/// <summary>
/// Close the ring bond with the specified 'rnum'.
/// </summary>
/// <param name="rnum">ring number</param>
/// <param name="buffer"></param>
/// <exception cref="InvalidSmilesException">bond types did not match</exception>
private void CloseRing(int rnum, CharBuffer buffer)
{
var rbond = rings[rnum];
rings[rnum] = null;
int u = rbond.u;
int v = stack.Peek();
if (u == v)
{
throw new InvalidSmilesException("Endpoints of ringbond are the same - loops are not allowed",
buffer);
}
if (g.Adjacent(u, v))
{
throw new InvalidSmilesException("Endpoints of ringbond are already connected - multi-edges are not allowed",
buffer);
}
bond = DecideBond(rbond.bond, bond.Inverse(), rbond.pos, buffer);
var e = new Edge(u, v, bond);
if (bond.IsDirectional)
{
BitArrays.EnsureCapacity(checkDirectionalBonds, Math.Max(u, v) + 1);
checkDirectionalBonds.Set(u, true);
checkDirectionalBonds.Set(v, true);
if (rbond.bond.IsDirectional)
{
bondStrPos[e] = rbond.pos;
}
else
{
bondStrPos[e] = lastBondPos;
}
}
g.AddEdge(e);
bond = Bond.Implicit;
// adjust the arrangement replacing where this ring number was openned
arrangement[rbond.u].Replace(-rnum, stack.Peek());
if (arrangement.ContainsKey(v))
{
arrangement[v].Add(rbond.u);
}
openRings--;
}
/// <summary>
/// Add an atom and bond with the atom on the stack (if available and non-dot bond).
/// </summary>
/// <param name="a">an atom to add</param>
/// <param name="buffer"></param>
private void AddAtom(IAtom a, CharBuffer buffer)
{
int v = g.AddAtom(a);
if (!stack.IsEmpty)
{
int u = stack.Pop();
if (bond != Bond.Dot)
{
var e = new Edge(u, v, bond);
if (bond.IsDirectional)
{
bondStrPos[e] = lastBondPos;
BitArrays.EnsureCapacity(checkDirectionalBonds, Math.Max(u, v) + 1);
checkDirectionalBonds.Set(u, true);
checkDirectionalBonds.Set(v, true);
}
g.AddEdge(e);
if (arrangement.ContainsKey(u))
{
arrangement[u].Add(v);
}
}
else
{
start.Add(v); // start of a new run
}
}
stack.Push(v);
bond = Bond.Implicit;
// configurations used to create topologies after parsing
if (configuration != Configuration.Unknown)
{
g.AddFlags(Graph.HAS_ATM_STRO);
configurations.Add(v, configuration);
configuration = Configuration.Unknown;
}
}
/// <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 || nDownV > 1)
{
int offset1 = -1, offset2 = -1;
foreach (var e in g.GetEdges(v))
{
if (e.Bond.IsDirectional)
{
if (offset1 < 0)
{
offset1 = bondStrPos[e];
}
else
{
offset2 = bondStrPos[e];
}
}
}
var errorPos = InvalidSmilesException.Display(buffer,
offset1 - buffer.Length,
offset2 - buffer.Length);
if (strict)
{
throw new InvalidSmilesException($"Ignored invalid Cis/Trans specification: {errorPos}");
}
else
{
warnings.Add($"Ignored invalid Cis/Trans specification: {errorPos}");
}
}
if (nUpW > 1 || nDownW > 1)
{
int offset1 = -1;
int offset2 = -1;
foreach (var e in g.GetEdges(w))
{
if (e.Bond.IsDirectional)
{
if (offset1 < 0)
{
offset1 = bondStrPos[e];
}
else
{
offset2 = bondStrPos[e];
}
}
}
var errorPos = InvalidSmilesException.Display(buffer,
offset1 - buffer.Length,
offset2 - buffer.Length);
if (strict)
{
throw new InvalidSmilesException($"Ignored invalid Cis/Trans specification: {errorPos}");
}
else
{
warnings.Add($"Ignored invalid Cis/Trans specification: {errorPos}");
}
}
}
}
/// <summary>
/// Adds a new node to the RGraph.
/// </summary>
/// <param name="newNode">The node to add to the graph</param>
public void AddNode(RNode newNode)
{
graph.Add(newNode);
BitArrays.EnsureCapacity(graphBitSet, graph.Count);
graphBitSet.Set(graph.Count - 1, true);
}
/// <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);
}
}
}