Examples with ILonePair org.openscience.cdk.interfaces.ILonePair used on opensource projects

Example 1 with ILonePair

use of org.openscience.cdk.interfaces.ILonePair in project ambit-mirror by ideaconsult.

the class SuppleAtomContainer method getConnectedLonePairsList.

public List<ILonePair> getConnectedLonePairsList(IAtom atom) {
    List<ILonePair> lps = new ArrayList<ILonePair>();
    Iterator<ILonePair> lp = lonePairs.iterator();
    while (lp.hasNext()) {
        ILonePair p = lp.next();
        if (p.contains(atom))
            lps.add(p);
    }
    return lps;
}

Example 2 with ILonePair

use of org.openscience.cdk.interfaces.ILonePair in project ambit-mirror by ideaconsult.

the class SuppleAtomContainer method removeLonePair.

public ILonePair removeLonePair(int position) {
    ILonePair lp = lonePairs.get(position);
    lp.removeListener(this);
    lonePairs.remove(lp);
    notifyChanged();
    return lp;
}

Example 3 with ILonePair

use of org.openscience.cdk.interfaces.ILonePair in project ambit-mirror by ideaconsult.

the class SuppleAtomContainer method removeAllElectronContainers.

public void removeAllElectronContainers() {
    removeAllBonds();
    for (ILonePair lp : lonePairs()) lp.removeListener(this);
    for (ISingleElectron se : singleElectrons) se.removeListener(this);
    lonePairs.clear();
    singleElectrons.clear();
    notifyChanged();
}

Example 4 with ILonePair

use of org.openscience.cdk.interfaces.ILonePair in project ambit-mirror by ideaconsult.

the class SuppleAtomContainer method init.

protected void init() {
    atoms = new FilteredList<IAtom>();
    bonds = new FilteredList<IBond>();
    lonePairs = new ArrayList<ILonePair>();
    singleElectrons = new ArrayList<ISingleElectron>();
    int atomCount = getAtomCount();
    stereoElements = new HashSet<IStereoElement>(atomCount / 2);
    for (IStereoElement element : stereoElements()) {
        addStereoElement(element);
    }
}

Example 5 with ILonePair

use of org.openscience.cdk.interfaces.ILonePair in project ambit-mirror by ideaconsult.

the class SuppleAtomContainerTest method testAddLonePair_ILonePair.

@Test
public void testAddLonePair_ILonePair() {
    IAtomContainer acetone = new SuppleAtomContainer();
    IAtom c = MoleculeTools.newAtom(builder, "C");
    IAtom o = MoleculeTools.newAtom(builder, "O");
    acetone.addAtom(c);
    acetone.addAtom(o);
    IBond b1 = MoleculeTools.newBond(builder, c, o, IBond.Order.DOUBLE);
    acetone.addBond(b1);
    ILonePair lp1 = MoleculeTools.newLonePair(builder, o);
    ILonePair lp2 = MoleculeTools.newLonePair(builder, o);
    acetone.addLonePair(lp1);
    acetone.addLonePair(lp2);
    Assert.assertEquals(2, acetone.getConnectedLonePairsCount(o));
    Assert.assertEquals(0, acetone.getConnectedLonePairsCount(c));
}