private void Parse(string smarts, SmartsFlaver flav)
{
var builder = CDK.Builder;
if (!Smarts.Parse(builder.NewAtomContainer(), smarts, flav))
{
throw new InvalidSmarts(Smarts.GetLastErrorMessage());
}
}
public void ErrorHandling()
{
var builder = CDK.Builder;
if (!Smarts.Parse(builder.NewAtomContainer(), "CCCJCCC"))
{
Assert.AreEqual("Unexpected character", Smarts.GetLastErrorMessage());
Assert.AreEqual("CCCJCCC\n ^\n", Smarts.GetLastErrorLocation());
}
}
// create a query container from a smarts pattern
// Note: only use simple constructs! the target properties will not
// currently be initialised. avoid aromaticity, rings etc.
protected static IAtomContainer Sma(string sma)
{
var query = new QueryAtomContainer(CDK.Builder);
if (!Smarts.Parse(query, sma))
{
throw new IOException(Smarts.GetLastErrorMessage());
}
query.Title = sma;
return(query);
}
public void TestUITSymmetricMatch()
{
var q = new QueryAtomContainer();
if (!Smarts.Parse(q, "C**C"))
{
Assert.Fail(Smarts.GetLastErrorMessage());
}
//Creating 'SCCS' target molecule
var target = builder.NewAtomContainer();
//atoms
var ta0 = builder.NewAtom("S");
target.Atoms.Add(ta0);
var ta1 = builder.NewAtom("C");
target.Atoms.Add(ta1);
var ta2 = builder.NewAtom("C");
target.Atoms.Add(ta2);
var ta3 = builder.NewAtom("S");
target.Atoms.Add(ta3);
//bonds
var tb0 = builder.NewBond();
tb0.SetAtoms(new IAtom[] { ta0, ta1 });
tb0.Order = BondOrder.Single;
target.Bonds.Add(tb0);
var tb1 = builder.NewBond();
tb1.SetAtoms(new IAtom[] { ta1, ta2 });
tb1.Order = BondOrder.Single;
target.Bonds.Add(tb1);
var tb2 = builder.NewBond();
tb2.SetAtoms(new IAtom[] { ta2, ta3 });
tb2.Order = BondOrder.Single;
target.Bonds.Add(tb2);
//Isomorphism check
var res = uiTester.IsSubgraph(target, q);
Assert.IsFalse(res, "C**C should not match SCCS");
}
public void TestSFBug1708336()
{
var atomContainer = builder.NewAtomContainer();
atomContainer.Atoms.Add(builder.NewAtom("C"));
atomContainer.Atoms.Add(builder.NewAtom("C"));
atomContainer.Atoms.Add(builder.NewAtom("N"));
atomContainer.AddBond(atomContainer.Atoms[0], atomContainer.Atoms[1], BondOrder.Single);
atomContainer.AddBond(atomContainer.Atoms[1], atomContainer.Atoms[2], BondOrder.Single);
var query = new QueryAtomContainer();
if (!Smarts.Parse(query, "C*C"))
{
Assert.Fail(Smarts.GetLastErrorMessage());
}
var list = uiTester.GetSubgraphMaps(atomContainer, query);
Assert.IsTrue(list.Count() == 0);
}
