public void TestAllSaturated_Formaldehyde()
{
// test Formaldehyde, CH2=O with explicit hydrogen
var m = new AtomContainer();
Atom c = new Atom("C");
Atom h1 = new Atom("H");
Atom h2 = new Atom("H");
Atom O = new Atom("O");
m.Atoms.Add(c);
m.Atoms.Add(h1);
m.Atoms.Add(h2);
m.Atoms.Add(O);
for (int i = 0; i < 2; i++)
{
LonePair lp = new LonePair(O);
m.LonePairs.Add(lp);
}
m.Bonds.Add(new Bond(c, h1));
m.Bonds.Add(new Bond(c, h2));
m.Bonds.Add(new Bond(c, O, BondOrder.Double));
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(m);
Assert.IsTrue(CDK.LonePairElectronChecker.IsSaturated(m));
}
public void TestAllSaturated_Methanethiol()
{
// test Methanethiol, CH4S
Atom c = new Atom("C")
{
ImplicitHydrogenCount = 3
};
Atom s = new Atom("S")
{
ImplicitHydrogenCount = 1
};
Bond b1 = new Bond(c, s, BondOrder.Single);
var m = new AtomContainer();
m.Atoms.Add(c);
m.Atoms.Add(s);
m.Bonds.Add(b1);
for (int i = 0; i < 1; i++)
{
LonePair lp = new LonePair(s);
m.LonePairs.Add(lp);
}
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(m);
Assert.IsFalse(CDK.LonePairElectronChecker.IsSaturated(m));
}
public void TestDontDeleteSingleElectrons()
{
AtomContainer atomCon = new AtomContainer();
// make two molecules; one with an LonePair, the other with a SingleElectron
IAtomContainer mol1 = new AtomContainer();
Atom atom1 = new Atom("C");
mol1.Atoms.Add(atom1);
LonePair lp1 = new LonePair(atom1);
mol1.LonePairs.Add(lp1);
// mol2
IAtomContainer mol2 = new AtomContainer();
Atom atom2 = new Atom("C");
mol2.Atoms.Add(atom2);
SingleElectron se2 = new SingleElectron(atom2);
mol2.SingleElectrons.Add(se2);
atomCon.Add(mol1);
atomCon.Add(mol2);
// now partition
IChemObjectSet <IAtomContainer> moleculeSet = ConnectivityChecker.PartitionIntoMolecules(atomCon);
Assert.IsNotNull(moleculeSet);
Assert.AreEqual(2, moleculeSet.Count);
Assert.IsTrue(ConnectivityChecker.IsConnected(moleculeSet[0]));
Assert.IsTrue(ConnectivityChecker.IsConnected(moleculeSet[1]));
// make sure
Assert.AreEqual(1, moleculeSet[0].Atoms.Count);
Assert.AreEqual(1, moleculeSet[0].GetElectronContainers().Count());
Assert.AreEqual(1, moleculeSet[1].Atoms.Count);
Assert.AreEqual(1, moleculeSet[1].GetElectronContainers().Count());
// we don't know which partition contains the LP and which the electron
Assert.IsTrue(moleculeSet[0].GetConnectedSingleElectrons(
moleculeSet[0].Atoms[0]).Count() == 0 ||
moleculeSet[1].GetConnectedSingleElectrons(
moleculeSet[1].Atoms[0]).Count() == 0);
Assert.IsTrue(moleculeSet[0].GetConnectedLonePairs(
moleculeSet[0].Atoms[0]).Count() == 0 ||
moleculeSet[1].GetConnectedLonePairs(
moleculeSet[1].Atoms[0]).Count() == 0);
}
