBonds.containsKey(key)) {
        this.bond = Extension.savedBonds.get(key);
    } else {
        this.bond = new Bond(c0, c1, ord);
        Extension.savedBonds.put(key, this.bond);
    }
}

Example 5 with Bond

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

the class Extension method clone.

public Extension clone() {
    Extension ext = new Extension();
    IAtom a0 = null, a1 = null;
    try {
        a0 = (IAtom) this.bond.getAtom(0).clone();
        a1 = (IAtom) this.bond.getAtom(1).clone();
    } catch (CloneNotSupportedException e) {
        e.printStackTrace();
    }
    ext.bond = new Bond(a0, a1, this.bond.getOrder());
    return ext;
}