public object Visit(ASTSimpleBond node, object data)
{
SMARTSBond bond = null;
switch (node.BondType)
{
case SMARTSParserConstants.S_BOND:
bond = new Smarts.OrderQueryBond(BondOrder.Single, builder);
break;
case SMARTSParserConstants.D_BOND:
bond = new Smarts.OrderQueryBond(BondOrder.Double, builder);
doubleBonds.Add(bond);
break;
case SMARTSParserConstants.T_BOND:
bond = new Smarts.OrderQueryBond(BondOrder.Triple, builder);
break;
case SMARTSParserConstants.DOLLAR:
bond = new Smarts.OrderQueryBond(BondOrder.Quadruple, builder);
break;
case SMARTSParserConstants.ANY_BOND:
bond = new Smarts.AnyOrderQueryBond(builder);
break;
case SMARTSParserConstants.AR_BOND:
bond = new Smarts.AromaticQueryBond(builder);
break;
case SMARTSParserConstants.R_BOND:
bond = new Smarts.RingBond(builder);
break;
case SMARTSParserConstants.UP_S_BOND:
bond = new Smarts.StereoBond(builder, StereoBond.Direction.Up, false);
stereoBonds.Add(bond);
break;
case SMARTSParserConstants.DN_S_BOND:
bond = new Smarts.StereoBond(builder, StereoBond.Direction.Down, false);
stereoBonds.Add(bond);
break;
case SMARTSParserConstants.UP_OR_UNSPECIFIED_S_BOND:
bond = new Smarts.StereoBond(builder, StereoBond.Direction.Up, true);
stereoBonds.Add(bond);
break;
case SMARTSParserConstants.DN_OR_UNSPECIFIED_S_BOND:
bond = new Smarts.StereoBond(builder, StereoBond.Direction.Down, true);
stereoBonds.Add(bond);
break;
default:
Trace.TraceError("Unparsed bond: " + node.ToString());
break;
}
return(bond);
}
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);
}