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

Example 6 with Bond

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

the class Chain method getMolecule.

/**
 * construct recursively a molecule corresponding to the bloc.
 * Attention, this function is not very efficient because of multiple molecules creation.
 * @return Bloc molecule. Can return null if there are problems of compatibility between sub-bloc and extension positions.
 */
public IMolecule getMolecule() {
    if (this.mol != null)
        return this.mol;
    IMolecule mol = null;
    this.atoms = new ArrayList<>();
    // Sub-bloc molecule
    if (this.getSize() > 1) {
        IMolecule subMol = this.subBlc.getMolecule();
        mol = new Molecule();
        for (IAtom a : subMol.atoms()) mol.addAtom(a);
        for (IBond b : subMol.bonds()) mol.addBond(b);
        for (IAtom a : this.subBlc.atoms) {
            IAtom cloneA = mol.getAtom(subMol.getAtomNumber(a));
            this.atoms.add(cloneA);
        }
    } else {
        mol = new Molecule();
    }
    // Extension of mol
    IAtom a1 = this.ext.getBond().getAtom(0);
    if (this.position1 == -1) {
        try {
            a1 = (IAtom) a1.clone();
        } catch (CloneNotSupportedException e) {
            e.printStackTrace();
        }
        mol.addAtom(a1);
        this.atoms.add(a1);
        // Hydrogens
        int hydrogens = this.ext.getBond().getAtom(0).getImplicitHydrogenCount();
        a1.setImplicitHydrogenCount(hydrogens);
        // Aromatic
        if (this.ext.getBond().getAtom(0).getFlag(CDKConstants.ISAROMATIC))
            a1.setFlag(CDKConstants.ISAROMATIC, true);
        else
            a1.setFlag(CDKConstants.ISAROMATIC, false);
    } else {
        if (a1.getAtomicNumber() == this.atoms.get(this.position1).getAtomicNumber())
            a1 = this.atoms.get(this.position1);
        else
            return null;
    }
    IAtom a2 = this.ext.getBond().getAtom(1);
    if (this.position2 == -1) {
        try {
            a2 = (IAtom) a2.clone();
        } catch (CloneNotSupportedException e) {
            e.printStackTrace();
        }
        mol.addAtom(a2);
        this.atoms.add(a2);
        // Hydrogen
        int hydrogens = this.ext.getBond().getAtom(1).getImplicitHydrogenCount();
        a2.setImplicitHydrogenCount(hydrogens);
        // Aromatic
        if (this.ext.getBond().getAtom(1).getFlag(CDKConstants.ISAROMATIC))
            a2.setFlag(CDKConstants.ISAROMATIC, true);
        else
            a2.setFlag(CDKConstants.ISAROMATIC, false);
    } else if (a2.getAtomicNumber() == this.atoms.get(this.position2).getAtomicNumber())
        a2 = this.atoms.get(this.position2);
    else
        return null;
    mol.addBond(new Bond(a1, a2, this.ext.getBond().getOrder()));
    this.mol = mol;
    return mol;
}