private static void AddExtendedCisTransConfig(ExtendedCisTrans ect, GraphBuilder gb,
Dictionary <IAtom, int> indices,
IAtomContainer container)
{
var ends = ExtendedCisTrans.FindTerminalAtoms(container, ect.Focus);
var carriers = ect.Carriers;
if (ends != null)
{
Configuration.ConfigurationDoubleBond config;
switch (ect.Configure)
{
case StereoConfigurations.Together:
config = Configuration.ConfigurationDoubleBond.Together;
break;
case StereoConfigurations.Opposite:
config = Configuration.ConfigurationDoubleBond.Opposite;
break;
default:
config = Configuration.ConfigurationDoubleBond.Unspecified;
break;
}
gb.CreateExtendedGeometric(indices[ends[0]], indices[ends[1]])
.Configure(indices[carriers[0].GetOther(ends[0])],
indices[carriers[1].GetOther(ends[1])],
config);
}
}
/// <summary>
/// Adjust the configuration of the cumulated double bonds to be
/// either Cis or Trans.
/// </summary>
/// <param name="elem">the stereo element to adjust</param>
private void Adjust(ExtendedCisTrans elem)
{
var middle = elem.Focus;
var ends = ExtendedCisTrans.FindTerminalAtoms(container, middle);
var bonds = elem.Carriers;
var left = ends[0];
var right = ends[1];
var p = Parity(elem.Configure);
var q = Parity(GetAtoms(left, bonds[0].GetOther(left), right))
* Parity(GetAtoms(right, bonds[1].GetOther(right), left));
// configuration is unspecified? then we add an unspecified bond.
// note: IDoubleBondStereochemistry doesn't indicate this yet
if (p == 0)
{
foreach (var bond in container.GetConnectedBonds(left))
{
bond.Stereo = BondStereo.None;
}
foreach (var bond in container.GetConnectedBonds(right))
{
bond.Stereo = BondStereo.None;
}
bonds[0].Stereo = BondStereo.UpOrDown;
return;
}
// configuration is already correct
if (p == q)
{
return;
}
Arrays.Fill(visited, false);
visited[atomToIndex[left]] = true;
if (ringSearch.Cyclic(atomToIndex[middle.Begin], atomToIndex[middle.End]))
{
return;
}
foreach (var w in graph[atomToIndex[right]])
{
if (!visited[w])
{
Reflect(w, middle);
}
}
}