public void TestDefineLigandImplicitHydrogen()
{
var molecule = smiles.ParseSmiles("CC(C)C(C#N)(C(=C)C)");
var ligand = CIPTool.DefineLigand(molecule, new VisitedAtoms(), 3, CIPTool.Hydrogen);
Assert.IsTrue(ligand is ImplicitHydrogenLigand);
}
public void TestTermination()
{
int ringSize = 7;
var ring = builder.NewAtomContainer();
for (int i = 0; i < ringSize; i++)
{
ring.Atoms.Add(builder.NewAtom("C"));
}
for (int j = 0; j < ringSize - 1; j++)
{
ring.AddBond(ring.Atoms[j], ring.Atoms[j + 1], BondOrder.Single);
}
ring.AddBond(ring.Atoms[ringSize - 1], ring.Atoms[0], BondOrder.Single);
ring.Atoms.Add(builder.NewAtom("Cl"));
ring.Atoms.Add(builder.NewAtom("F"));
ring.AddBond(ring.Atoms[0], ring.Atoms[ringSize], BondOrder.Single);
ring.AddBond(ring.Atoms[0], ring.Atoms[ringSize + 1], BondOrder.Single);
ring.Atoms.Add(builder.NewAtom("O"));
ring.AddBond(ring.Atoms[1], ring.Atoms[ringSize + 2], BondOrder.Single);
var atoms = new IAtom[] { ring.Atoms[ringSize], ring.Atoms[ringSize + 1], ring.Atoms[ringSize - 1], ring.Atoms[1] };
var stereoCenter = new TetrahedralChirality(ring.Atoms[0], atoms, TetrahedralStereo.AntiClockwise);
ring.StereoElements.Add(stereoCenter);
SmilesGenerator generator = new SmilesGenerator();
CIPTool.GetCIPChirality(ring, stereoCenter);
}
/// <summary>
/// Get the CIP labelling for a container with a single stereo element.
/// </summary>
/// <param name="container">input container</param>
/// <returns>the labelling</returns>
CIPTool.CIPChirality Label(IAtomContainer container)
{
var elements = new List <IStereoElement <IChemObject, IChemObject> >();
foreach (var element in container.StereoElements)
{
elements.Add(element);
}
if (elements.Count != 1)
{
Assert.Fail($"expected 1 stereo-element, found - {elements.Count}");
}
foreach (var element in elements)
{
if (element is ITetrahedralChirality)
{
return(CIPTool.GetCIPChirality(container, (ITetrahedralChirality)element));
}
else if (element is IDoubleBondStereochemistry)
{
return(CIPTool.GetCIPChirality(container, (IDoubleBondStereochemistry)element));
}
}
throw new InvalidOperationException();
}
public void TestTwoVersusDoubleBondedOxygenR()
{
var molecule = smiles.ParseSmiles("OC(O)C([H])(C)C=O");
LigancyFourChirality chirality = CIPTool.DefineLigancyFourChirality(molecule, 3, 4, 5, 1, 6, TetrahedralStereo.Clockwise);
Assert.AreEqual(CIPTool.CIPChirality.R, CIPTool.GetCIPChirality(chirality));
}
public void TestGetCIPChirality()
{
var chirality = new LigancyFourChirality(molecule.Atoms[1], ligands, TetrahedralStereo.Clockwise);
var rsChirality = CIPTool.GetCIPChirality(chirality);
Assert.AreEqual(CIPTool.CIPChirality.S, rsChirality);
}
public void Test()
{
var molecule = smiles.ParseSmiles("ClC(Br)(I)[H]");
LigancyFourChirality chirality = CIPTool.DefineLigancyFourChirality(molecule, 1, 4, 0, 2, 3, TetrahedralStereo.Clockwise);
Assert.AreEqual(CIPTool.CIPChirality.R, CIPTool.GetCIPChirality(chirality));
}
public void Test2methylbutanolR()
{
var molecule = smiles.ParseSmiles("OCC([H])(C)CC");
LigancyFourChirality chirality = CIPTool.DefineLigancyFourChirality(molecule, 2, 3, 1, 4, 5, TetrahedralStereo.Clockwise);
Assert.AreEqual(CIPTool.CIPChirality.R, CIPTool.GetCIPChirality(chirality));
}
public void TestTetraHalogenMethane()
{
var molecule = smiles.ParseSmiles("FC(Br)(Cl)I");
LigancyFourChirality chirality = CIPTool.DefineLigancyFourChirality(molecule, 1, 0, 4, 2, 3,
TetrahedralStereo.AntiClockwise);
Assert.AreEqual(CIPTool.CIPChirality.R, CIPTool.GetCIPChirality(chirality));
}
public void TestDefineLigand()
{
var ligand = CIPTool.DefineLigand(molecule, new VisitedAtoms(), 1, 2);
Assert.AreEqual(molecule, ligand.AtomContainer);
Assert.AreEqual(molecule.Atoms[1], ligand.CentralAtom);
Assert.AreEqual(molecule.Atoms[2], ligand.LigandAtom);
}
public void TestImplicitHydrogen()
{
var molecule = smiles.ParseSmiles("CCC(C)CCC");
LigancyFourChirality chirality = CIPTool.DefineLigancyFourChirality(molecule, 2, CIPTool.Hydrogen, 3, 1, 4,
TetrahedralStereo.AntiClockwise);
Assert.AreEqual(CIPTool.CIPChirality.S, CIPTool.GetCIPChirality(chirality));
}
public void TestOrder()
{
var ligandCopy = CIPTool.Order(ligands);
Assert.AreEqual("H", ligandCopy[0].LigandAtom.Symbol);
Assert.AreEqual("Cl", ligandCopy[1].LigandAtom.Symbol);
Assert.AreEqual("Br", ligandCopy[2].LigandAtom.Symbol);
Assert.AreEqual("I", ligandCopy[3].LigandAtom.Symbol);
}
public void TestGetCIPChiralityAnti()
{
var antiLigands = new ILigand[] { ligands[0], ligands[1], ligands[3], ligands[2] };
var chirality = new LigancyFourChirality(molecule.Atoms[1], antiLigands, TetrahedralStereo.AntiClockwise);
var rsChirality = CIPTool.GetCIPChirality(chirality);
Assert.AreEqual(CIPTool.CIPChirality.S, rsChirality);
}
// 5 seconds should be enough
public void TestTermination2()
{
var mol = smiles.ParseSmiles("OC1CCC[C@](F)(CC1)Cl");
var stereoElements = mol.StereoElements;
var stereo = stereoElements.First();
Assert.IsNotNull(stereo);
Assert.IsTrue(stereo is ITetrahedralChirality);
CIPTool.GetCIPChirality(mol, (ITetrahedralChirality)stereo);
}
public void Label()
{
var container = CDK.SmilesParser.ParseSmiles("C/C=C/[C@@H](C)C(/C)=C(/C)C[C@H](C)O");
CIPTool.Label(container);
Assert.AreEqual("R", container.Atoms[3].GetCIPDescriptor());
Assert.AreEqual("S", container.Atoms[10].GetCIPDescriptor());
Assert.AreEqual("E", container.GetBond(container.Atoms[1], container.Atoms[2]).GetCIPDescriptor());
Assert.AreEqual("Z", container.GetBond(container.Atoms[5], container.Atoms[7]).GetCIPDescriptor());
}
public void TestCID42475007S()
{
var mol = smiles.ParseSmiles("C[NH+](C)CCN(C1=NC2=C(S1)C=C(C=C2)Br)C(=O)[C@@H]3COC4=CC=CC=C4O3");
var stereoElements = mol.StereoElements;
var stereo = stereoElements.First();
Assert.IsNotNull(stereo);
Assert.IsTrue(stereo is ITetrahedralChirality);
Assert.AreEqual(CIPTool.CIPChirality.S, CIPTool.GetCIPChirality(mol, (ITetrahedralChirality)stereo));
}
public void SSulfinyl()
{
var mol = smiles.ParseSmiles("CCC[S@](C)=O");
var stereoElements = mol.StereoElements;
var stereo = stereoElements.First();
Assert.IsNotNull(stereo);
Assert.IsTrue(stereo is ITetrahedralChirality);
Assert.AreEqual(CIPTool.CIPChirality.S, CIPTool.GetCIPChirality(mol, (ITetrahedralChirality)stereo));
}
// 5 seconds should be enough
public void TestTermination()
{
IAtomContainer mol = smiles
.ParseSmiles("[H]O[C@]([H])(C1([H])(C([H])([H])C([H])([H])C1([H])([H])))C2([H])(C([H])([H])C2([H])([H]))");
var stereoElements = mol.StereoElements;
var stereo = stereoElements.First();
Assert.IsNotNull(stereo);
Assert.IsTrue(stereo is ITetrahedralChirality);
CIPTool.GetCIPChirality(mol, (ITetrahedralChirality)stereo);
}
public void TestGetLigandLigandsVisitedTracking()
{
var molecule = smiles.ParseSmiles("CC(C)C(CC)(C(C)(C)C)[H]");
var ligand = CIPTool.DefineLigand(molecule, new VisitedAtoms(), 3, 1);
var sideChains = CIPTool.GetLigandLigands(ligand);
foreach (var ligand2 in sideChains)
{
Assert.AreNotSame(ligand.VisitedAtoms, ligand2.VisitedAtoms);
}
}
public void Main()
{
IAtomContainer mol = new AtomContainer();
IAtom centralAtom = new Atom();
#region
IAtom[] ligandAtoms = mol.GetConnectedAtoms(centralAtom).ToArray();
ITetrahedralChirality tetraStereo = new TetrahedralChirality(centralAtom, ligandAtoms, TetrahedralStereo.AntiClockwise);
CIPChirality cipChirality = CIPTool.GetCIPChirality(mol, tetraStereo);
#endregion
}
public void TestGetCIPChiralityDoubleBondOpposite()
{
var container = CDK.SmilesParser.ParseSmiles("CCC(C)=C(C)CC");
var label = CIPTool.GetCIPChirality(
container,
new DoubleBondStereochemistry(
container.GetBond(container.Atoms[2], container.Atoms[4]),
new[] { container.GetBond(container.Atoms[2], container.Atoms[3]), container.GetBond(container.Atoms[4], container.Atoms[6]) },
DoubleBondConformation.Opposite));
Assert.AreEqual(CIPTool.CIPChirality.Z, label);
}
public void TestGetCIPChiralityILigancyFourChirality()
{
var ligandAtoms = new List <IAtom>();
foreach (var ligand in ligands)
{
ligandAtoms.Add(ligand.LigandAtom);
}
var chirality = new TetrahedralChirality(molecule.Atoms[1], ligandAtoms, TetrahedralStereo.Clockwise);
var rsChirality = CIPTool.GetCIPChirality(molecule, chirality);
Assert.AreEqual(CIPTool.CIPChirality.S, rsChirality);
}
public void TestGetLigandLigandsDoubleTriple()
{
var molecule = smiles.ParseSmiles("CC(C)C(C#N)(C(=C)C)[H]");
var ligand = CIPTool.DefineLigand(molecule, new VisitedAtoms(), 3, 1);
var sideChains = CIPTool.GetLigandLigands(ligand);
Assert.AreEqual(2, sideChains.Count);
ligand = CIPTool.DefineLigand(molecule, new VisitedAtoms(), 3, 4);
sideChains = CIPTool.GetLigandLigands(ligand);
Assert.AreEqual(3, sideChains.Count);
ligand = CIPTool.DefineLigand(molecule, new VisitedAtoms(), 3, 6);
sideChains = CIPTool.GetLigandLigands(ligand);
Assert.AreEqual(3, sideChains.Count);
ligand = CIPTool.DefineLigand(molecule, new VisitedAtoms(), 3, 9);
sideChains = CIPTool.GetLigandLigands(ligand);
Assert.AreEqual(0, sideChains.Count);
}
public void TestDefineLigancyFourChirality()
{
var chirality = CIPTool.DefineLigancyFourChirality(molecule, 1, 0, 2, 3, 4, TetrahedralStereo.AntiClockwise);
Assert.AreEqual(molecule.Atoms[1], chirality.ChiralAtom);
Assert.AreEqual(TetrahedralStereo.AntiClockwise, chirality.Stereo);
var ligands = chirality.Ligands;
Assert.AreEqual(molecule, ligands[0].AtomContainer);
Assert.AreEqual(molecule.Atoms[0], ligands[0].LigandAtom);
Assert.AreEqual(molecule.Atoms[1], ligands[0].CentralAtom);
Assert.AreEqual(molecule, ligands[1].AtomContainer);
Assert.AreEqual(molecule.Atoms[2], ligands[1].LigandAtom);
Assert.AreEqual(molecule.Atoms[1], ligands[1].CentralAtom);
Assert.AreEqual(molecule, ligands[2].AtomContainer);
Assert.AreEqual(molecule.Atoms[3], ligands[2].LigandAtom);
Assert.AreEqual(molecule.Atoms[1], ligands[2].CentralAtom);
Assert.AreEqual(molecule, ligands[3].AtomContainer);
Assert.AreEqual(molecule.Atoms[4], ligands[3].LigandAtom);
Assert.AreEqual(molecule.Atoms[1], ligands[3].CentralAtom);
}
public void TestOla28()
{
var filename = "NCDK.Data.CML.mol28.cml";
IChemFile file;
IAtomContainer mol;
using (var reader = new CMLReader(ResourceLoader.GetAsStream(filename)))
{
file = reader.Read(builder.NewChemFile());
mol = ChemFileManipulator.GetAllAtomContainers(file).First();
}
foreach (var atom in mol.Atoms)
{
var neighbors = mol.GetConnectedAtoms(atom).ToReadOnlyList();
if (neighbors.Count == 4)
{
var stereo = StereoTool.GetStereo(neighbors[0], neighbors[1], neighbors[2], neighbors[3]);
ITetrahedralChirality stereoCenter = new TetrahedralChirality(mol.Atoms[0], neighbors, stereo);
CIPTool.CIPChirality chirality = CIPTool.GetCIPChirality(mol, stereoCenter);
}
}
}
public void TestSteroid()
{
var mol = builder.NewAtomContainer();
var a1 = builder.NewAtom("F");
a1.FormalCharge = 0;
a1.Point3D = new Vector3(7.0124, 2.5853, -0.9016);
mol.Atoms.Add(a1);
var a2 = builder.NewAtom("O");
a2.FormalCharge = 0;
a2.Point3D = new Vector3(-0.5682, -0.2861, 2.1733);
mol.Atoms.Add(a2);
var a3 = builder.NewAtom("O");
a3.FormalCharge = 0;
a3.Point3D = new Vector3(2.2826, -2.9598, -0.5754);
mol.Atoms.Add(a3);
var a4 = builder.NewAtom("O");
a4.FormalCharge = 0;
a4.Point3D = new Vector3(-6.6808, -1.9515, 0.4596);
mol.Atoms.Add(a4);
var a5 = builder.NewAtom("O");
a5.FormalCharge = 0;
a5.Point3D = new Vector3(4.2201, -1.7701, -1.7827);
mol.Atoms.Add(a5);
var a6 = builder.NewAtom("O");
a6.FormalCharge = 0;
a6.Point3D = new Vector3(-7.0886, 0.761, 0.0885);
mol.Atoms.Add(a6);
var a7 = builder.NewAtom("O");
a7.FormalCharge = 0;
a7.Point3D = new Vector3(-3.3025, 3.5973, -0.657);
mol.Atoms.Add(a7);
var a8 = builder.NewAtom("C");
a8.FormalCharge = 0;
a8.Point3D = new Vector3(0.4862, -0.9146, 0.0574);
mol.Atoms.Add(a8);
var a9 = builder.NewAtom("C");
a9.FormalCharge = 0;
a9.Point3D = new Vector3(-0.1943, 0.2177, 0.8706);
mol.Atoms.Add(a9);
var a10 = builder.NewAtom("C");
a10.FormalCharge = 0;
a10.Point3D = new Vector3(1.7596, -1.1559, 0.9089);
mol.Atoms.Add(a10);
var a11 = builder.NewAtom("C");
a11.FormalCharge = 0;
a11.Point3D = new Vector3(-2.4826, -0.4593, -0.073);
mol.Atoms.Add(a11);
var a12 = builder.NewAtom("C");
a12.FormalCharge = 0;
a12.Point3D = new Vector3(-3.7166, 0.0102, -0.941);
mol.Atoms.Add(a12);
var a13 = builder.NewAtom("C");
a13.FormalCharge = 0;
a13.Point3D = new Vector3(-0.4659, -2.1213, 0.0044);
mol.Atoms.Add(a13);
var a14 = builder.NewAtom("C");
a14.FormalCharge = 0;
a14.Point3D = new Vector3(-1.485, 0.6715, 0.2231);
mol.Atoms.Add(a14);
var a15 = builder.NewAtom("C");
a15.FormalCharge = 0;
a15.Point3D = new Vector3(0.9729, 1.1842, 1.122);
mol.Atoms.Add(a15);
var a16 = builder.NewAtom("C");
a16.FormalCharge = 0;
a16.Point3D = new Vector3(2.1976, 0.2666, 1.3272);
mol.Atoms.Add(a16);
var a17 = builder.NewAtom("C");
a17.FormalCharge = 0;
a17.Point3D = new Vector3(-1.8034, -1.7401, -0.6501);
mol.Atoms.Add(a17);
var a18 = builder.NewAtom("C");
a18.FormalCharge = 0;
a18.Point3D = new Vector3(-4.2265, 1.3894, -0.4395);
mol.Atoms.Add(a18);
var a19 = builder.NewAtom("C");
a19.FormalCharge = 0;
a19.Point3D = new Vector3(2.8802, -1.9484, 0.2485);
mol.Atoms.Add(a19);
var a20 = builder.NewAtom("C");
a20.FormalCharge = 0;
a20.Point3D = new Vector3(0.862, -0.4809, -1.3862);
mol.Atoms.Add(a20);
var a21 = builder.NewAtom("C");
a21.FormalCharge = 0;
a21.Point3D = new Vector3(-4.8907, -1.0078, -0.8633);
mol.Atoms.Add(a21);
var a22 = builder.NewAtom("C");
a22.FormalCharge = 0;
a22.Point3D = new Vector3(-1.7576, 1.9697, 0.0241);
mol.Atoms.Add(a22);
var a23 = builder.NewAtom("C");
a23.FormalCharge = 0;
a23.Point3D = new Vector3(-4.9064, 1.3293, 0.9405);
mol.Atoms.Add(a23);
var a24 = builder.NewAtom("C");
a24.FormalCharge = 0;
a24.Point3D = new Vector3(-3.339, 0.1527, -2.4408);
mol.Atoms.Add(a24);
var a25 = builder.NewAtom("C");
a25.FormalCharge = 0;
a25.Point3D = new Vector3(-3.1038, 2.4096, -0.4054);
mol.Atoms.Add(a25);
var a26 = builder.NewAtom("C");
a26.FormalCharge = 0;
a26.Point3D = new Vector3(-5.5668, -1.0627, 0.5104);
mol.Atoms.Add(a26);
var a27 = builder.NewAtom("C");
a27.FormalCharge = 0;
a27.Point3D = new Vector3(3.7564, -1.0338, -0.652);
mol.Atoms.Add(a27);
var a28 = builder.NewAtom("C");
a28.FormalCharge = 0;
a28.Point3D = new Vector3(-6.0498, 0.3154, 0.9627);
mol.Atoms.Add(a28);
var a29 = builder.NewAtom("C");
a29.FormalCharge = 0;
a29.Point3D = new Vector3(3.6914, -2.6828, 1.3258);
mol.Atoms.Add(a29);
var a30 = builder.NewAtom("C");
a30.FormalCharge = 0;
a30.Point3D = new Vector3(4.9535, -0.3812, 0.0661);
mol.Atoms.Add(a30);
var a31 = builder.NewAtom("C");
a31.FormalCharge = 0;
a31.Point3D = new Vector3(5.4727, 0.8461, -0.696);
mol.Atoms.Add(a31);
var a32 = builder.NewAtom("C");
a32.FormalCharge = 0;
a32.Point3D = new Vector3(6.7079, 1.5265, -0.0844);
mol.Atoms.Add(a32);
var a33 = builder.NewAtom("C");
a33.FormalCharge = 0;
a33.Point3D = new Vector3(6.4387, 2.104, 1.3013);
mol.Atoms.Add(a33);
var a34 = builder.NewAtom("C");
a34.FormalCharge = 0;
a34.Point3D = new Vector3(7.9342, 0.6197, -0.0661);
mol.Atoms.Add(a34);
var a35 = builder.NewAtom("H");
a35.FormalCharge = 0;
a35.Point3D = new Vector3(1.4474, -1.6941, 1.8161);
mol.Atoms.Add(a35);
var a36 = builder.NewAtom("H");
a36.FormalCharge = 0;
a36.Point3D = new Vector3(-2.8575, -0.7521, 0.9166);
mol.Atoms.Add(a36);
var a37 = builder.NewAtom("H");
a37.FormalCharge = 0;
a37.Point3D = new Vector3(-0.0529, -2.952, -0.5733);
mol.Atoms.Add(a37);
var a38 = builder.NewAtom("H");
a38.FormalCharge = 0;
a38.Point3D = new Vector3(-0.6583, -2.5149, 1.01);
mol.Atoms.Add(a38);
var a39 = builder.NewAtom("H");
a39.FormalCharge = 0;
a39.Point3D = new Vector3(1.1462, 1.8516, 0.2703);
mol.Atoms.Add(a39);
var a40 = builder.NewAtom("H");
a40.FormalCharge = 0;
a40.Point3D = new Vector3(0.8186, 1.8095, 2.0087);
mol.Atoms.Add(a40);
var a41 = builder.NewAtom("H");
a41.FormalCharge = 0;
a41.Point3D = new Vector3(2.5044, 0.2648, 2.3797);
mol.Atoms.Add(a41);
var a42 = builder.NewAtom("H");
a42.FormalCharge = 0;
a42.Point3D = new Vector3(2.9822, 0.7582, 0.7671);
mol.Atoms.Add(a42);
var a43 = builder.NewAtom("H");
a43.FormalCharge = 0;
a43.Point3D = new Vector3(-2.4854, -2.5906, -0.5319);
mol.Atoms.Add(a43);
var a44 = builder.NewAtom("H");
a44.FormalCharge = 0;
a44.Point3D = new Vector3(-1.6353, -1.6475, -1.7261);
mol.Atoms.Add(a44);
var a45 = builder.NewAtom("H");
a45.FormalCharge = 0;
a45.Point3D = new Vector3(-4.9616, 1.7691, -1.1638);
mol.Atoms.Add(a45);
var a46 = builder.NewAtom("H");
a46.FormalCharge = 0;
a46.Point3D = new Vector3(-0.0354, -0.2446, -1.9684);
mol.Atoms.Add(a46);
var a47 = builder.NewAtom("H");
a47.FormalCharge = 0;
a47.Point3D = new Vector3(1.3691, -1.2574, -1.9625);
mol.Atoms.Add(a47);
var a48 = builder.NewAtom("H");
a48.FormalCharge = 0;
a48.Point3D = new Vector3(1.4296, 0.4511, -1.4252);
mol.Atoms.Add(a48);
var a49 = builder.NewAtom("H");
a49.FormalCharge = 0;
a49.Point3D = new Vector3(-4.5596, -2.0138, -1.147);
mol.Atoms.Add(a49);
var a50 = builder.NewAtom("H");
a50.FormalCharge = 0;
a50.Point3D = new Vector3(-5.6512, -0.7511, -1.6149);
mol.Atoms.Add(a50);
var a51 = builder.NewAtom("H");
a51.FormalCharge = 0;
a51.Point3D = new Vector3(-1.0464, 2.7559, 0.2488);
mol.Atoms.Add(a51);
var a52 = builder.NewAtom("H");
a52.FormalCharge = 0;
a52.Point3D = new Vector3(-4.1786, 1.0807, 1.7222);
mol.Atoms.Add(a52);
var a53 = builder.NewAtom("H");
a53.FormalCharge = 0;
a53.Point3D = new Vector3(-5.2947, 2.3265, 1.1848);
mol.Atoms.Add(a53);
var a54 = builder.NewAtom("H");
a54.FormalCharge = 0;
a54.Point3D = new Vector3(-2.421, 0.7311, -2.5838);
mol.Atoms.Add(a54);
var a55 = builder.NewAtom("H");
a55.FormalCharge = 0;
a55.Point3D = new Vector3(-3.2008, -0.8224, -2.9194);
mol.Atoms.Add(a55);
var a56 = builder.NewAtom("H");
a56.FormalCharge = 0;
a56.Point3D = new Vector3(-4.1353, 0.658, -3.0004);
mol.Atoms.Add(a56);
var a57 = builder.NewAtom("H");
a57.FormalCharge = 0;
a57.Point3D = new Vector3(-4.8758, -1.4669, 1.2574);
mol.Atoms.Add(a57);
var a58 = builder.NewAtom("H");
a58.FormalCharge = 0;
a58.Point3D = new Vector3(-0.9312, 0.4562, 2.6867);
mol.Atoms.Add(a58);
var a59 = builder.NewAtom("H");
a59.FormalCharge = 0;
a59.Point3D = new Vector3(3.1882, -0.2287, -1.0977);
mol.Atoms.Add(a59);
var a60 = builder.NewAtom("H");
a60.FormalCharge = 0;
a60.Point3D = new Vector3(-6.4869, 0.2469, 1.965);
mol.Atoms.Add(a60);
var a61 = builder.NewAtom("H");
a61.FormalCharge = 0;
a61.Point3D = new Vector3(4.102, -2.0082, 2.0826);
mol.Atoms.Add(a61);
var a62 = builder.NewAtom("H");
a62.FormalCharge = 0;
a62.Point3D = new Vector3(4.5162, -3.2434, 0.8708);
mol.Atoms.Add(a62);
var a63 = builder.NewAtom("H");
a63.FormalCharge = 0;
a63.Point3D = new Vector3(3.0747, -3.4251, 1.8469);
mol.Atoms.Add(a63);
var a64 = builder.NewAtom("H");
a64.FormalCharge = 0;
a64.Point3D = new Vector3(1.8961, -3.6368, 0.0058);
mol.Atoms.Add(a64);
var a65 = builder.NewAtom("H");
a65.FormalCharge = 0;
a65.Point3D = new Vector3(5.7631, -1.1204, 0.1084);
mol.Atoms.Add(a65);
var a66 = builder.NewAtom("H");
a66.FormalCharge = 0;
a66.Point3D = new Vector3(4.743, -0.1036, 1.1001);
mol.Atoms.Add(a66);
var a67 = builder.NewAtom("H");
a67.FormalCharge = 0;
a67.Point3D = new Vector3(-6.3482, -2.8223, 0.1828);
mol.Atoms.Add(a67);
var a68 = builder.NewAtom("H");
a68.FormalCharge = 0;
a68.Point3D = new Vector3(4.6594, -1.153, -2.3908);
mol.Atoms.Add(a68);
var a69 = builder.NewAtom("H");
a69.FormalCharge = 0;
a69.Point3D = new Vector3(-7.3836, 1.6319, 0.4047);
mol.Atoms.Add(a69);
var a70 = builder.NewAtom("H");
a70.FormalCharge = 0;
a70.Point3D = new Vector3(5.716, 0.5715, -1.7297);
mol.Atoms.Add(a70);
var a71 = builder.NewAtom("H");
a71.FormalCharge = 0;
a71.Point3D = new Vector3(4.6721, 1.5926, -0.7787);
mol.Atoms.Add(a71);
var b1 = builder.NewBond(a1, a32, BondOrder.Single);
mol.Bonds.Add(b1);
var b2 = builder.NewBond(a2, a9, BondOrder.Single);
mol.Bonds.Add(b2);
var b3 = builder.NewBond(a2, a58, BondOrder.Single);
mol.Bonds.Add(b3);
var b4 = builder.NewBond(a3, a19, BondOrder.Single);
mol.Bonds.Add(b4);
var b5 = builder.NewBond(a3, a64, BondOrder.Single);
mol.Bonds.Add(b5);
var b6 = builder.NewBond(a4, a26, BondOrder.Single);
mol.Bonds.Add(b6);
var b7 = builder.NewBond(a4, a67, BondOrder.Single);
mol.Bonds.Add(b7);
var b8 = builder.NewBond(a5, a27, BondOrder.Single);
mol.Bonds.Add(b8);
var b9 = builder.NewBond(a5, a68, BondOrder.Single);
mol.Bonds.Add(b9);
var b10 = builder.NewBond(a6, a28, BondOrder.Single);
mol.Bonds.Add(b10);
var b11 = builder.NewBond(a6, a69, BondOrder.Single);
mol.Bonds.Add(b11);
var b12 = builder.NewBond(a7, a25, BondOrder.Double);
mol.Bonds.Add(b12);
var b13 = builder.NewBond(a8, a9, BondOrder.Single);
mol.Bonds.Add(b13);
var b14 = builder.NewBond(a8, a10, BondOrder.Single);
mol.Bonds.Add(b14);
var b15 = builder.NewBond(a8, a13, BondOrder.Single);
mol.Bonds.Add(b15);
var b16 = builder.NewBond(a8, a20, BondOrder.Single);
mol.Bonds.Add(b16);
var b17 = builder.NewBond(a9, a14, BondOrder.Single);
mol.Bonds.Add(b17);
var b18 = builder.NewBond(a9, a15, BondOrder.Single);
mol.Bonds.Add(b18);
var b19 = builder.NewBond(a10, a16, BondOrder.Single);
mol.Bonds.Add(b19);
var b20 = builder.NewBond(a10, a19, BondOrder.Single);
mol.Bonds.Add(b20);
var b21 = builder.NewBond(a10, a35, BondOrder.Single);
mol.Bonds.Add(b21);
var b22 = builder.NewBond(a11, a12, BondOrder.Single);
mol.Bonds.Add(b22);
var b23 = builder.NewBond(a11, a14, BondOrder.Single);
mol.Bonds.Add(b23);
var b24 = builder.NewBond(a11, a17, BondOrder.Single);
mol.Bonds.Add(b24);
var b25 = builder.NewBond(a11, a36, BondOrder.Single);
mol.Bonds.Add(b25);
var b26 = builder.NewBond(a12, a18, BondOrder.Single);
mol.Bonds.Add(b26);
var b27 = builder.NewBond(a12, a21, BondOrder.Single);
mol.Bonds.Add(b27);
var b28 = builder.NewBond(a12, a24, BondOrder.Single);
mol.Bonds.Add(b28);
var b29 = builder.NewBond(a13, a17, BondOrder.Single);
mol.Bonds.Add(b29);
var b30 = builder.NewBond(a13, a37, BondOrder.Single);
mol.Bonds.Add(b30);
var b31 = builder.NewBond(a13, a38, BondOrder.Single);
mol.Bonds.Add(b31);
var b32 = builder.NewBond(a14, a22, BondOrder.Double);
mol.Bonds.Add(b32);
var b33 = builder.NewBond(a15, a16, BondOrder.Single);
mol.Bonds.Add(b33);
var b34 = builder.NewBond(a15, a39, BondOrder.Single);
mol.Bonds.Add(b34);
var b35 = builder.NewBond(a15, a40, BondOrder.Single);
mol.Bonds.Add(b35);
var b36 = builder.NewBond(a16, a41, BondOrder.Single);
mol.Bonds.Add(b36);
var b37 = builder.NewBond(a16, a42, BondOrder.Single);
mol.Bonds.Add(b37);
var b38 = builder.NewBond(a17, a43, BondOrder.Single);
mol.Bonds.Add(b38);
var b39 = builder.NewBond(a17, a44, BondOrder.Single);
mol.Bonds.Add(b39);
var b40 = builder.NewBond(a18, a23, BondOrder.Single);
mol.Bonds.Add(b40);
var b41 = builder.NewBond(a18, a25, BondOrder.Single);
mol.Bonds.Add(b41);
var b42 = builder.NewBond(a18, a45, BondOrder.Single);
mol.Bonds.Add(b42);
var b43 = builder.NewBond(a19, a27, BondOrder.Single);
mol.Bonds.Add(b43);
var b44 = builder.NewBond(a19, a29, BondOrder.Single);
mol.Bonds.Add(b44);
var b45 = builder.NewBond(a20, a46, BondOrder.Single);
mol.Bonds.Add(b45);
var b46 = builder.NewBond(a20, a47, BondOrder.Single);
mol.Bonds.Add(b46);
var b47 = builder.NewBond(a20, a48, BondOrder.Single);
mol.Bonds.Add(b47);
var b48 = builder.NewBond(a21, a26, BondOrder.Single);
mol.Bonds.Add(b48);
var b49 = builder.NewBond(a21, a49, BondOrder.Single);
mol.Bonds.Add(b49);
var b50 = builder.NewBond(a21, a50, BondOrder.Single);
mol.Bonds.Add(b50);
var b51 = builder.NewBond(a22, a25, BondOrder.Single);
mol.Bonds.Add(b51);
var b52 = builder.NewBond(a22, a51, BondOrder.Single);
mol.Bonds.Add(b52);
var b53 = builder.NewBond(a23, a28, BondOrder.Single);
mol.Bonds.Add(b53);
var b54 = builder.NewBond(a23, a52, BondOrder.Single);
mol.Bonds.Add(b54);
var b55 = builder.NewBond(a23, a53, BondOrder.Single);
mol.Bonds.Add(b55);
var b56 = builder.NewBond(a24, a54, BondOrder.Single);
mol.Bonds.Add(b56);
var b57 = builder.NewBond(a24, a55, BondOrder.Single);
mol.Bonds.Add(b57);
var b58 = builder.NewBond(a24, a56, BondOrder.Single);
mol.Bonds.Add(b58);
var b59 = builder.NewBond(a26, a28, BondOrder.Single);
mol.Bonds.Add(b59);
var b60 = builder.NewBond(a26, a57, BondOrder.Single);
mol.Bonds.Add(b60);
var b61 = builder.NewBond(a27, a30, BondOrder.Single);
mol.Bonds.Add(b61);
var b62 = builder.NewBond(a27, a59, BondOrder.Single);
mol.Bonds.Add(b62);
var b63 = builder.NewBond(a28, a60, BondOrder.Single);
mol.Bonds.Add(b63);
var b64 = builder.NewBond(a29, a61, BondOrder.Single);
mol.Bonds.Add(b64);
var b65 = builder.NewBond(a29, a62, BondOrder.Single);
mol.Bonds.Add(b65);
var b66 = builder.NewBond(a29, a63, BondOrder.Single);
mol.Bonds.Add(b66);
var b67 = builder.NewBond(a30, a31, BondOrder.Single);
mol.Bonds.Add(b67);
var b68 = builder.NewBond(a30, a65, BondOrder.Single);
mol.Bonds.Add(b68);
var b69 = builder.NewBond(a30, a66, BondOrder.Single);
mol.Bonds.Add(b69);
var b70 = builder.NewBond(a31, a32, BondOrder.Single);
mol.Bonds.Add(b70);
var b71 = builder.NewBond(a31, a70, BondOrder.Single);
mol.Bonds.Add(b71);
var b72 = builder.NewBond(a31, a71, BondOrder.Single);
mol.Bonds.Add(b72);
var b73 = builder.NewBond(a32, a33, BondOrder.Single);
mol.Bonds.Add(b73);
var b74 = builder.NewBond(a32, a34, BondOrder.Single);
mol.Bonds.Add(b74);
var ligandAtoms = new IAtom[4];
ligandAtoms[0] = a1; // F
ligandAtoms[1] = a33; // Me
ligandAtoms[2] = a34; // Me
ligandAtoms[3] = a31; // rest of molecule
var stereo = StereoTool.GetStereo(ligandAtoms[0], ligandAtoms[1], ligandAtoms[2], ligandAtoms[3]);
var tetraStereo = new TetrahedralChirality(a32, ligandAtoms, stereo);
Assert.AreEqual(CIPTool.CIPChirality.None, CIPTool.GetCIPChirality(mol, tetraStereo));
}
public void TestCheckIfAllLigandsAreDifferent()
{
Assert.IsTrue(CIPTool.CheckIfAllLigandsAreDifferent(ligands));
}
public void TestCheckIfAllLigandsAreDifferentFalse()
{
var sameLigands = new ILigand[] { ligands[0], ligands[0], ligands[1], ligands[2] };
Assert.IsFalse(CIPTool.CheckIfAllLigandsAreDifferent(sameLigands));
}
