public void BondStereoCisTrans()
{
var mol = new QueryAtomContainer(null);
Assert.IsTrue(Smarts.Parse(mol, "C/C=C/,\\C"));
Assert.AreEqual("C/C=C/,\\C", Smarts.Generate(mol));
}
public void AtomStereo()
{
var mol = new QueryAtomContainer(null);
Assert.IsTrue(Smarts.Parse(mol, "C[C@H](O)CC"));
Assert.AreEqual("C[C@H1](O)CC", Smarts.Generate(mol));
}
public void TestAliphaticSymbols()
{
foreach (var e in ChemicalElement.Values)
{
switch (e.Symbol)
{
case "R":
continue;
default:
int len = e.Symbol.Length;
if (len == 1 || len == 2)
{
string smarts = $"[{e.Symbol}]";
var mol = new QueryAtomContainer();
Assert.IsTrue(Smarts.Parse(mol, smarts), smarts);
var expr = GetAtomExpr(mol.Atoms[0]);
var ee = new Expr(ExprType.Element, e.AtomicNumber);
var ea = new Expr(AliphaticElement, e.AtomicNumber);
Assert.IsTrue(expr.Equals(ee) || expr.Equals(ea));
}
break;
}
}
}
public void BondFalse()
{
var mol = new QueryAtomContainer(null);
Assert.IsTrue(Smarts.Parse(mol, "C!~C"));
Assert.AreEqual("C!~C", Smarts.Generate(mol));
}
public void BondTrue()
{
var mol = new QueryAtomContainer();
Assert.IsTrue(Smarts.Parse(mol, "C~C~N(~O)~O"));
Assert.AreEqual("C~C~N(~O)~O", Smarts.Generate(mol));
}
public void RoundTripStereo()
{
var mol = new QueryAtomContainer();
Smarts.Parse(mol, "O1.[S@]=1(C)CC");
Assert.AreEqual("O=[S@@](C)CC", Smarts.Generate(mol));
}
public void AromaticBond()
{
var mol = new QueryAtomContainer();
Assert.IsTrue(Smarts.Parse(mol, "[#6]:[#6]"));
Assert.AreEqual("[#6]:[#6]", Smarts.Generate(mol));
}
public static IAtomContainer MolFromSmarts(string smarts)
{
var mol = CDK.Builder.NewAtomContainer();
Smarts.Parse(mol, smarts, SmartsFlaver.Daylight);
return(mol);
}
public void BondStereoCisThenTransUnspecWithNbrComplex()
{
var mol = new QueryAtomContainer();
Assert.IsTrue(Smarts.Parse(mol, "C/?C=C(C)\\C=C\\O"));
Assert.AreEqual("C/?C=C(C)/C=C/O", Smarts.Generate(mol));
}
public void RingClosureExprs3()
{
var mol = new QueryAtomContainer();
Assert.IsTrue(Smarts.Parse(mol, "C1-,=CCCC1"));
Assert.AreEqual("C1CCCC-,=1", Smarts.Generate(mol));
}
public void BondStereoUnspec()
{
var mol = new QueryAtomContainer();
Assert.IsTrue(Smarts.Parse(mol, "C/C=C/?\\?C"));
Assert.AreEqual("C/C=C!/!\\C", Smarts.Generate(mol));
}
public void CompGroupingOnAgent()
{
var mol = new QueryAtomContainer();
Assert.IsTrue(Smarts.Parse(mol, ">(c1ccccc1[O-].[Na+])>"));
Assert.AreEqual(">(c1c(cccc1)[O-].[Na+])>", Smarts.Generate(mol));
}
public void AtomStereoOrUnspec()
{
var mol = new QueryAtomContainer();
Assert.IsTrue(Smarts.Parse(mol, "C[C@?H](O)CC"));
Assert.AreEqual("C[CH1@?](O)CC", Smarts.Generate(mol));
}
public void ReactionWithMaps()
{
var mol = new QueryAtomContainer();
Assert.IsTrue(Smarts.Parse(mol, "c1cccc[c:1]1[NH2:2]>>c1cccc[c:1]1[N:2](~O)~O"));
Assert.AreEqual("c1[c:1](cccc1)[NH2:2]>>c1[c:1](cccc1)[N:2](~O)~O", Smarts.Generate(mol));
}
public void CompGrouping()
{
var mol = new QueryAtomContainer();
Assert.IsTrue(Smarts.Parse(mol, "([Na+].[Cl-]).c1ccccc1"));
Assert.AreEqual("c1ccccc1.([Na+].[Cl-])", Smarts.Generate(mol));
}
public void NotTripleBond()
{
var mol = new QueryAtomContainer();
Assert.IsTrue(Smarts.Parse(mol, "C!#C"));
Assert.AreEqual("C!#C", Smarts.Generate(mol));
}
public void Reaction()
{
var mol = new QueryAtomContainer();
Assert.IsTrue(Smarts.Parse(mol, "c1ccccc1[NH2]>>c1ccccc1N(~O)~O"));
Assert.AreEqual("c1c(cccc1)[NH2]>>c1c(cccc1)N(~O)~O", Smarts.Generate(mol));
}
static IAtomContainer Sma(string smarts)
{
var query = new QueryAtomContainer(null);
Smarts.Parse(query, smarts);
return(query);
}
public void BondInRing()
{
var mol = new QueryAtomContainer();
Assert.IsTrue(Smarts.Parse(mol, "C@C"));
Assert.AreEqual("C@C", Smarts.Generate(mol));
}
static Expr GetBondExpr(string sma, SmartsFlaver flav)
{
var mol = new AtomContainer();
Assert.IsTrue(Smarts.Parse(mol, sma, flav));
return(GetBondExpr(mol.Bonds[0]));
}
public void BondStereoCisThenTransWithNbr()
{
var mol = new QueryAtomContainer();
Assert.IsTrue(Smarts.Parse(mol, "C/C=C(C)\\C=C\\C"));
Assert.AreEqual("C/C=C(C)\\C=C\\C", Smarts.Generate(mol));
}
public void AtomMaps()
{
var mol = new QueryAtomContainer();
Assert.IsFalse(Smarts.Parse(mol, "[:10]"));
Assert.IsTrue(Smarts.Parse(mol, "[*:10]"));
Assert.AreEqual(10, mol.Atoms[0].GetProperty <int>(CDKPropertyName.AtomAtomMapping));
}
public void MultipleReads()
{
var mol = new QueryAtomContainer();
Assert.IsTrue(Smarts.Parse(mol, "C/C=C/C"));
Assert.IsTrue(Smarts.Parse(mol, "C/C=C\\C"));
Assert.AreEqual("C/C=C/C.C/C=C\\C", Smarts.Generate(mol));
}
public void TestRecursive()
{
Assert.IsTrue(Smarts.Parse(new QueryAtomContainer(), "[$(*OC)]"));
Assert.IsFalse(Smarts.Parse(new QueryAtomContainer(), "[$*OC)]"));
Assert.IsFalse(Smarts.Parse(new QueryAtomContainer(), "[$(*OC]"));
Assert.IsTrue(Smarts.Parse(new QueryAtomContainer(), "[$((*[O-].[Na+]))]"));
Assert.IsFalse(Smarts.Parse(new QueryAtomContainer(), "[$([J])]"));
}
public void IndoleWithExprRoundTrip()
{
var mol = new QueryAtomContainer();
Assert.IsTrue(Smarts.Parse(mol, "[n;$(*C),$(*OC)]1ccc2c1cccc2"));
// CDK choice of data structures lose local arrangement but
// output is still indole
Assert.AreEqual("[n;$(*C),$(*OC)]1c2c(cc1)cccc2", Smarts.Generate(mol));
}
public void TrailingOperator()
{
var mol = new AtomContainer();
Assert.IsFalse(Smarts.Parse(mol, "[a#6,]"));
Assert.IsFalse(Smarts.Parse(mol, "[a#6;]"));
Assert.IsFalse(Smarts.Parse(mol, "[a#6&]"));
Assert.IsFalse(Smarts.Parse(mol, "[a#6!]"));
}
public void LeadingBondOperator()
{
var mol = new AtomContainer();
Assert.IsFalse(Smarts.Parse(mol, "*,-*"));
Assert.IsFalse(Smarts.Parse(mol, "*;-*"));
Assert.IsFalse(Smarts.Parse(mol, "*&-*"));
Assert.IsTrue(Smarts.Parse(mol, "*!-*"));
}
public void RingSmallestInvalid()
{
var mol = new AtomContainer();
Assert.IsTrue(Smarts.Parse(mol, "[r0]")); // not in ring
Assert.IsFalse(Smarts.Parse(mol, "[r1]"));
Assert.IsFalse(Smarts.Parse(mol, "[r2]"));
Assert.IsTrue(Smarts.Parse(mol, "[r3]"));
}
public void LeadingOperator()
{
var mol = new AtomContainer();
Assert.IsFalse(Smarts.Parse(mol, "[,a#6]"));
Assert.IsFalse(Smarts.Parse(mol, "[;a#6]"));
Assert.IsFalse(Smarts.Parse(mol, "[&a#6]"));
Assert.IsTrue(Smarts.Parse(mol, "[!a#6]"));
}
public void TrailingBondOperator()
{
var mol = new AtomContainer();
Assert.IsFalse(Smarts.Parse(mol, "*-,*"));
Assert.IsFalse(Smarts.Parse(mol, "*-;*"));
Assert.IsFalse(Smarts.Parse(mol, "*-&*"));
Assert.IsFalse(Smarts.Parse(mol, "*-!*"));
}
