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 Guanine_std()
{
var smipar = new SmilesParser(builder);
var smiles = "NC1=NC2=C(N=CN2)C(=O)N1";
var mol = smipar.ParseSmiles(smiles);
var inchiFact = InChIGeneratorFactory.Instance;
InChIGenerator inchigen = inchiFact.GetInChIGenerator(mol);
Assert.AreEqual(InChIReturnCode.Ok, inchigen.ReturnStatus);
Assert.AreEqual("InChI=1S/C5H5N5O/c6-5-9-3-2(4(11)10-5)7-1-8-3/h1H,(H4,6,7,8,9,10,11)", inchigen.InChI);
}
public void TestSMILESConversion_TopologicalCentre()
{
// (2R,3R,4S,5R,6S)-3,5-dimethylheptane-2,4,6-triol
var parser = CDK.SmilesParser;
var container = parser.ParseSmiles("C[C@@H](O)[C@@H](C)[C@@H](O)[C@H](C)[C@H](C)O");
InChIGenerator generator = InChIGeneratorFactory.Instance.GetInChIGenerator(container);
string expected = "InChI=1S/C9H20O3/c1-5(7(3)10)9(12)6(2)8(4)11/h5-12H,1-4H3/t5-,6-,7-,8+,9-/m1/s1";
string actual = generator.InChI;
Assert.AreEqual(expected, actual, "Incorrect InCHI generated for topological centre");
}
public void TestGetStandardInChIEandZ12Dichloroethene2D()
{
// (E)-1,2-dichloroethene
var acE = builder.NewAtomContainer();
var a1E = builder.NewAtom("C", new Vector2(2.866, -0.250));
var a2E = builder.NewAtom("C", new Vector2(3.732, 0.250));
var a3E = builder.NewAtom("Cl", new Vector2(2.000, 2.500));
var a4E = builder.NewAtom("Cl", new Vector2(4.598, -0.250));
a1E.ImplicitHydrogenCount = 1;
a2E.ImplicitHydrogenCount = 1;
acE.Atoms.Add(a1E);
acE.Atoms.Add(a2E);
acE.Atoms.Add(a3E);
acE.Atoms.Add(a4E);
acE.Bonds.Add(builder.NewBond(a1E, a2E, BondOrder.Double));
acE.Bonds.Add(builder.NewBond(a1E, a2E, BondOrder.Double));
acE.Bonds.Add(builder.NewBond(a1E, a3E, BondOrder.Single));
acE.Bonds.Add(builder.NewBond(a2E, a4E, BondOrder.Single));
var genE = factory.GetInChIGenerator(acE);
Assert.AreEqual(InChIReturnCode.Ok, genE.ReturnStatus);
Assert.AreEqual("InChI=1S/C2H2Cl2/c3-1-2-4/h1-2H/b2-1+", genE.InChI);
// (Z)-1,2-dichloroethene
var acZ = builder.NewAtomContainer();
var a1Z = builder.NewAtom("C", new Vector2(2.866, -0.440));
var a2Z = builder.NewAtom("C", new Vector2(3.732, 0.060));
var a3Z = builder.NewAtom("Cl", new Vector2(2.000, 0.060));
var a4Z = builder.NewAtom("Cl", new Vector2(3.732, 1.060));
a1Z.ImplicitHydrogenCount = 1;
a2Z.ImplicitHydrogenCount = 1;
acZ.Atoms.Add(a1Z);
acZ.Atoms.Add(a2Z);
acZ.Atoms.Add(a3Z);
acZ.Atoms.Add(a4Z);
acZ.Bonds.Add(builder.NewBond(a1Z, a2Z, BondOrder.Double));
acZ.Bonds.Add(builder.NewBond(a1Z, a2Z, BondOrder.Double));
acZ.Bonds.Add(builder.NewBond(a1Z, a3Z, BondOrder.Single));
acZ.Bonds.Add(builder.NewBond(a2Z, a4Z, BondOrder.Single));
InChIGenerator genZ = factory.GetInChIGenerator(acZ);
Assert.AreEqual(InChIReturnCode.Ok, genZ.ReturnStatus);
Assert.AreEqual("InChI=1S/C2H2Cl2/c3-1-2-4/h1-2H/b2-1-", genZ.InChI);
}
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;
}
}
