public void TestPartitionIntoMolecules_IAtomContainer()
{
//Debug.WriteLine(atomCon);
AtomContainer atomCon = new AtomContainer();
atomCon.Add(TestMoleculeFactory.Make4x3CondensedRings());
atomCon.Add(TestMoleculeFactory.MakeAlphaPinene());
atomCon.Add(TestMoleculeFactory.MakeSpiroRings());
IChemObjectSet <IAtomContainer> moleculeSet = ConnectivityChecker.PartitionIntoMolecules(atomCon);
Assert.IsNotNull(moleculeSet);
Assert.AreEqual(3, moleculeSet.Count);
}
public static void Main(string[] args)
{
{
var mol = new AtomContainer();
#region Detect
Atom a0 = new Atom("C"); mol.Atoms.Add(a0);
Atom a1 = new Atom("C"); mol.Atoms.Add(a1);
Atom a2 = new Atom("C"); mol.Atoms.Add(a2);
Atom h1 = new Atom("H"); mol.Atoms.Add(h1);
Atom h2 = new Atom("H"); mol.Atoms.Add(h2);
Atom h3 = new Atom("H"); mol.Atoms.Add(h3);
Atom h4 = new Atom("H"); mol.Atoms.Add(h4);
Atom h5 = new Atom("H"); mol.Atoms.Add(h5);
mol.AddBond(a0, a1, BondOrder.Double);
mol.AddBond(a1, a2, BondOrder.Single);
mol.AddBond(a0, h1, BondOrder.Single);
mol.AddBond(a0, h2, BondOrder.Single);
mol.AddBond(a1, h3, BondOrder.Single);
mol.AddBond(a2, h4, BondOrder.Single);
mol.AddBond(a2, h5, BondOrder.Single);
SingleElectron se = new SingleElectron(a2);
mol.Add(se);
var pi_systems = ConjugatedPiSystemsDetector.Detect(mol);
#endregion
}
}
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);
}
public void Main()
{
{
#region
AtomContainer radical = new AtomContainer();
Atom carbon = new Atom("C");
carbon.ImplicitHydrogenCount = 3;
radical.Add(new SingleElectron(carbon));
#endregion
}
}