public virtual void TestGetLonePairCount_Molecule()
{
IAtomContainer acetone = (IAtomContainer)NewChemObject();
IAtom c1 = acetone.Builder.NewAtom("C");
IAtom c2 = acetone.Builder.NewAtom("C");
IAtom o = acetone.Builder.NewAtom("O");
IAtom c3 = acetone.Builder.NewAtom("C");
acetone.Atoms.Add(c1);
acetone.Atoms.Add(c2);
acetone.Atoms.Add(c3);
acetone.Atoms.Add(o);
IBond b1 = acetone.Builder.NewBond(c1, c2, BondOrder.Single);
IBond b2 = acetone.Builder.NewBond(c1, o, BondOrder.Double);
IBond b3 = acetone.Builder.NewBond(c1, c3, BondOrder.Single);
acetone.Bonds.Add(b1);
acetone.Bonds.Add(b2);
acetone.Bonds.Add(b3);
// add lone pairs on oxygen
ILonePair lp1 = acetone.Builder.NewLonePair(o);
ILonePair lp2 = acetone.Builder.NewLonePair(o);
acetone.LonePairs.Add(lp1);
acetone.LonePairs.Add(lp2);
Assert.AreEqual(2, acetone.LonePairs.Count);
}
public void TestMatchAgainstItself()
{
var m_bond1 = new Mock <ILonePair>(); ILonePair bond1 = m_bond1.Object;
string result = LonePairDiff.Diff(bond1, bond1);
AssertZeroLength(result);
}
public void TestNewLonePair_IAtom()
{
IChemObjectBuilder builder = RootObject.Builder;
ILonePair lonePair = builder.NewLonePair(builder.NewAtom());
Assert.IsNotNull(lonePair);
}
public override void TestClone()
{
ILonePair lp = (ILonePair)NewChemObject();
object clone = lp.Clone();
Assert.IsTrue(clone is ILonePair);
}
public virtual void TestContains_IAtom()
{
ILonePair lp = (ILonePair)NewChemObject();
IAtom atom = lp.Builder.NewAtom("N");
lp.Atom = atom;
Assert.IsTrue(lp.Contains(atom));
}
public virtual void TestSetAtom_IAtom()
{
ILonePair lp = (ILonePair)NewChemObject();
IAtom atom = lp.Builder.NewAtom("N");
lp.Atom = atom;
Assert.AreEqual(atom, lp.Atom);
}
public override void TestGetElectronCount()
{
ILonePair lp = (ILonePair)NewChemObject();
Assert.AreEqual(2, lp.ElectronCount.Value);
lp = lp.Builder.NewLonePair(lp.Builder.NewAtom("N"));
Assert.AreEqual(2, lp.ElectronCount.Value);
}
public override void TestToString()
{
ILonePair lp = (ILonePair)NewChemObject();
string description = lp.ToString();
for (int i = 0; i < description.Length; i++)
{
Assert.IsTrue(description[i] != '\n');
Assert.IsTrue(description[i] != '\r');
}
}
public virtual void TestClone_IAtom()
{
ILonePair lp = (ILonePair)NewChemObject();
IAtom atom = lp.Builder.NewAtom("N");
lp.Atom = atom;
// test cloning of atom
ILonePair clone = (ILonePair)lp.Clone();
Assert.AreNotSame(atom, clone.Atom);
}
public void TestDifference()
{
var m_carbon = new Mock <IAtom>(); IAtom carbon = m_carbon.Object;
var m_oxygen = new Mock <IAtom>(); IAtom oxygen = m_oxygen.Object;
m_carbon.SetupGet(n => n.Symbol).Returns("C");
m_oxygen.SetupGet(n => n.Symbol).Returns("O");
var m_bond1 = new Mock <ILonePair>(); ILonePair bond1 = m_bond1.Object;
var m_bond2 = new Mock <ILonePair>(); ILonePair bond2 = m_bond2.Object;
m_bond1.SetupGet(n => n.Atom).Returns(carbon);
m_bond2.SetupGet(n => n.Atom).Returns(oxygen);
IDifference difference = LonePairDiff.Difference(bond1, bond2);
Assert.IsNotNull(difference);
}
/// <summary>
/// Compare two <see cref="IChemObject"/> classes and return the difference as an <see cref="IDifference"/>.
/// </summary>
/// <param name="first">the first of the two classes to compare</param>
/// <param name="second">the second of the two classes to compare</param>
/// <returns>an <see cref="IDifference"/> representation of the difference between the first and second <see cref="IChemObject"/>.</returns>
public static IDifference Difference(IChemObject first, IChemObject second)
{
if (!(first is ILonePair && second is ILonePair))
{
return(null);
}
ILonePair firstB = (ILonePair)first;
ILonePair secondB = (ILonePair)second;
IDifferenceList totalDiff = new ChemObjectDifference("LonePairDiff");
totalDiff.AddChild(AtomDiff.Difference(firstB.Atom, secondB.Atom));
totalDiff.AddChild(ElectronContainerDiff.Difference(first, second));
if (totalDiff.ChildCount() > 0)
{
return(totalDiff);
}
else
{
return(null);
}
}
public void TestDiff()
{
var m_carbon = new Mock <IAtom>(); IAtom carbon = m_carbon.Object;
var m_oxygen = new Mock <IAtom>(); IAtom oxygen = m_oxygen.Object;
m_carbon.SetupGet(n => n.Symbol).Returns("C");
m_oxygen.SetupGet(n => n.Symbol).Returns("O");
var m_bond1 = new Mock <ILonePair>(); ILonePair bond1 = m_bond1.Object;
var m_bond2 = new Mock <ILonePair>(); ILonePair bond2 = m_bond2.Object;
m_bond1.SetupGet(n => n.Atom).Returns(carbon);
m_bond2.SetupGet(n => n.Atom).Returns(oxygen);
string result = LonePairDiff.Diff(bond1, bond2);
Assert.IsNotNull(result);
Assert.AreNotSame(0, result.Length);
AssertContains(result, "LonePairDiff");
AssertContains(result, "AtomDiff");
AssertContains(result, "C/O");
}
public static bool replaceAtomByAtom(IAtomContainer container, IAtom atom, IAtom newAtom)
{
if (!container.contains(atom))
{
// it should complain
return(false);
}
else
{
container.setAtomAt(container.getAtomNumber(atom), newAtom);
IElectronContainer[] electronContainers = container.ElectronContainers;
for (int i = 0; i < electronContainers.Length; i++)
{
if (electronContainers[i] is IBond)
{
IBond bond = (IBond)electronContainers[i];
if (bond.contains(atom))
{
for (int j = 0; j < bond.AtomCount; j++)
{
if (atom.Equals(bond.getAtomAt(j)))
{
bond.setAtomAt(newAtom, j);
}
}
}
}
else if (electronContainers[i] is ILonePair)
{
ILonePair lonePair = (ILonePair)electronContainers[i];
if (atom.Equals(lonePair.Atom))
{
lonePair.Atom = newAtom;
}
}
}
return(true);
}
}
public bool Contains(ILonePair lonePair) => false;
