public void R_penta_2_3_diene()
{
var parser = new InChIToStructure("InChI=1S/C5H8/c1-3-5-4-2/h3-4H,1-2H3/t5-/m0/s1", CDK.Builder);
var container = parser.AtomContainer;
var ses = container.StereoElements.GetEnumerator();
Assert.IsInstanceOfType(container, CDK.Builder.NewAtomContainer().GetType());
var f = ses.MoveNext();
Assert.IsTrue(f);
var se = ses.Current;
Assert.IsInstanceOfType(se, typeof(ExtendedTetrahedral));
ExtendedTetrahedral element = (ExtendedTetrahedral)se;
Assert.IsTrue(
Compares.AreEqual(
new IAtom[] {
container.Atoms[5], container.Atoms[0], container.Atoms[1], container.Atoms[6]
},
element.Peripherals));
Assert.AreEqual(container.Atoms[4], element.Focus);
Assert.AreEqual(TetrahedralStereo.AntiClockwise, element.Winding);
}
public void TestGetMessage()
{
var parser = new InChIToStructure("InChI=1S/CH5/h1H4", builder);
var container = parser.AtomContainer;
string message = parser.Message;
Assert.IsNotNull(message);
}
public void TestGetAtomContainer()
{
var parser = new InChIToStructure("InChI=1S/CH4/h1H4", builder);
var container = parser.AtomContainer;
Assert.IsNotNull(container);
Assert.AreEqual(1, container.Atoms.Count);
}
public void TestGetReturnStatus_EOF()
{
var parser = new InChIToStructure("InChI=1S", builder);
var container = parser.AtomContainer;
var returnStatus = parser.ReturnStatus;
Assert.IsNotNull(returnStatus);
Assert.AreEqual(InChIReturnCode.EOF, returnStatus);
}
public void Diazene()
{
InChIToStructure parse = new InChIToStructure("InChI=1S/H2N2/c1-2/h1-2H/b2-1+",
CDK.Builder);
IAtomContainer mol = parse.AtomContainer;
Assert.AreEqual(4, mol.Atoms.Count);
Assert.AreEqual(true, mol.StereoElements.Any());
}
public void AtomicOxygen()
{
var parser = new InChIToStructure("InChI=1S/O", builder);
var container = parser.AtomContainer;
Assert.IsInstanceOfType(container, builder.NewAtomContainer().GetType());
Assert.IsNotNull(container.Atoms[0].ImplicitHydrogenCount);
Assert.AreEqual(0, container.Atoms[0].ImplicitHydrogenCount);
}
public void TestGetAtomContainer_IChemObjectBuilder()
{
var parser = new InChIToStructure("InChI=1S/CH5/h1H4", builder);
var container = parser.AtomContainer;
// test if the created IAtomContainer is done with the Silent module...
// OK, this is not typical use, but maybe the above generate method should be private
Assert.IsInstanceOfType(container, builder.NewAtomContainer().GetType());
}
public void TestGetWarningFlags()
{
var parser = new InChIToStructure("InChI=1S/CH5/h1H4", builder);
var container = parser.AtomContainer;
var flags = parser.WarningFlags;
Assert.IsNotNull(flags);
Assert.AreEqual(4, flags.Count);
}
public void TestFixedHydrogens()
{
var parser = new InChIToStructure("InChI=1/CH2O2/c2-1-3/h1H,(H,2,3)/f/h2H", builder);
var container = parser.AtomContainer;
Assert.IsNotNull(container);
Assert.AreEqual(3, container.Atoms.Count);
Assert.AreEqual(2, container.Bonds.Count);
Assert.IsTrue(container.Bonds[0].Order == BondOrder.Double || container.Bonds[1].Order == BondOrder.Double);
}
public void HeavyOxygenWater()
{
var parser = new InChIToStructure("InChI=1S/H2O/h1H2/i1+2", builder);
var container = parser.AtomContainer;
Assert.IsNotNull(container.Atoms[0].ImplicitHydrogenCount);
Assert.IsInstanceOfType(container, builder.NewAtomContainer().GetType());
Assert.IsNotNull(container.Atoms[0].ImplicitHydrogenCount);
Assert.AreEqual(2, container.Atoms[0].ImplicitHydrogenCount);
Assert.AreEqual(18, container.Atoms[0].MassNumber);
}
public void NonNullAtomicNumbers()
{
var parser = new InChIToStructure("InChI=1S/CH4/h1H4", builder);
var container = parser.AtomContainer;
foreach (var atom in container.Atoms)
{
Assert.IsNotNull(atom.AtomicNumber);
}
Assert.IsNotNull(container);
Assert.AreEqual(1, container.Atoms.Count);
}
public void Z_bute_2_ene()
{
var parser = new InChIToStructure("InChI=1/C4H8/c1-3-4-2/h3-4H,1-2H3/b4-3-", builder);
var container = parser.AtomContainer;
var ses = container.StereoElements.GetEnumerator();
Assert.IsInstanceOfType(container, builder.NewAtomContainer().GetType());
Assert.IsTrue(ses.MoveNext());
var se = ses.Current;
Assert.IsInstanceOfType(se, typeof(IDoubleBondStereochemistry));
Assert.AreEqual(DoubleBondConformation.Together, ((IDoubleBondStereochemistry)se).Stereo);
}
static void Main()
{
string inchi = "inchi";
#region
// Get InChIToStructure
InChIToStructure intostruct = InChIToStructure.FromInChI(inchi, ChemObjectBuilder.Instance);
InChIReturnCode ret = intostruct.ReturnStatus;
if (ret == InChIReturnCode.Warning)
{
// Structure generated, but with warning message
Console.WriteLine($"InChI warning: {intostruct.Message}");
}
else if (ret != InChIReturnCode.Ok)
{
// Structure generation failed
throw new CDKException($"Structure generation failed: {ret.ToString()} [{intostruct.Message}]");
}
IAtomContainer container = intostruct.AtomContainer;
#endregion
}
public void TestConstructor_String_IChemObjectBuilder()
{
var parser = new InChIToStructure("InChI=1S/CH4/h1H4", builder);
Assert.IsNotNull(parser);
}
public void TestGetInChIToStructure_String_IChemObjectBuilder_List()
{
var parser = InChIToStructure.FromInChI("InChI=1/ClH/h1H", ChemObjectBuilder.Instance, new List <string>());
Assert.IsNotNull(parser);
}
public void TestGetInChIToStructure_String_IChemObjectBuilder_NullList()
{
InChIToStructure.FromInChI("InChI=1/ClH/h1H", ChemObjectBuilder.Instance, (List <string>)null);
}