/// <summary>
/// Second traversal writes the bonds and atoms to the SMILES string.
/// </summary>
/// <param name="u">a vertex</param>
/// <param name="p">previous vertex</param>
/// <param name="b">the bond from the previous vertex to this vertex</param>
public void Write(int u, int p, Bond b)
{
visitedAt[u] = nVisit++;
int remaining = g.Degree(u);
if (u != p)
{
remaining--;
}
// assign ring numbers
if (rings.TryGetValue(u, out IList <RingClosure> closures))
{
foreach (var rc in closures)
{
// as we are composing tokens, make sure apply in reverse
int rnum = rnums.Next();
if (rc.Register(rnum))
{
int v = rc.Other(u);
tokens[u] = new RingNumberToken(new RingBondToken(tokens[u],
rc.GetBond(u)),
rnum);
rnums.Use(rnum);
}
else
{
tokens[u] = new RingNumberToken(tokens[u],
rc.RNum);
rnums.Free(rc.RNum);
}
remaining--;
}
}
sb.Append(b.Token);
tokens[u].Append(sb);
int d = g.Degree(u);
for (int j = 0; j < d; ++j)
{
Edge e = g.EdgeAt(u, j);
int v = e.Other(u);
if (visitedAt[v] < 0)
{
if (--remaining > 0)
{
sb.Append('(');
Write(v, u, e.GetBond(u));
sb.Append(')');
}
else
{
Write(v, u, e.GetBond(u));
}
}
}
}
/// <summary>
/// First traversal of the molecule assigns ring bonds (numbered later) and
/// configures topologies.
/// </summary>
/// <param name="u">the vertex to visit</param>
/// <param name="p">the atom we came from</param>
void Prepare(int u, int p)
{
visitedAt[u] = nVisit++;
tokens[u] = g.GetAtom(u).Token;
tokens[u].Graph = g;
tokens[u].Index = u;
int d = g.Degree(u);
for (int j = 0; j < d; ++j)
{
Edge e = g.EdgeAt(u, j);
int v = e.Other(u);
if (visitedAt[v] < 0)
{
Prepare(v, u);
}
else if (v != p && visitedAt[v] < visitedAt[u])
{
CyclicEdge(v, u, e.GetBond(v));
}
}
PrepareStereochemistry(u, p);
}
private Bond FirstDirectionalLabel(int u, int x, BitArray adjToDb)
{
Edge e = g.CreateEdge(u, x);
Bond b = e.GetBond(u);
// the edge is next to another double bond configuration, we
// need to consider its assignment
if (adjToDb[x] && g.Degree(x) > 2)
{
foreach (var f in g.GetEdges(x))
{
if (f.Other(x) != u && f.Bond != Bond.Double && f.Bond.IsDirectional)
{
return(f.GetBond(x));
}
}
}
// consider other labels on this double-bond
if (g.Degree(u) > 2)
{
foreach (var f in g.GetEdges(u))
{
if (f.Other(u) != x && f.Bond != Bond.Double && f.Bond.IsDirectional)
{
return(f.GetBond(u).Inverse());
}
}
}
return(b.IsDirectional ? b : Bond.Down);
}
/// <summary>
/// Given a double bond edge traverse the neighbors of one of the endpoints
/// and accumulate any explicit replacements in the <paramref name="acc"/> accumulator.
/// </summary>
/// <param name="g">the chemical graph</param>
/// <param name="e">a edge in the graph ('double bond type')</param>
/// <param name="u">a endpoint of the edge <paramref name="e"/></param>
/// <param name="acc">accumulator for new edges</param>
/// <returns>does the edge <paramref name="e"/> need to be reconsidered later</returns>
/// <exception cref="InvalidSmilesException">thrown if the edge could not be converted</exception>
private bool ReplaceImplWithExpl(Graph g,
Edge e,
int u,
Dictionary <Edge, Edge> acc)
{
Edge implicit_ = null;
Edge explicit_ = null;
foreach (var f in g.GetEdges(u))
{
Edge f2 = acc.ContainsKey(f) ? acc[f] : f;
var aa = f2.GetBond(u);
if (aa == Bond.Single || aa == Bond.Implicit)
{
if (implicit_ != null)
{
return(true);
}
implicit_ = f;
}
else if (aa == Bond.Double)
{
if (!f.Equals(e))
{
return(false);
}
}
else if (aa == Bond.Up || aa == Bond.Down)
{
if (explicit_ != null)
{
if (acc.ContainsKey(explicit_))
{
explicit_ = acc[explicit_];
}
// original bonds are invalid
if ((f.Bond == Bond.Up || f.Bond == Bond.Down) &&
explicit_.GetBond(u).Inverse() != f.GetBond(u))
{
throw new InvalidSmilesException("invalid double bond configuration");
}
if (explicit_.GetBond(u).Inverse() != f2.GetBond(u))
{
acc[f] = f2.Inverse();
BitArray visited = new BitArray(g.Order);
visited.Set(u, true);
InvertExistingDirectionalLabels(g, visited, acc, f2
.Other(u));
}
return(false);
}
explicit_ = f;
}
}
// no implicit or explicit bond? don't do anything
if (implicit_ == null || explicit_ == null)
{
return(false);
}
if (acc.ContainsKey(explicit_))
{
explicit_ = acc[explicit_];
}
int v = implicit_.Other(u);
if (!acc.TryGetValue(implicit_, out Edge existing))
{
existing = null;
}
acc[implicit_] = new Edge(u,
v,
explicit_.GetBond(u)
.Inverse());
if (existing != null && existing.GetBond(u) != explicit_.GetBond(u).Inverse())
{
throw new InvalidSmilesException("unable to assign explicit type for " + implicit_);
}
return(false);
}
/// <summary>
/// Create the topologies (stereo configurations) for the chemical graph. The
/// topologies define spacial arrangement around atoms.
/// </summary>
private void CreateTopologies(CharBuffer buffer)
{
// create topologies (stereo configurations)
foreach (var e in configurations)
{
AddTopology(e.Key,
Topology.ToExplicit(g, e.Key, e.Value));
}
for (int v = BitArrays.NextSetBit(checkDirectionalBonds, 0); v >= 0; v = BitArrays.NextSetBit(checkDirectionalBonds, v + 1))
{
int nUpV = 0;
int nDownV = 0;
int nUpW = 0;
int nDownW = 0;
int w = -1;
{
int d = g.Degree(v);
for (int j = 0; j < d; ++j)
{
Edge e = g.EdgeAt(v, j);
Bond bond = e.GetBond(v);
if (bond == Bond.Up)
{
nUpV++;
}
else if (bond == Bond.Down)
{
nDownV++;
}
else if (bond == Bond.Double)
{
w = e.Other(v);
}
}
}
if (w < 0)
{
continue;
}
BitArrays.EnsureCapacity(checkDirectionalBonds, w + 1);
checkDirectionalBonds.Set(w, false);
{
int d = g.Degree(w);
for (int j = 0; j < d; ++j)
{
Edge e = g.EdgeAt(w, j);
Bond bond = e.GetBond(w);
if (bond == Bond.Up)
{
nUpW++;
}
else if (bond == Bond.Down)
{
nDownW++;
}
}
}
if (nUpV + nDownV == 0 || nUpW + nDownW == 0)
{
continue;
}
if (nUpV > 1)
{
throw new InvalidSmilesException("Multiple directional bonds on atom " + v, buffer);
}
if (nDownV > 1)
{
throw new InvalidSmilesException("Multiple directional bonds on atom " + v, buffer);
}
if (nUpW > 1)
{
throw new InvalidSmilesException("Multiple directional bonds on atom " + w, buffer);
}
if (nDownW > 1)
{
throw new InvalidSmilesException("Multiple directional bonds on atom " + w, buffer);
}
}
}
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!
}
}