public void FormalCharges()
{
Assert.AreEqual("[-2]", Smarts.GenerateAtom(GetExpr(ExprType.FormalCharge, -2)));
Assert.AreEqual("[-]", Smarts.GenerateAtom(GetExpr(ExprType.FormalCharge, -1)));
Assert.AreEqual("[+0]", Smarts.GenerateAtom(GetExpr(ExprType.FormalCharge, 0)));
Assert.AreEqual("[+]", Smarts.GenerateAtom(GetExpr(ExprType.FormalCharge, 1)));
Assert.AreEqual("[+2]", Smarts.GenerateAtom(GetExpr(ExprType.FormalCharge, 2)));
}
public void UsrRecrNot()
{
var expr = new Expr(ExprType.Element, 9)
.Or(new Expr(ExprType.Element, 17))
.Or(new Expr(ExprType.Element, 35))
.Negate();
Assert.AreEqual("[!$([F,Cl,Br])]", Smarts.GenerateAtom(expr));
}
public void AtomicNumHighWeightElements()
{
Assert.AreEqual("[#110]", Smarts.GenerateAtom(GetExpr(ExprType.Element, AtomicNumbers.Darmstadtium)));
Assert.AreEqual("[#117]", Smarts.GenerateAtom(GetExpr(ExprType.Element, AtomicNumbers.Tennessine)));
Assert.AreEqual("[#113]", Smarts.GenerateAtom(GetExpr(ExprType.Element, AtomicNumbers.Nihonium)));
Assert.AreEqual("[#110]", Smarts.GenerateAtom(GetExpr(ExprType.AliphaticElement, AtomicNumbers.Darmstadtium)));
Assert.AreEqual("[#117]", Smarts.GenerateAtom(GetExpr(ExprType.AliphaticElement, AtomicNumbers.Tennessine)));
Assert.AreEqual("[#113]", Smarts.GenerateAtom(GetExpr(ExprType.AliphaticElement, AtomicNumbers.Nihonium)));
}
public void UsrRecrOr()
{
var expr = GetOr(
GetAnd(
GetOr(
GetExpr(ExprType.Element, 6),
GetExpr(ExprType.Element, 7)),
GetExpr(ExprType.IsInRing)),
GetExpr(ExprType.IsAromatic));
Assert.AreEqual("[$([#6,#7])R,a]", Smarts.GenerateAtom(expr));
}
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
}
}
public void AtomicNum()
{
Assert.AreEqual("[#0]", Smarts.GenerateAtom(GetExpr(ExprType.Element, 0)));
Assert.AreEqual("[#0]", Smarts.GenerateAtom(GetExpr(ExprType.AliphaticElement, 0)));
Assert.AreEqual("[#0]", Smarts.GenerateAtom(GetExpr(ExprType.AromaticElement, 0)));
Assert.AreEqual("[#1]", Smarts.GenerateAtom(GetExpr(ExprType.Element, 1)));
Assert.AreEqual("[#1]", Smarts.GenerateAtom(GetExpr(ExprType.AliphaticElement, 1)));
Assert.AreEqual("[#1]", Smarts.GenerateAtom(GetExpr(ExprType.AromaticElement, 1)));
Assert.AreEqual("[He]", Smarts.GenerateAtom(GetExpr(ExprType.Element, 2)));
Assert.AreEqual("[Li]", Smarts.GenerateAtom(GetExpr(ExprType.Element, 3)));
Assert.AreEqual("[#6]", Smarts.GenerateAtom(GetExpr(ExprType.Element, 6)));
Assert.AreEqual("[#7]", Smarts.GenerateAtom(GetExpr(ExprType.Element, 7)));
Assert.AreEqual("[#8]", Smarts.GenerateAtom(GetExpr(ExprType.Element, 8)));
Assert.AreEqual("F", Smarts.GenerateAtom(GetExpr(ExprType.Element, 9)));
Assert.AreEqual("[Ne]", Smarts.GenerateAtom(GetExpr(ExprType.Element, 10)));
Assert.AreEqual("[Na]", Smarts.GenerateAtom(GetExpr(ExprType.Element, 11)));
Assert.AreEqual("[Mg]", Smarts.GenerateAtom(GetExpr(ExprType.Element, 12)));
// Ds, Ts and Nh etc write as #<num>
Assert.AreEqual("[#110]", Smarts.GenerateAtom(GetExpr(ExprType.Element, AtomicNumbers.Darmstadtium)));
Assert.AreEqual("[#117]", Smarts.GenerateAtom(GetExpr(ExprType.Element, AtomicNumbers.Tennessine)));
Assert.AreEqual("[#113]", Smarts.GenerateAtom(GetExpr(ExprType.Element, AtomicNumbers.Nihonium)));
}
public void Helium()
{
var expr = new Expr(ExprType.Element, 2);
Assert.AreEqual("[He]", Smarts.GenerateAtom(expr));
}
public void Carbon()
{
var expr = new Expr(ExprType.Element, 6);
Assert.AreEqual("[#6]", Smarts.GenerateAtom(expr));
}
public void UseExplAnd2()
{
var expr = new Expr(ExprType.Degree, 1).And(new Expr(ExprType.Isotope, 2));
Assert.AreEqual("[D&2]", Smarts.GenerateAtom(expr));
}
public void UseExplAnd1()
{
var expr = new Expr(ExprType.AliphaticElement, 6).And(new Expr(ExprType.RingSmallest, 6));
Assert.AreEqual("[C&r6]", Smarts.GenerateAtom(expr));
}
public void RingMembership()
{
Assert.AreEqual("[R]", Smarts.GenerateAtom(GetExpr(ExprType.IsInRing)));
Assert.AreEqual("[!R]", Smarts.GenerateAtom(GetExpr(ExprType.IsInChain)));
}
public void RingCount()
{
Assert.AreEqual("[R2]", Smarts.GenerateAtom(GetExpr(ExprType.RingCount, 2)));
}
public void UseImplAnd()
{
var expr = new Expr(ExprType.AromaticElement, 7).And(new Expr(ExprType.Degree, 2).And(new Expr(ExprType.HasImplicitHydrogen)));
Assert.AreEqual("[nD2h]", Smarts.GenerateAtom(expr));
}
public void UseLowPrecedenceAnd()
{
var expr = new Expr(ExprType.Element, 8).And(new Expr(ExprType.Degree, 2).Or(new Expr(ExprType.Degree, 1)));
Assert.AreEqual("[#8;D2,D]", Smarts.GenerateAtom(expr));
}
public void Connectivity()
{
Assert.AreEqual("[X]", Smarts.GenerateAtom(GetExpr(ExprType.TotalDegree, 1)));
Assert.AreEqual("[X2]", Smarts.GenerateAtom(GetExpr(ExprType.TotalDegree, 2)));
}
public void Degree()
{
Assert.AreEqual("[D]", Smarts.GenerateAtom(GetExpr(ExprType.Degree, 1)));
Assert.AreEqual("[D2]", Smarts.GenerateAtom(GetExpr(ExprType.Degree, 2)));
}
public void Valence()
{
Assert.AreEqual("[v]", Smarts.GenerateAtom(GetExpr(ExprType.Valence, 1)));
Assert.AreEqual("[v2]", Smarts.GenerateAtom(GetExpr(ExprType.Valence, 2)));
}
public void RingSmallest()
{
Assert.AreEqual("[r4]", Smarts.GenerateAtom(GetExpr(ExprType.RingSmallest, 4)));
}
public void Isotopes()
{
Assert.AreEqual("[13]", Smarts.GenerateAtom(GetExpr(ExprType.Isotope, 13)));
Assert.AreEqual("[0]", Smarts.GenerateAtom(GetExpr(ExprType.HasUnspecifiedIsotope)));
Assert.AreEqual("[!0]", Smarts.GenerateAtom(GetExpr(ExprType.HasIsotope)));
}
public void TotalHCount()
{
Assert.AreEqual("[H1]", Smarts.GenerateAtom(GetExpr(ExprType.TotalHCount, 1)));
Assert.AreEqual("[H2]", Smarts.GenerateAtom(GetExpr(ExprType.TotalHCount, 2)));
}
public void AromaticElement()
{
Assert.AreEqual("c", Smarts.GenerateAtom(GetExpr(ExprType.AromaticElement, 6)));
Assert.AreEqual("n", Smarts.GenerateAtom(GetExpr(ExprType.AromaticElement, 7)));
}