/// <summary>
/// Decide the bond to use for a ring bond. The bond symbol can be present on
/// either or both bonded atoms. This method takes those bonds, chooses the
/// correct one or reports an error if there is a conflict.
/// </summary>
/// <remarks>
/// Equivalent SMILES:
/// <list type="bullet">
/// <item>C=1CCCCC=1</item>
/// <item>C=1CCCCC1 (preferred)</item>
/// <item>C1CCCCC=1</item>
/// </list>
/// </remarks>
/// <param name="a">a bond</param>
/// <param name="b">other bond</param>
/// <param name="pos">the position in the string of bond <paramref name="a"/></param>
/// <param name="buffer"></param>
/// <returns>the bond to use for this edge</returns>
/// <exception cref="InvalidSmilesException">ring bonds did not match</exception>
public Bond DecideBond(Bond a, Bond b, int pos, CharBuffer buffer)
{
if (a == b)
{
return(a);
}
else if (a == Bond.Implicit)
{
return(b);
}
else if (b == Bond.Implicit)
{
return(a);
}
if (strict || a.Inverse() != b)
{
throw new InvalidSmilesException($"Ring closure bonds did not match, '{a}'!='{b}':" +
InvalidSmilesException.Display(buffer,
pos - buffer.Position,
lastBondPos - buffer.Position));
}
warnings.Add("Ignored invalid Cis/Trans on ring closure, should flip:" +
InvalidSmilesException.Display(buffer,
pos - buffer.Position,
lastBondPos - buffer.Position));
return(Bond.Implicit);
}
private void SetDirection(Edge e, int u, Bond b)
{
if (e.Either() == u)
{
e.SetBond(b);
}
else
{
e.SetBond(b.Inverse());
}
}
public Bond GetBond(int x)
{
if (x == u)
{
return(b);
}
else if (x == v)
{
return(b.Inverse());
}
throw new ArgumentException("invalid endpoint");
}
private void AssignDirectionalLabels()
{
if (!builders.Any())
{
return;
}
// handle extended geometric configurations first
var buildersToRemove = new List <GeometricBuilder>();
foreach (var builder in builders)
{
if (!builder.Extended)
{
continue;
}
buildersToRemove.Add(builder);
Edge e = FindDoubleBond(g, builder.u);
Edge f = FindDoubleBond(g, builder.v);
if (e == null || f == null)
{
continue;
}
Edge eRef = g.CreateEdge(builder.u, builder.X);
Edge fRef = g.CreateEdge(builder.v, builder.Y);
Edge eLab = FindBondToLabel(g, builder.u);
Edge fLab = FindBondToLabel(g, builder.v);
// adjust for reference
Configuration.ConfigurationDoubleBond config = builder.c;
if ((eLab == eRef) != (fRef == fLab))
{
if (config == Configuration.ConfigurationDoubleBond.Together)
{
config = Configuration.ConfigurationDoubleBond.Opposite;
}
else if (config == Configuration.ConfigurationDoubleBond.Opposite)
{
config = Configuration.ConfigurationDoubleBond.Together;
}
}
if (eLab.Bond.IsDirectional)
{
if (fLab.Bond.IsDirectional)
{
// can't do anything, may be incorrect
}
else
{
if (config == Configuration.ConfigurationDoubleBond.Together)
{
SetDirection(fLab, builder.v, eLab.GetBond(builder.u));
}
else if (config == Configuration.ConfigurationDoubleBond.Opposite)
{
SetDirection(fLab, builder.v, eLab.GetBond(builder.u));
}
}
}
else
{
if (fLab.Bond.IsDirectional)
{
if (config == Configuration.ConfigurationDoubleBond.Together)
{
SetDirection(eLab, builder.v, fLab.GetBond(builder.u));
}
else if (config == Configuration.ConfigurationDoubleBond.Opposite)
{
SetDirection(eLab, builder.v, fLab.GetBond(builder.u));
}
}
else
{
SetDirection(eLab, builder.u, Bond.Down);
if (config == Configuration.ConfigurationDoubleBond.Together)
{
SetDirection(fLab, builder.v, Bond.Down);
}
else if (config == Configuration.ConfigurationDoubleBond.Opposite)
{
SetDirection(fLab, builder.v, Bond.Up);
}
}
}
}
foreach (var builder in buildersToRemove)
{
builders.Remove(builder);
}
if (!builders.Any())
{
return;
}
// store the vertices which are adjacent to pi bonds with a config
BitArray pibonded = new BitArray(g.Order);
BitArray unspecified = new BitArray(g.Order);
var unspecEdges = new HashSet <Edge>();
// clear existing directional labels, if build is called multiple times
// this can cause problems
if (g.GetFlags(Graph.HAS_BND_STRO) != 0)
{
foreach (Edge edge in g.Edges)
{
if (edge.Bond.IsDirectional)
{
edge.SetBond(Bond.Implicit);
}
}
}
foreach (Edge e in g.Edges)
{
int u = e.Either();
int v = e.Other(u);
if (e.Bond.Order == 2 && g.Degree(u) >= 2 && g.Degree(v) >= 2)
{
unspecified.Set(u, true);
unspecified.Set(v, true);
pibonded.Set(u, true);
pibonded.Set(v, true);
unspecEdges.Add(e);
}
}
foreach (var builder in builders)
{
g.AddFlags(Graph.HAS_BND_STRO);
// unspecified only used for getting not setting configuration
if (builder.c == Configuration.ConfigurationDoubleBond.Unspecified)
{
continue;
}
CheckGeometricBuilder(builder); // check required vertices are adjacent
int u = builder.u, v = builder.v, x = builder.X, y = builder.Y;
if (x == y)
{
continue;
}
unspecEdges.Remove(g.CreateEdge(u, v));
unspecified.Set(u, false);
unspecified.Set(v, false);
Fix(g, u, v, pibonded);
Fix(g, v, u, pibonded);
Bond first = FirstDirectionalLabel(u, x, pibonded);
Bond second = builder.c == Configuration.ConfigurationDoubleBond.Together ? first : first.Inverse();
// check if the second label would cause a conflict
if (CheckDirectionalAssignment(second, v, y, pibonded))
{
// okay to assign the labels as they are
g.Replace(g.CreateEdge(u, x), new Edge(u, x, first));
g.Replace(g.CreateEdge(v, y), new Edge(v, y, second));
}
// there will be a conflict - check if we invert the first one...
else if (CheckDirectionalAssignment(first.Inverse(), u, x, pibonded))
{
g.Replace(g.CreateEdge(u, x), new Edge(u, x, (first = first.Inverse())));
g.Replace(g.CreateEdge(v, y), new Edge(v, y, (second = second.Inverse())));
}
else
{
BitArray visited = new BitArray(g.Order);
visited.Set(v, true);
InvertExistingDirectionalLabels(pibonded, visited, v, u);
if (!CheckDirectionalAssignment(first, u, x, pibonded) ||
!CheckDirectionalAssignment(second, v, y, pibonded))
{
throw new ArgumentException("cannot assign geometric configuration");
}
g.Replace(g.CreateEdge(u, x), new Edge(u, x, first));
g.Replace(g.CreateEdge(v, y), new Edge(v, y, second));
}
// propagate bond directions to other adjacent bonds
foreach (var e in g.GetEdges(u))
{
if (e.Bond != Bond.Double && !e.Bond.IsDirectional)
{
e.SetBond(e.Either() == u ? first.Inverse() : first);
}
}
foreach (var e in g.GetEdges(v))
{
if (e.Bond != Bond.Double && !e.Bond.IsDirectional)
{
e.SetBond(e.Either() == v ? second.Inverse() : second);
}
}
}
// unspecified pibonds should "not" have a configuration, if they
// do we try to eliminate it
foreach (Edge unspecEdge in unspecEdges)
{
int u = unspecEdge.Either();
int v = unspecEdge.Other(u);
// no problem if one side isn't defined
if (!HasDirectional(g, u) || !HasDirectional(g, v))
{
continue;
}
foreach (Edge e in g.GetEdges(u))
{
if (IsRedundantDirectionalEdge(g, e, unspecified))
{
e.SetBond(Bond.Implicit);
}
}
if (!HasDirectional(g, u))
{
continue;
}
foreach (Edge e in g.GetEdges(v))
{
if (IsRedundantDirectionalEdge(g, e, unspecified))
{
e.SetBond(Bond.Implicit);
}
}
// if (hasDirectional(g, v))
// could generate warning!
}
}