private void SetDirection(Edge e, int u, Bond b)
{
if (e.Either() == u)
{
e.SetBond(b);
}
else
{
e.SetBond(b.Inverse());
}
}
// invariant, m is a perfect matching
private static Graph Assign(Graph g, BitArray subset, BitArray aromatic, Matching m)
{
g.SetFlags(g.GetFlags() & ~Graph.HAS_AROM);
for (int u = BitArrays.NextSetBit(aromatic, 0); u >= 0; u = BitArrays.NextSetBit(aromatic, u + 1))
{
g.SetAtom(u, g.GetAtom(u).AsAliphaticForm());
int deg = g.Degree(u);
for (int j = 0; j < deg; ++j)
{
Edge e = g.EdgeAt(u, j);
int v = e.Other(u);
if (v < u)
{
var aa = e.Bond;
if (aa == Bond.Single)
{
if (aromatic[u] && aromatic[v])
{
e.SetBond(Bond.Single);
}
else
{
e.SetBond(Bond.Implicit);
}
}
else if (aa == Bond.Aromatic)
{
if (subset[u] && m.Other(u) == v)
{
e.SetBond(Bond.DoubleAromatic);
g.UpdateBondedValence(u, +1);
g.UpdateBondedValence(v, +1);
}
else if (aromatic[v])
{
e.SetBond(Bond.ImplicitAromatic);
}
else
{
e.SetBond(Bond.Implicit);
}
}
else if (aa == Bond.Implicit)
{
if (subset[u] && m.Other(u) == v)
{
e.SetBond(Bond.DoubleAromatic);
g.UpdateBondedValence(u, +1);
g.UpdateBondedValence(v, +1);
}
else if (aromatic[u] && aromatic[v])
{
e.SetBond(Bond.ImplicitAromatic);
}
}
}
}
}
return(g);
}
/// <summary>
/// Add an edge to the graph.
/// </summary>
/// <param name="e">the edge to add</param>
/// <returns>graph builder for adding more atoms/connections</returns>
public GraphBuilder Add(Edge e)
{
Bond b = e.Bond;
int u = e.Either();
int v = e.Other(u);
if (b == Bond.Single && (!g.GetAtom(u).IsAromatic() || !g.GetAtom(v).IsAromatic()))
{
e.SetBond(Bond.Implicit);
}
else if (b == Bond.Aromatic && g.GetAtom(u).IsAromatic() && g.GetAtom(v).IsAromatic())
{
e.SetBond(Bond.Implicit);
}
g.AddEdge(e);
valence[u] += b.Order;
valence[v] += b.Order;
return(this);
}
public static Graph Resonate(Graph g, BitArray cyclic, bool ordered)
{
BitArray subset = new BitArray(g.Order);
for (int u = BitArrays.NextSetBit(cyclic, 0); u >= 0; u = BitArrays.NextSetBit(cyclic, u + 1))
{
// candidates must have a bonded
// valence of one more than their degree
// and in a ring
int uExtra = g.BondedValence(u) - g.Degree(u);
if (uExtra > 0)
{
int other = -1;
Edge target = null;
int d = g.Degree(u);
for (int j = 0; j < d; ++j)
{
Edge e = g.EdgeAt(u, j);
int v = e.Other(u);
// check for bond validity
if (e.Bond.Order == 2)
{
int vExtra = g.BondedValence(v) - g.Degree(v);
if (cyclic[v] && vExtra > 0)
{
if (HasAdjDirectionalLabels(g, e, cyclic) && !InSmallRing(g, e))
{
other = -1;
break;
}
if (vExtra > 1 && HasAdditionalCyclicDoubleBond(g, cyclic, u, v))
{
other = -1;
break;
}
if (other == -1)
{
other = v; // first one
target = e;
}
else
{
other = -2; // found more than one
}
}
// only one double bond don't check any more
if (uExtra == 1)
{
break;
}
}
}
if (other >= 0)
{
subset.Set(u, true);
subset.Set(other, true);
target.SetBond(Bond.Implicit);
}
}
}
if (!ordered)
{
g = g.Sort(new Graph.CanOrderFirst());
}
Matching m = Matching.CreateEmpty(g);
int n = BitArrays.Cardinality(subset);
int nMatched = ArbitraryMatching.Dfs(g, m, subset);
if (nMatched < n)
{
if (n - nMatched == 2)
{
nMatched = ArbitraryMatching.AugmentOnce(g, m, nMatched, subset);
}
if (nMatched < n)
{
nMatched = MaximumMatching.Maximise(g, m, nMatched, IntSet.FromBitArray(subset));
}
if (nMatched < n)
{
throw new ApplicationException("Could not Kekulise");
}
}
// assign new double bonds
for (int v = BitArrays.NextSetBit(subset, 0); v >= 0; v = BitArrays.NextSetBit(subset, v + 1))
{
int w = m.Other(v);
subset.Set(w, false);
g.CreateEdge(v, w).SetBond(Bond.Double);
}
return(g);
}
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!
}
}