public void WaterAtom()
{
IAtom a = g2c.ToCDKAtom(AtomBuilder.Aliphatic(Beam.Element.Oxygen).NumOfHydrogens(2).Build(), 2);
Assert.AreEqual("O", a.Symbol);
Assert.AreEqual(2, a.ImplicitHydrogenCount);
}
public void MethaneAtom()
{
IAtom a = g2c.ToCDKAtom(AtomBuilder.Aliphatic(Beam.Element.Carbon).NumOfHydrogens(4).Build(), 4);
Assert.AreEqual("C", a.Symbol);
Assert.AreEqual(4, a.ImplicitHydrogenCount);
}
public void NewUnknownAtom()
{
IAtom a = g2c.NewCDKAtom(AtomBuilder.Aliphatic(Beam.Element.Unknown).Build());
Assert.IsInstanceOfType(a, typeof(IPseudoAtom));
Assert.AreEqual("*", ((IPseudoAtom)a).Label);
}
public void AzaniumAtom()
{
IAtom a = g2c.ToCDKAtom(AtomBuilder.Aliphatic(Beam.Element.Nitrogen).NumOfHydrogens(4).Cation.Build(), 4);
Assert.AreEqual("N", a.Symbol);
Assert.AreEqual(4, a.ImplicitHydrogenCount);
Assert.AreEqual(+1, a.FormalCharge);
}
public void Oxidanide()
{
IAtom a = g2c.ToCDKAtom(AtomBuilder.Aliphatic(Beam.Element.Oxygen).NumOfHydrogens(1).Anion.Build(), 1);
Assert.AreEqual("O", a.Symbol);
Assert.AreEqual(1, a.ImplicitHydrogenCount);
Assert.AreEqual(-1, a.FormalCharge);
}
public void NewNitrogenAtom()
{
IAtom a = g2c.NewCDKAtom(AtomBuilder.Aliphatic(Beam.Element.Nitrogen).Build());
Assert.IsInstanceOfType(a, typeof(IAtom));
Assert.IsNotInstanceOfType(a, typeof(IPseudoAtom));
Assert.AreEqual("N", a.Symbol);
}
/// <summary>
/// Convert an CDK <see cref="IAtom"/> to a Beam Atom. The symbol and implicit
/// hydrogen count are not optional. If the symbol is not supported by the
/// SMILES notation (e.g. 'R1') the element will automatically default to
/// Unknown ('*').
/// </summary>
/// <param name="a">cdk Atom instance</param>
/// <returns>a Beam atom</returns>
/// <exception cref="NullReferenceException">the atom had an undefined symbol or implicit hydrogen count</exception>
static Beam.IAtom ToBeamAtom(IAtom a, SmiFlavors flavour)
{
var aromatic = SmiFlavorTool.IsSet(flavour, SmiFlavors.UseAromaticSymbols) && a.IsAromatic;
var charge = a.FormalCharge;
string symbol = CheckNotNull(a.Symbol, "An atom had an undefined symbol");
var element = Beam.Element.OfSymbol(symbol);
if (element == null)
{
element = Beam.Element.Unknown;
}
var ab = aromatic ? AtomBuilder.Aromatic(element) : AtomBuilder.Aliphatic(element);
// CDK leaves nulls on pseudo atoms - we need to check this special case
var hCount = a.ImplicitHydrogenCount;
if (element == Beam.Element.Unknown)
{
ab.NumOfHydrogens(hCount ?? 0);
}
else
{
ab.NumOfHydrogens(CheckNotNull(hCount, "One or more atoms had an undefined number of implicit hydrogens"));
}
if (charge.HasValue)
{
ab.Charge(charge.Value);
}
// use the mass number to specify isotope?
if (SmiFlavorTool.IsSet(flavour, SmiFlavors.AtomicMass | SmiFlavors.AtomicMassStrict))
{
var massNumber = a.MassNumber;
if (massNumber != null)
{
ab.Isotope(massNumber.Value);
}
}
var atomClass = a.GetProperty <int?>(CDKPropertyName.AtomAtomMapping);
if (SmiFlavorTool.IsSet(flavour, SmiFlavors.AtomAtomMap) && atomClass != null)
{
ab.AtomClass(atomClass.Value);
}
return(ab.Build());
}
public void Carbon_14()
{
IAtom a = g2c.ToCDKAtom(AtomBuilder.Aliphatic(Beam.Element.Carbon).NumOfHydrogens(4).Isotope(14).Build(), 4);
Assert.AreEqual(14, a.MassNumber);
}
public void UnspecifiedMass()
{
IAtom a = g2c.ToCDKAtom(AtomBuilder.Aliphatic(Beam.Element.Carbon).NumOfHydrogens(4).Build(), 4);
Assert.IsNull(a.MassNumber);
}