/// <summary>
/// Create a new CDK <see cref="IAtom"/> from the Beam Atom. If the element is
/// unknown (i.e. '*') then an pseudo atom is created.
/// </summary>
/// <param name="atom">an Atom from the Beam Graph</param>
/// <returns>the CDK atom to have it's properties set</returns>
public IAtom NewCDKAtom(Beam.IAtom atom)
{
var element = atom.Element;
var unknown = element == Beam.Element.Unknown;
if (unknown)
{
var pseudoAtom = builder.NewPseudoAtom(element.Symbol);
pseudoAtom.Symbol = element.Symbol;
pseudoAtom.Label = atom.Label;
return(pseudoAtom);
}
return(CreateAtom(element));
}
/// <summary>
/// Create a new CDK <see cref="IAtom"/> from the Beam Atom.
/// </summary>
/// <param name="beamAtom">an Atom from the Beam ChemicalGraph</param>
/// <param name="hCount">hydrogen count for the atom</param>
/// <returns>the CDK atom to have it's properties set</returns>
public IAtom ToCDKAtom(Beam.IAtom beamAtom, int hCount)
{
var cdkAtom = NewCDKAtom(beamAtom);
cdkAtom.ImplicitHydrogenCount = hCount;
cdkAtom.FormalCharge = beamAtom.Charge;
if (beamAtom.Isotope >= 0)
{
cdkAtom.MassNumber = beamAtom.Isotope;
}
if (beamAtom.IsAromatic())
{
cdkAtom.IsAromatic = true;
}
if (beamAtom.AtomClass > 0)
{
cdkAtom.SetProperty(CDKPropertyName.AtomAtomMapping, beamAtom.AtomClass);
}
return(cdkAtom);
}
