/// <summary>
/// Internal - create a query atom container that exactly matches the molecule provided.
/// Similar to <see cref="QueryAtomContainerCreator"/>
/// but we can't access SMARTS query classes from that module (cdk-isomorphism).
/// </summary>
/// <param name="mol">molecule</param>
/// <returns>query container</returns>
/// <seealso cref="QueryAtomContainerCreator"/>
private static IQueryAtomContainer MatchExact(IAtomContainer mol)
{
var bldr = mol.Builder;
var qry = new QueryAtomContainer();
var atmmap = new Dictionary <IAtom, IAtom>();
foreach (var atom in mol.Atoms)
{
var qatom = MatchExact(mol, atom);
if (qatom != null)
{
atmmap[atom] = qatom;
qry.Atoms.Add(qatom);
}
}
foreach (var bond in mol.Bonds)
{
var beg = atmmap[bond.Begin];
var end = atmmap[bond.End];
// attach bond skipped
if (beg == null || end == null)
{
continue;
}
var qbond = new QueryBond(beg, end, ExprType.True);
qry.Bonds.Add(qbond);
}
return(qry);
}
public static QueryAtomContainer CreateSymbolChargeIDQueryContainer(IAtomContainer container)
{
var queryContainer = new QueryAtomContainer(container.Builder);
for (int i = 0; i < container.Atoms.Count; i++)
{
queryContainer.Atoms.Add(new SymbolChargeIDQueryAtom(container.Atoms[i]));
}
foreach (var bond in container.Bonds)
{
int index1 = container.Atoms.IndexOf(bond.Begin);
int index2 = container.Atoms.IndexOf(bond.End);
if (bond.IsAromatic)
{
QueryBond qbond = new QueryBond(queryContainer.Atoms[index1],
queryContainer.Atoms[index2],
ExprType.IsAromatic);
queryContainer.Bonds.Add(qbond);
}
else
{
QueryBond qbond = new QueryBond(queryContainer.Atoms[index1],
queryContainer.Atoms[index2],
ExprType.Order,
bond.Order.Numeric())
{
Order = bond.Order // backwards compatibility
};
queryContainer.Bonds.Add(qbond);
}
}
return(queryContainer);
}
static void Main()
{
IAtomContainer mol = null;
#region 1
if (Smarts.Parse(mol, "[aD3]a-a([aD3])[aD3]"))
{
var smarts = Smarts.Generate(mol);
}
#endregion
{
#region GenerateAtom
var expr = new Expr(ExprType.Degree, 4).And(
new Expr(ExprType.IsAromatic));
var aExpr = Smarts.GenerateAtom(expr);
// aExpr = "[D4a]"
#endregion
}
{
#region GenerateBond
var expr = new Expr(ExprType.True);
var bExpr = Smarts.GenerateBond(expr);
// // bExpr='~'
#endregion
}
{
#region Generate
var qatom1 = new QueryAtom();
var qatom2 = new QueryAtom();
var qbond = new QueryBond();
qatom1.Expression = new Expr(ExprType.IsAromatic);
qatom2.Expression = new Expr(ExprType.IsAromatic);
qbond.Expression = new Expr(ExprType.IsAliphatic);
qbond.SetAtoms(new IAtom[] { qatom1, qatom2 });
mol.Atoms.Add(qatom1);
mol.Atoms.Add(qatom2);
mol.Bonds.Add(qbond);
var smartsStr = Smarts.Generate(mol);
// smartsStr = 'a!:a'
#endregion
}
}