/// <summary> Says if an atom is the start of a double bond configuration
///
/// </summary>
/// <param name="a"> The atom which is the start of configuration
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <param name="parent"> The atom we came from
/// </param>
/// <param name="doubleBondConfiguration"> The array indicating where double bond
/// configurations are specified (this method ensures that there is
/// actually the possibility of a double bond configuration)
/// </param>
/// <returns> false=is not start of configuration, true=is
/// </returns>
private static bool isStartOfDoubleBond(IAtomContainer container, IAtom a, IAtom parent, bool[] doubleBondConfiguration)
{
int lengthAtom = container.getConnectedAtoms(a).Length + a.getHydrogenCount();
if (lengthAtom != 3 && (lengthAtom != 2 && (System.Object)a.Symbol != (System.Object)("N")))
{
return(false);
}
IAtom[] atoms = container.getConnectedAtoms(a);
IAtom one = null;
IAtom two = null;
bool doubleBond = false;
IAtom nextAtom = null;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i] != parent && container.getBond(atoms[i], a).Order == CDKConstants.BONDORDER_DOUBLE && isEndOfDoubleBond(container, atoms[i], a, doubleBondConfiguration))
{
doubleBond = true;
nextAtom = atoms[i];
}
if (atoms[i] != nextAtom && one == null)
{
one = atoms[i];
}
else if (atoms[i] != nextAtom && one != null)
{
two = atoms[i];
}
}
System.String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
if (one != null && ((!a.Symbol.Equals("N") && two != null && !morgannumbers[container.getAtomNumber(one)].Equals(morgannumbers[container.getAtomNumber(two)]) && doubleBond && doubleBondConfiguration[container.getBondNumber(a, nextAtom)]) || (doubleBond && a.Symbol.Equals("N") && System.Math.Abs(giveAngleBothMethods(nextAtom, a, parent, true)) > System.Math.PI / 10)))
{
return(true);
}
else
{
return(false);
}
}
/// <summary> Says if an atom is the end of a double bond configuration
///
/// </summary>
/// <param name="atom"> The atom which is the end of configuration
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <param name="parent"> The atom we came from
/// </param>
/// <param name="doubleBondConfiguration"> The array indicating where double bond
/// configurations are specified (this method ensures that there is
/// actually the possibility of a double bond configuration)
/// </param>
/// <returns> false=is not end of configuration, true=is
/// </returns>
private static bool isEndOfDoubleBond(IAtomContainer container, IAtom atom, IAtom parent, bool[] doubleBondConfiguration)
{
if (container.getBondNumber(atom, parent) == -1 || doubleBondConfiguration.Length <= container.getBondNumber(atom, parent) || !doubleBondConfiguration[container.getBondNumber(atom, parent)])
{
return(false);
}
int lengthAtom = container.getConnectedAtoms(atom).Length + atom.getHydrogenCount();
int lengthParent = container.getConnectedAtoms(parent).Length + parent.getHydrogenCount();
if (container.getBond(atom, parent) != null)
{
if (container.getBond(atom, parent).Order == CDKConstants.BONDORDER_DOUBLE && (lengthAtom == 3 || (lengthAtom == 2 && atom.Symbol.Equals("N"))) && (lengthParent == 3 || (lengthParent == 2 && parent.Symbol.Equals("N"))))
{
IAtom[] atoms = container.getConnectedAtoms(atom);
IAtom one = null;
IAtom two = null;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i] != parent && one == null)
{
one = atoms[i];
}
else if (atoms[i] != parent && one != null)
{
two = atoms[i];
}
}
System.String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
if ((one != null && two == null && atom.Symbol.Equals("N") && System.Math.Abs(giveAngleBothMethods(parent, atom, one, true)) > System.Math.PI / 10) || (!atom.Symbol.Equals("N") && one != null && two != null && !morgannumbers[container.getAtomNumber(one)].Equals(morgannumbers[container.getAtomNumber(two)])))
{
return(true);
}
else
{
return(false);
}
}
}
return(false);
}
