public object Visit(ASTSmarts node, object data)
{
System.Console.Out.WriteLine(IndentString() + node);
++indent;
data = node.ChildrenAccept(this, data);
--indent;
return(data);
}
public object Visit(ASTSmarts node, object data)
{
string local = "";
for (int i = 0; i < node.JjtGetNumChildren(); i++)
{
INode child = node.JjtGetChild(i);
if (child is ASTAtom)
{
local = (string)child.JjtAccept(this, local);
}
else if (child is ASTLowAndBond)
{
i++;
INode nextChild = node.JjtGetChild(i); // the next child should
// be another smarts
string bond = (string)child.JjtAccept(this, local);
local = local + bond;
local = (string)nextChild.JjtAccept(this, local);
}
else if (child is ASTSmarts)
{ // implicit single bond
if (local.Length != 0)
{
local = local + "-";
}
local = (string)child.JjtAccept(this, local);
}
else if (child is ASTExplicitAtom)
{
if (local.Length != 0)
{
local = local + "-";
}
local = (string)child.JjtAccept(this, local);
}
}
return(data + local);
}
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);
}
public object Visit(ASTGroup node, object data)
{
IAtomContainer fullQuery = (IAtomContainer)data;
if (fullQuery == null)
{
fullQuery = new QueryAtomContainer(builder);
}
// keeps track of component grouping
var components = fullQuery.GetProperty <int[]>("COMPONENT.GROUPING", Array.Empty <int>());
int maxId = 0;
if (components.Length > 0)
{
foreach (int id in components)
{
if (id > maxId)
{
maxId = id;
}
}
}
for (int i = 0; i < node.JjtGetNumChildren(); i++)
{
ASTSmarts smarts = (ASTSmarts)node.JjtGetChild(i);
ringAtoms = new RingIdentifierAtom[10];
query = new QueryAtomContainer(builder);
smarts.JjtAccept(this, null);
// update component info
if (components.Length > 0 || smarts.ComponentId > 0)
{
components = Arrays.CopyOf(components, 1 + fullQuery.Atoms.Count + query.Atoms.Count);
int id = smarts.ComponentId;
Arrays.Fill(components, fullQuery.Atoms.Count, components.Length, id);
if (id > maxId)
{
maxId = id;
}
}
fullQuery.Add(query);
}
// only store if there was a component grouping
if (maxId > 0)
{
components[components.Length - 1] = maxId; // we left space to store how many groups there were
fullQuery.SetProperty("COMPONENT.GROUPING", components);
}
// create tetrahedral elements
foreach (var atom in neighbors.Keys)
{
IList <IAtom> localNeighbors = neighbors[atom];
if (localNeighbors.Count == 4)
{
fullQuery.StereoElements.Add(new TetrahedralChirality(atom, localNeighbors.ToArray(),
TetrahedralStereo.Clockwise)); // <- to be modified later
}
else if (localNeighbors.Count == 5)
{
localNeighbors.Remove(atom); // remove central atom (which represented implicit part)
fullQuery.StereoElements.Add(new TetrahedralChirality(atom, localNeighbors.ToArray(),
TetrahedralStereo.Clockwise)); // <- to be modified later
}
}
// for each double bond, find the stereo bonds. Currently doesn't
// handle logical bonds i.e. C/C-,=C/C
foreach (var bond in doubleBonds)
{
IAtom left = bond.Begin;
IAtom right = bond.End;
StereoBond leftBond = FindStereoBond(left);
StereoBond rightBond = FindStereoBond(right);
if (leftBond == null || rightBond == null)
{
continue;
}
DoubleBondConformation conformation = leftBond.GetDirection(left) == rightBond.GetDirection(right) ? DoubleBondConformation.Together
: DoubleBondConformation.Opposite;
fullQuery.StereoElements.Add(new DoubleBondStereochemistry(bond, new IBond[] { leftBond, rightBond },
conformation));
}
return(fullQuery);
}
