public void TestPseudoAtoms()
{
var filename = "NCDK.Data.MDL.pseudoatoms.sdf";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins);
var mol = builder.NewAtomContainer();
mol = reader.Read(mol);
Assert.IsNotNull(mol);
// check that there are some pseudo-atoms
bool hasPseudo = false;
foreach (var atom in mol.Atoms)
{
if (atom is IPseudoAtom)
{
hasPseudo = true;
}
}
Assert.IsTrue(hasPseudo, "The molecule should have one or more pseudo atoms");
EquivalentClassPartitioner partitioner = new EquivalentClassPartitioner(mol);
Assert.IsNotNull(partitioner);
int[] classes = partitioner.GetTopoEquivClassbyHuXu(mol);
}
public void TestImidazole()
{
var mol = TestMoleculeFactory.MakeImidazole();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
Aromaticity.CDKLegacy.Apply(mol);
Assert.IsNotNull(mol, "Created molecule was null");
var it = new EquivalentClassPartitioner(mol);
var equivalentClass = it.GetTopoEquivClassbyHuXu(mol);
var arrEquivalent = new char[mol.Atoms.Count];
for (int i = 1; i < equivalentClass.Length; i++)
{
arrEquivalent[i - 1] = equivalentClass[i].ToString()[0];
}
string strEquivalent = new string(arrEquivalent);
Assert.IsNotNull(equivalentClass, "Equivalent class was null");
Assert.AreEqual(3, equivalentClass[0], "Wrong number of equivalent classes");
Assert.AreEqual("12321", strEquivalent, "Wrong class assignment");
}
public void TestEquivalent()
{
var C40C3V = builder.NewAtomContainer();
C40C3V.Atoms.Add(builder.NewAtom("C")); // 1
C40C3V.Atoms.Add(builder.NewAtom("C")); // 2
C40C3V.Atoms.Add(builder.NewAtom("C")); // 3
C40C3V.Atoms.Add(builder.NewAtom("C")); // 4
C40C3V.Atoms.Add(builder.NewAtom("C")); // 5
C40C3V.Atoms.Add(builder.NewAtom("C")); // 6
C40C3V.Atoms.Add(builder.NewAtom("C")); // 7
C40C3V.Atoms.Add(builder.NewAtom("C")); // 8
C40C3V.Atoms.Add(builder.NewAtom("C")); // 9
C40C3V.Atoms.Add(builder.NewAtom("C")); // 10
C40C3V.Atoms.Add(builder.NewAtom("C")); // 11
C40C3V.Atoms.Add(builder.NewAtom("C")); // 12
C40C3V.Atoms.Add(builder.NewAtom("C")); // 13
C40C3V.Atoms.Add(builder.NewAtom("C")); // 14
C40C3V.Atoms.Add(builder.NewAtom("C")); // 15
C40C3V.Atoms.Add(builder.NewAtom("C")); // 16
C40C3V.Atoms.Add(builder.NewAtom("C")); // 17
C40C3V.Atoms.Add(builder.NewAtom("C")); // 18
C40C3V.Atoms.Add(builder.NewAtom("C")); // 19
C40C3V.Atoms.Add(builder.NewAtom("C")); // 20
C40C3V.Atoms.Add(builder.NewAtom("C")); // 21
C40C3V.Atoms.Add(builder.NewAtom("C")); // 22
C40C3V.Atoms.Add(builder.NewAtom("C")); // 23
C40C3V.Atoms.Add(builder.NewAtom("C")); // 24
C40C3V.Atoms.Add(builder.NewAtom("C")); // 25
C40C3V.Atoms.Add(builder.NewAtom("C")); // 26
C40C3V.Atoms.Add(builder.NewAtom("C")); // 27
C40C3V.Atoms.Add(builder.NewAtom("C")); // 28
C40C3V.Atoms.Add(builder.NewAtom("C")); // 29
C40C3V.Atoms.Add(builder.NewAtom("C")); // 30
C40C3V.Atoms.Add(builder.NewAtom("C")); // 31
C40C3V.Atoms.Add(builder.NewAtom("C")); // 32
C40C3V.Atoms.Add(builder.NewAtom("C")); // 33
C40C3V.Atoms.Add(builder.NewAtom("C")); // 34
C40C3V.Atoms.Add(builder.NewAtom("C")); // 35
C40C3V.Atoms.Add(builder.NewAtom("C")); // 36
C40C3V.Atoms.Add(builder.NewAtom("C")); // 37
C40C3V.Atoms.Add(builder.NewAtom("C")); // 38
C40C3V.Atoms.Add(builder.NewAtom("C")); // 39
C40C3V.Atoms.Add(builder.NewAtom("C")); // 40
C40C3V.AddBond(C40C3V.Atoms[0], C40C3V.Atoms[1], BondOrder.Single); // 1
C40C3V.AddBond(C40C3V.Atoms[0], C40C3V.Atoms[5], BondOrder.Single); // 2
C40C3V.AddBond(C40C3V.Atoms[0], C40C3V.Atoms[8], BondOrder.Single); // 3
C40C3V.AddBond(C40C3V.Atoms[1], C40C3V.Atoms[2], BondOrder.Single); // 4
C40C3V.AddBond(C40C3V.Atoms[1], C40C3V.Atoms[25], BondOrder.Single); // 5
C40C3V.AddBond(C40C3V.Atoms[2], C40C3V.Atoms[3], BondOrder.Single); // 6
C40C3V.AddBond(C40C3V.Atoms[2], C40C3V.Atoms[6], BondOrder.Single); // 7
C40C3V.AddBond(C40C3V.Atoms[3], C40C3V.Atoms[4], BondOrder.Single); // 8
C40C3V.AddBond(C40C3V.Atoms[3], C40C3V.Atoms[24], BondOrder.Single); // 9
C40C3V.AddBond(C40C3V.Atoms[4], C40C3V.Atoms[7], BondOrder.Single); // 10
C40C3V.AddBond(C40C3V.Atoms[4], C40C3V.Atoms[8], BondOrder.Single); // 11
C40C3V.AddBond(C40C3V.Atoms[5], C40C3V.Atoms[21], BondOrder.Single); // 12
C40C3V.AddBond(C40C3V.Atoms[5], C40C3V.Atoms[28], BondOrder.Single); // 13
C40C3V.AddBond(C40C3V.Atoms[6], C40C3V.Atoms[22], BondOrder.Single); // 14
C40C3V.AddBond(C40C3V.Atoms[6], C40C3V.Atoms[27], BondOrder.Single); // 15
C40C3V.AddBond(C40C3V.Atoms[7], C40C3V.Atoms[20], BondOrder.Single); // 16
C40C3V.AddBond(C40C3V.Atoms[7], C40C3V.Atoms[23], BondOrder.Single); // 17
C40C3V.AddBond(C40C3V.Atoms[8], C40C3V.Atoms[26], BondOrder.Single); // 18
C40C3V.AddBond(C40C3V.Atoms[9], C40C3V.Atoms[12], BondOrder.Single); // 19
C40C3V.AddBond(C40C3V.Atoms[9], C40C3V.Atoms[37], BondOrder.Single); // 20
C40C3V.AddBond(C40C3V.Atoms[9], C40C3V.Atoms[39], BondOrder.Single); // 21
C40C3V.AddBond(C40C3V.Atoms[10], C40C3V.Atoms[14], BondOrder.Single); // 22
C40C3V.AddBond(C40C3V.Atoms[10], C40C3V.Atoms[38], BondOrder.Single); // 23
C40C3V.AddBond(C40C3V.Atoms[10], C40C3V.Atoms[39], BondOrder.Single); // 24
C40C3V.AddBond(C40C3V.Atoms[11], C40C3V.Atoms[13], BondOrder.Single); // 25
C40C3V.AddBond(C40C3V.Atoms[11], C40C3V.Atoms[36], BondOrder.Single); // 26
C40C3V.AddBond(C40C3V.Atoms[11], C40C3V.Atoms[39], BondOrder.Single); // 27
C40C3V.AddBond(C40C3V.Atoms[12], C40C3V.Atoms[35], BondOrder.Single); // 28
C40C3V.AddBond(C40C3V.Atoms[12], C40C3V.Atoms[38], BondOrder.Single); // 29
C40C3V.AddBond(C40C3V.Atoms[13], C40C3V.Atoms[34], BondOrder.Single); // 30
C40C3V.AddBond(C40C3V.Atoms[13], C40C3V.Atoms[37], BondOrder.Single); // 31
C40C3V.AddBond(C40C3V.Atoms[14], C40C3V.Atoms[33], BondOrder.Single); // 32
C40C3V.AddBond(C40C3V.Atoms[14], C40C3V.Atoms[36], BondOrder.Single); // 33
C40C3V.AddBond(C40C3V.Atoms[15], C40C3V.Atoms[29], BondOrder.Single); // 34
C40C3V.AddBond(C40C3V.Atoms[15], C40C3V.Atoms[17], BondOrder.Single); // 35
C40C3V.AddBond(C40C3V.Atoms[15], C40C3V.Atoms[37], BondOrder.Single); // 36
C40C3V.AddBond(C40C3V.Atoms[16], C40C3V.Atoms[19], BondOrder.Single); // 37
C40C3V.AddBond(C40C3V.Atoms[16], C40C3V.Atoms[30], BondOrder.Single); // 38
C40C3V.AddBond(C40C3V.Atoms[16], C40C3V.Atoms[36], BondOrder.Single); // 39
C40C3V.AddBond(C40C3V.Atoms[17], C40C3V.Atoms[20], BondOrder.Single); // 40
C40C3V.AddBond(C40C3V.Atoms[17], C40C3V.Atoms[35], BondOrder.Single); // 41
C40C3V.AddBond(C40C3V.Atoms[18], C40C3V.Atoms[22], BondOrder.Single); // 42
C40C3V.AddBond(C40C3V.Atoms[18], C40C3V.Atoms[32], BondOrder.Single); // 43
C40C3V.AddBond(C40C3V.Atoms[18], C40C3V.Atoms[33], BondOrder.Single); // 44
C40C3V.AddBond(C40C3V.Atoms[19], C40C3V.Atoms[28], BondOrder.Single); // 45
C40C3V.AddBond(C40C3V.Atoms[19], C40C3V.Atoms[34], BondOrder.Single); // 46
C40C3V.AddBond(C40C3V.Atoms[20], C40C3V.Atoms[26], BondOrder.Single); // 47
C40C3V.AddBond(C40C3V.Atoms[21], C40C3V.Atoms[26], BondOrder.Single); // 48
C40C3V.AddBond(C40C3V.Atoms[21], C40C3V.Atoms[29], BondOrder.Single); // 49
C40C3V.AddBond(C40C3V.Atoms[22], C40C3V.Atoms[24], BondOrder.Single); // 50
C40C3V.AddBond(C40C3V.Atoms[23], C40C3V.Atoms[24], BondOrder.Single); // 51
C40C3V.AddBond(C40C3V.Atoms[23], C40C3V.Atoms[31], BondOrder.Single); // 52
C40C3V.AddBond(C40C3V.Atoms[25], C40C3V.Atoms[27], BondOrder.Single); // 53
C40C3V.AddBond(C40C3V.Atoms[25], C40C3V.Atoms[28], BondOrder.Single); // 54
C40C3V.AddBond(C40C3V.Atoms[27], C40C3V.Atoms[30], BondOrder.Single); // 55
C40C3V.AddBond(C40C3V.Atoms[29], C40C3V.Atoms[34], BondOrder.Single); // 56
C40C3V.AddBond(C40C3V.Atoms[30], C40C3V.Atoms[33], BondOrder.Single); // 57
C40C3V.AddBond(C40C3V.Atoms[31], C40C3V.Atoms[32], BondOrder.Single); // 58
C40C3V.AddBond(C40C3V.Atoms[31], C40C3V.Atoms[35], BondOrder.Single); // 59
C40C3V.AddBond(C40C3V.Atoms[32], C40C3V.Atoms[38], BondOrder.Single); // 60
var it = new EquivalentClassPartitioner(C40C3V);
var equivalentClass = it.GetTopoEquivClassbyHuXu(C40C3V);
var arrEquivalent = new char[39];
for (int i = 1; i < equivalentClass.Length - 1; i++)
{
arrEquivalent[i - 1] = equivalentClass[i].ToString()[0];
}
string strEquivalent = new string(arrEquivalent);
Assert.IsNotNull(equivalentClass);
Assert.IsTrue(equivalentClass[0] == 10);//number of Class
Assert.IsTrue(equivalentClass[40] == 10);
Assert.AreEqual("111112221333444556667878222879995555444", strEquivalent);
}
public void TestFullereneC24D6D()
{
var C24D6D = builder.NewAtomContainer();
C24D6D.Atoms.Add(builder.NewAtom("C")); // 1
C24D6D.Atoms.Add(builder.NewAtom("C")); // 2
C24D6D.Atoms.Add(builder.NewAtom("C")); // 3
C24D6D.Atoms.Add(builder.NewAtom("C")); // 4
C24D6D.Atoms.Add(builder.NewAtom("C")); // 5
C24D6D.Atoms.Add(builder.NewAtom("C")); // 6
C24D6D.Atoms.Add(builder.NewAtom("C")); // 7
C24D6D.Atoms.Add(builder.NewAtom("C")); // 8
C24D6D.Atoms.Add(builder.NewAtom("C")); // 9
C24D6D.Atoms.Add(builder.NewAtom("C")); // 10
C24D6D.Atoms.Add(builder.NewAtom("C")); // 11
C24D6D.Atoms.Add(builder.NewAtom("C")); // 12
C24D6D.Atoms.Add(builder.NewAtom("C")); // 13
C24D6D.Atoms.Add(builder.NewAtom("C")); // 14
C24D6D.Atoms.Add(builder.NewAtom("C")); // 15
C24D6D.Atoms.Add(builder.NewAtom("C")); // 16
C24D6D.Atoms.Add(builder.NewAtom("C")); // 17
C24D6D.Atoms.Add(builder.NewAtom("C")); // 18
C24D6D.Atoms.Add(builder.NewAtom("C")); // 19
C24D6D.Atoms.Add(builder.NewAtom("C")); // 20
C24D6D.Atoms.Add(builder.NewAtom("C")); // 21
C24D6D.Atoms.Add(builder.NewAtom("C")); // 22
C24D6D.Atoms.Add(builder.NewAtom("C")); // 23
C24D6D.Atoms.Add(builder.NewAtom("C")); // 24
C24D6D.AddBond(C24D6D.Atoms[0], C24D6D.Atoms[1], BondOrder.Single); // 1
C24D6D.AddBond(C24D6D.Atoms[0], C24D6D.Atoms[5], BondOrder.Single); // 2
C24D6D.AddBond(C24D6D.Atoms[0], C24D6D.Atoms[11], BondOrder.Single); // 3
C24D6D.AddBond(C24D6D.Atoms[1], C24D6D.Atoms[2], BondOrder.Single); // 4
C24D6D.AddBond(C24D6D.Atoms[1], C24D6D.Atoms[10], BondOrder.Single); // 5
C24D6D.AddBond(C24D6D.Atoms[2], C24D6D.Atoms[3], BondOrder.Single); // 6
C24D6D.AddBond(C24D6D.Atoms[2], C24D6D.Atoms[9], BondOrder.Single); // 7
C24D6D.AddBond(C24D6D.Atoms[3], C24D6D.Atoms[4], BondOrder.Single); // 8
C24D6D.AddBond(C24D6D.Atoms[3], C24D6D.Atoms[8], BondOrder.Single); // 9
C24D6D.AddBond(C24D6D.Atoms[4], C24D6D.Atoms[5], BondOrder.Single); // 10
C24D6D.AddBond(C24D6D.Atoms[4], C24D6D.Atoms[7], BondOrder.Single); // 11
C24D6D.AddBond(C24D6D.Atoms[5], C24D6D.Atoms[6], BondOrder.Single); // 12
C24D6D.AddBond(C24D6D.Atoms[6], C24D6D.Atoms[16], BondOrder.Single); // 13
C24D6D.AddBond(C24D6D.Atoms[6], C24D6D.Atoms[17], BondOrder.Single); // 14
C24D6D.AddBond(C24D6D.Atoms[7], C24D6D.Atoms[15], BondOrder.Single); // 15
C24D6D.AddBond(C24D6D.Atoms[7], C24D6D.Atoms[16], BondOrder.Single); // 16
C24D6D.AddBond(C24D6D.Atoms[8], C24D6D.Atoms[14], BondOrder.Single); // 17
C24D6D.AddBond(C24D6D.Atoms[8], C24D6D.Atoms[15], BondOrder.Single); // 18
C24D6D.AddBond(C24D6D.Atoms[9], C24D6D.Atoms[13], BondOrder.Single); // 19
C24D6D.AddBond(C24D6D.Atoms[9], C24D6D.Atoms[14], BondOrder.Single); // 20
C24D6D.AddBond(C24D6D.Atoms[10], C24D6D.Atoms[12], BondOrder.Single); // 21
C24D6D.AddBond(C24D6D.Atoms[10], C24D6D.Atoms[13], BondOrder.Single); // 22
C24D6D.AddBond(C24D6D.Atoms[11], C24D6D.Atoms[12], BondOrder.Single); // 23
C24D6D.AddBond(C24D6D.Atoms[11], C24D6D.Atoms[17], BondOrder.Single); // 24
C24D6D.AddBond(C24D6D.Atoms[12], C24D6D.Atoms[19], BondOrder.Single); // 25
C24D6D.AddBond(C24D6D.Atoms[13], C24D6D.Atoms[20], BondOrder.Single); // 26
C24D6D.AddBond(C24D6D.Atoms[14], C24D6D.Atoms[21], BondOrder.Single); // 27
C24D6D.AddBond(C24D6D.Atoms[15], C24D6D.Atoms[22], BondOrder.Single); // 28
C24D6D.AddBond(C24D6D.Atoms[16], C24D6D.Atoms[23], BondOrder.Single); // 29
C24D6D.AddBond(C24D6D.Atoms[17], C24D6D.Atoms[18], BondOrder.Single); // 30
C24D6D.AddBond(C24D6D.Atoms[18], C24D6D.Atoms[19], BondOrder.Single); // 31
C24D6D.AddBond(C24D6D.Atoms[18], C24D6D.Atoms[23], BondOrder.Single); // 32
C24D6D.AddBond(C24D6D.Atoms[19], C24D6D.Atoms[20], BondOrder.Single); // 33
C24D6D.AddBond(C24D6D.Atoms[20], C24D6D.Atoms[21], BondOrder.Single); // 34
C24D6D.AddBond(C24D6D.Atoms[21], C24D6D.Atoms[22], BondOrder.Single); // 35
C24D6D.AddBond(C24D6D.Atoms[22], C24D6D.Atoms[23], BondOrder.Single); // 36
var it = new EquivalentClassPartitioner(C24D6D);
var equivalentClass = it.GetTopoEquivClassbyHuXu(C24D6D);
var arrEquivalent = new char[24];
for (int i = 1; i < equivalentClass.Length; i++)
{
arrEquivalent[i - 1] = equivalentClass[i].ToString()[0];
}
string strEquivalent = new string(arrEquivalent);
Assert.IsNotNull(equivalentClass);
Assert.IsTrue(equivalentClass[0] == 2);//number of Class
Assert.AreEqual("111111222222222222111111", strEquivalent);
}