/// <summary>
/// Verify the tetrahedral stereochemistry (clockwise/anticlockwise) of atom
/// <paramref name="u"/> is preserved in the target when the <paramref name="mapping"/> is used.
/// </summary>
/// <param name="u">tetrahedral index in the target</param>
/// <param name="mapping">mapping of vertices</param>
/// <returns>the tetrahedral configuration is preserved</returns>
private bool CheckTetrahedral(int u, int[] mapping)
{
int v = mapping[u];
if (targetTypes[v] != StereoType.Unset && targetTypes[v] != StereoType.Tetrahedral)
{
return(false);
}
ITetrahedralChirality queryElement = (ITetrahedralChirality)queryElements[u];
ITetrahedralChirality targetElement = (ITetrahedralChirality)targetElements[v];
SMARTSAtom queryAtom = (SMARTSAtom)query.Atoms[u];
IAtom targetAtom = target.Atoms[v];
int[] us = Neighbors(queryElement, queryMap);
us = Map(u, v, us, mapping);
int p = PermutationParity(us);
// check if unspecified was allowed
if (targetTypes[v] == StereoType.Unset)
{
if (queryAtom is SMARTSAtom)
{
return(((SMARTSAtom)queryAtom).ChiralityMatches(targetAtom, 0, p));
}
else
{
return(((QueryAtom)queryAtom).Expression.Matches(targetAtom, 0));
}
}
// target was non-tetrahedral
if (targetTypes[v] != StereoType.Tetrahedral)
{
return(false);
}
int[] vs = Neighbors(targetElement, targetMap);
int q = PermutationParity(vs) * Parity(targetElement.Stereo);
if (queryAtom is SMARTSAtom)
{
return(((SMARTSAtom)queryAtom).ChiralityMatches(targetAtom, q, p));
}
else
{
q *= p;
if (q < 0)
{
return(((QueryAtom)queryAtom).Expression.Matches(targetAtom, (int)StereoConfigurations.Left));
}
else if (q > 0)
{
return(((QueryAtom)queryAtom).Expression.Matches(targetAtom, (int)StereoConfigurations.Right));
}
else
{
return(((QueryAtom)queryAtom).Expression.Matches(targetAtom, 0));
}
}
}
public object Visit(ASTSmarts node, object data)
{
SMARTSAtom atom = null;
SMARTSBond bond = null;
ASTAtom first = (ASTAtom)node.JjtGetChild(0);
atom = (SMARTSAtom)first.JjtAccept(this, null);
if (data != null)
{ // this is a sub smarts
bond = (SMARTSBond)((object[])data)[1];
IAtom prev = (SMARTSAtom)((object[])data)[0];
if (bond == null)
{ // since no bond was specified it could be aromatic or single
bond = new AromaticOrSingleQueryBond(builder);
bond.SetAtoms(new[] { prev, atom });
}
else
{
bond.SetAtoms(new[] { prev, atom });
}
if (neighbors.ContainsKey(prev))
{
neighbors[prev].Add(atom);
}
query.Bonds.Add(bond);
bond = null;
}
// first ATOM in expression
query.Atoms.Add(atom);
if (BitArrays.GetValue(tetrahedral, query.Atoms.Count - 1))
{
List <IAtom> localNeighbors = new List <IAtom>(query.GetConnectedAtoms(atom))
{
atom
};
neighbors[atom] = localNeighbors;
}
// now process the rest of the bonds/atoms
for (int i = 1; i < node.JjtGetNumChildren(); i++)
{
INode child = node.JjtGetChild(i);
if (child is ASTLowAndBond)
{
bond = (SMARTSBond)child.JjtAccept(this, data);
}
else if (child is ASTAtom)
{
SMARTSAtom newAtom = (SMARTSAtom)child.JjtAccept(this, null);
if (bond == null)
{ // since no bond was specified it could be aromatic or single
bond = new AromaticOrSingleQueryBond(builder);
}
bond.SetAtoms(new[] { atom, newAtom });
query.Bonds.Add(bond);
query.Atoms.Add(newAtom);
if (neighbors.ContainsKey(atom))
{
neighbors[atom].Add(newAtom);
}
if (BitArrays.GetValue(tetrahedral, query.Atoms.Count - 1))
{
List <IAtom> localNeighbors = new List <IAtom>(query.GetConnectedAtoms(newAtom))
{
newAtom
};
neighbors[newAtom] = localNeighbors;
}
atom = newAtom;
bond = null;
}
else if (child is ASTSmarts)
{ // another smarts
child.JjtAccept(this, new object[] { atom, bond });
bond = null;
}
else if (child is ASTRingIdentifier)
{
HandleRingClosure(atom, (ASTRingIdentifier)child);
}
else
{
throw new InvalidOperationException("Unhandled node type: " + child.GetType());
}
}
return(query);
}
