void Main()
{
IAtomContainer container = null;
#region
// Generate factory - if native code does not load
InChIGeneratorFactory factory = new InChIGeneratorFactory();
// Get InChIGenerator
InChIGenerator gen = factory.GetInChIGenerator(container);
InChIReturnCode ret = gen.ReturnStatus;
if (ret == InChIReturnCode.Warning)
{
// InChI generated, but with warning message
Console.WriteLine($"InChI warning: {gen.Message}");
}
else if (ret != InChIReturnCode.Ok)
{
// InChI generation failed
throw new CDKException($"InChI failed: {ret.ToString()} [{gen.Message}]");
}
string inchi = gen.InChI;
string auxinfo = gen.AuxInfo;
#endregion
}
public void TestInChIGenerator_AromaticBonds()
{
try
{
// create a fairly complex aromatic molecule
IAtomContainer tetrazole = TestMoleculeFactory.MakeTetrazole();
foreach (IAtom atom in tetrazole.Atoms)
{
atom.ImplicitHydrogenCount = null;
}
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(tetrazole);
Aromaticity.CDKLegacy.Apply(tetrazole);
InChIGeneratorFactory inchiFactory = InChIGeneratorFactory.Instance;
inchiFactory.IgnoreAromaticBonds = false;
// include aromatic bonds by default
InChIGenerator genAromaticity1 = inchiFactory.GetInChIGenerator(tetrazole);
// exclude aromatic bonds
Assert.IsFalse(inchiFactory.IgnoreAromaticBonds);
inchiFactory.IgnoreAromaticBonds = true;
Assert.IsTrue(inchiFactory.IgnoreAromaticBonds);
InChIGenerator genNoAromaticity = inchiFactory.GetInChIGenerator(tetrazole);
// include aromatic bonds again
inchiFactory.IgnoreAromaticBonds = false;
Assert.IsFalse(inchiFactory.IgnoreAromaticBonds);
InChIGenerator genAromaticity2 = inchiFactory.GetInChIGenerator(tetrazole);
// with the aromatic bonds included, no InChI can be generated
Assert.AreEqual(InChIReturnCode.Error, genAromaticity1.ReturnStatus, "return status was not in error");
Assert.AreEqual(InChIReturnCode.Error, genAromaticity2.ReturnStatus, "return status was not in error");
// excluding the aromatic bonds gives the normal InChI
Assert.AreEqual(InChIReturnCode.Ok, genNoAromaticity.ReturnStatus, "return status was not okay");
Assert.AreEqual("InChI=1S/CH2N4/c1-2-4-5-3-1/h1H,(H,2,3,4,5)",
genNoAromaticity.InChI, "InChIs did not match");
}
finally
{
InChIGeneratorFactory.Instance.IgnoreAromaticBonds = true;
}
}
public void TestGetInChIFromChlorineAtom()
{
var ac = builder.NewAtomContainer();
ac.Atoms.Add(builder.NewAtom("ClH"));
var gen = factory.GetInChIGenerator(ac, "FixedH");
Assert.AreEqual(gen.ReturnStatus, InChIReturnCode.Ok);
Assert.AreEqual("InChI=1/ClH/h1H", gen.InChI);
}