/// <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)
{
var bondNumber = container.Bonds.IndexOf(container.GetBond(atom, parent));
if (bondNumber == -1 ||
doubleBondConfiguration.Length <= bondNumber ||
!doubleBondConfiguration[bondNumber])
{
return(false);
}
int hcount = atom.ImplicitHydrogenCount ?? 0;
int lengthAtom = container.GetConnectedAtoms(atom).Count() + hcount;
hcount = parent.ImplicitHydrogenCount ?? 0;
int lengthParent = container.GetConnectedAtoms(parent).Count() + hcount;
if (container.GetBond(atom, parent) != null)
{
if (container.GetBond(atom, parent).Order == BondOrder.Double &&
(lengthAtom == 3 || (lengthAtom == 2 && atom.AtomicNumber.Equals(AtomicNumbers.N))) &&
(lengthParent == 3 || (lengthParent == 2 && parent.AtomicNumber.Equals(AtomicNumbers.N))))
{
var atoms = container.GetConnectedAtoms(atom);
IAtom one = null;
IAtom two = null;
foreach (var conAtom in atoms)
{
if (conAtom != parent && one == null)
{
one = conAtom;
}
else if (conAtom != parent && one != null)
{
two = conAtom;
}
}
string[] morgannumbers = MorganNumbersTools.GetMorganNumbersWithElementSymbol(container);
if ((one != null && two == null &&
atom.AtomicNumber.Equals(AtomicNumbers.N) &&
Math.Abs(GiveAngleBothMethods(parent, atom, one, true)) > Math.PI / 10) ||
(!atom.AtomicNumber.Equals(AtomicNumbers.N) &&
one != null && two != null &&
!morgannumbers[container.Atoms.IndexOf(one)].Equals(morgannumbers[container.Atoms.IndexOf(two)], StringComparison.Ordinal)))
{
return(true);
}
else
{
return(false);
}
}
}
return(false);
}
/// <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 hcount;
hcount = a.ImplicitHydrogenCount ?? 0;
int lengthAtom = container.GetConnectedAtoms(a).Count() + hcount;
if (lengthAtom != 3 && (lengthAtom != 2 && !(a.AtomicNumber.Equals(AtomicNumbers.N))))
{
return(false);
}
var atoms = container.GetConnectedAtoms(a);
IAtom one = null;
IAtom two = null;
bool doubleBond = false;
IAtom nextAtom = null;
foreach (var atom in atoms)
{
if (atom != parent && container.GetBond(atom, a).Order == BondOrder.Double &&
IsEndOfDoubleBond(container, atom, a, doubleBondConfiguration))
{
doubleBond = true;
nextAtom = atom;
}
if (atom != nextAtom && one == null)
{
one = atom;
}
else if (atom != nextAtom && one != null)
{
two = atom;
}
}
string[] morgannumbers = MorganNumbersTools.GetMorganNumbersWithElementSymbol(container);
if (one != null &&
((!a.AtomicNumber.Equals(AtomicNumbers.N) &&
two != null &&
!morgannumbers[container.Atoms.IndexOf(one)].Equals(morgannumbers[container.Atoms.IndexOf(two)], StringComparison.Ordinal) &&
doubleBond &&
doubleBondConfiguration[container.Bonds.IndexOf(container.GetBond(a, nextAtom))]) ||
(doubleBond && a.AtomicNumber.Equals(AtomicNumbers.N) &&
Math.Abs(GiveAngleBothMethods(nextAtom, a, parent, true)) > Math.PI / 10)))
{
return(true);
}
else
{
return(false);
}
}