/// <summary>
/// Is the {@code atom} a suppressible hydrogen and can be represented as
/// implicit. A hydrogen is suppressible if it is not an ion, not the major
/// isotope (i.e. it is a deuterium or tritium atom) and is not molecular
/// hydrogen.
/// </summary>
/// <param name="container"> the structure </param>
/// <param name="atom"> an atom in the structure </param>
/// <returns> the atom is a hydrogen and it can be suppressed (implicit) </returns>
private static bool suppressibleHydrogen(IAtomContainer container, IAtom atom)
{
// is the atom a hydrogen
if (!"H".Equals(atom.getSymbol()))
{
return(false);
}
// is the hydrogen an ion?
if (GetFormalCharge(atom) != 0)
{
return(false);
}
// is the hydrogen deuterium / tritium?
if (GetMassNumber(atom) != 1)
{
return(false);
}
// molecule hydrogen with implicit H?
if (atom.getImplicitHydrogenCount() != null && atom.getImplicitHydrogenCount().intValue() != 0)
{
return(false);
}
// molecule hydrogen
List <IAtom> neighbors = container.getConnectedAtomsList(atom) as List <IAtom>;
if (neighbors.Count == 1 && neighbors[0].getSymbol().Equals("H"))
{
return(false);
}
// what about bridging hydrogens?
// hydrogens with atom-atom mapping?
return(true);
}
/// <summary>
/// Get integer ImplicitHydrogenCount for an atom
/// </summary>
/// <param name="atom"></param>
/// <returns></returns>
public static int GetImplicitHydrogenCount(IAtom atom)
{
if (atom.getImplicitHydrogenCount() == null)
{
return(0);
}
else
{
return(atom.getImplicitHydrogenCount().intValue());
}
}
/// <summary>
/// Increment the implicit hydrogen count of the provided atom. If the atom
/// was a non-pseudo atom and had an unset hydrogen count an exception is
/// thrown.
/// </summary>
/// <param name="atom"> an atom to increment the hydrogen count of </param>
private static void incrementImplHydrogenCount(IAtom atom)
{
int?hCount = atom.getImplicitHydrogenCount().intValue();
if (hCount == null)
{
if (!(atom is IPseudoAtom))
{
throw new System.ArgumentException("a non-pseudo atom had an unset hydrogen count");
}
hCount = 0;
}
atom.setImplicitHydrogenCount(new java.lang.Integer((int)hCount + 1));
}