public void TotalBondEnergy_WhenThereAreBondRings_ReturnsTheSumOfAllBonds()
{
// Arrange
var molecule = new AtomContainer();
// Bonds: 5 carbon ring, each with an H bonded by C-H
molecule.addAtom(new Atom(new Element("C")));
molecule.addAtom(new Atom(new Element("C")));
molecule.addAtom(new Atom(new Element("C")));
molecule.addAtom(new Atom(new Element("C")));
molecule.addAtom(new Atom(new Element("C")));
molecule.addAtom(new Atom(new Element("H")));
molecule.addAtom(new Atom(new Element("H")));
molecule.addAtom(new Atom(new Element("H")));
molecule.addAtom(new Atom(new Element("H")));
molecule.addAtom(new Atom(new Element("H")));
// Ring
molecule.addBond(0, 1, IBond.Order.SINGLE);
molecule.addBond(1, 2, IBond.Order.SINGLE);
molecule.addBond(2, 3, IBond.Order.SINGLE);
molecule.addBond(3, 4, IBond.Order.SINGLE);
molecule.addBond(4, 0, IBond.Order.SINGLE);
// C-H bonds
molecule.addBond(0, 5, IBond.Order.SINGLE);
molecule.addBond(1, 6, IBond.Order.SINGLE);
molecule.addBond(2, 7, IBond.Order.SINGLE);
molecule.addBond(3, 8, IBond.Order.SINGLE);
molecule.addBond(4, 9, IBond.Order.SINGLE);
var calculator = new BondEnergyCalculator(molecule);
// Act
var bondEnergy = calculator.TotalBondEnergy();
// Assert
Assert.That(bondEnergy, Is.EqualTo(5 * 348 + 5 * 412));
}
public void TotalBondEnergy_WhenThereAreBonds_ReturnsSumOfTheBondEnergies()
{
// Arrange
var molecule = new AtomContainer();
// Bonds: C=C, C-H, C~N
molecule.addAtom(new Atom(new Element("C")));
molecule.addAtom(new Atom(new Element("C")));
molecule.addAtom(new Atom(new Element("H")));
molecule.addAtom(new Atom(new Element("N")));
molecule.addBond(0, 1, IBond.Order.DOUBLE);
molecule.addBond(1, 2, IBond.Order.SINGLE);
molecule.addBond(1, 3, IBond.Order.TRIPLE);
var calculator = new BondEnergyCalculator(molecule);
// Act
var bondEnergy = calculator.TotalBondEnergy();
// Assert
Assert.That(bondEnergy, Is.EqualTo(612 + 412 + 890));
}
public void TotalBondEnergy_WhenThereAreUnknownBonds_ReplacesUnknownsWithC_CBond()
{
// Arrange
var molecule = new AtomContainer();
// Bonds: C=C, C-H, C~N, N~X (Unknown)
molecule.addAtom(new Atom(new Element("C")));
molecule.addAtom(new Atom(new Element("C")));
molecule.addAtom(new Atom(new Element("H")));
molecule.addAtom(new Atom(new Element("N")));
molecule.addAtom(new Atom(new Element("X")));
molecule.addBond(0, 1, IBond.Order.DOUBLE);
molecule.addBond(1, 2, IBond.Order.SINGLE);
molecule.addBond(1, 3, IBond.Order.TRIPLE);
molecule.addBond(3, 4, IBond.Order.TRIPLE);
var calculator = new BondEnergyCalculator(molecule);
// Act
var bondEnergy = calculator.TotalBondEnergy();
// Assert
Assert.That(bondEnergy, Is.EqualTo(612 + 412 + 890 + 348));
}
private IAtomContainer makeAtomContainer(IAtom atom, List<IBond> parts)
{
IAtomContainer partContainer = new AtomContainer();
partContainer.addAtom(atom);
foreach (var aBond in parts)
{
foreach (var bondedAtom in aBond.atoms().ToWindowsEnumerable<IAtom>())
{
if (!partContainer.contains(bondedAtom))
{
partContainer.addAtom(bondedAtom);
}
}
partContainer.addBond(aBond);
}
return partContainer;
}