public void DodecahedraneTest()
{
var mol = new Molecule();
for (int i = 0; i < 20; i++)
{
mol.AddAtom("C");
}
mol.AddSingleBond(0, 1);
mol.AddSingleBond(0, 4);
mol.AddSingleBond(1, 2);
mol.AddSingleBond(2, 7);
mol.AddSingleBond(3, 4);
mol.AddSingleBond(3, 8);
mol.AddSingleBond(5, 10);
mol.AddSingleBond(5, 11);
mol.AddSingleBond(6, 11);
mol.AddSingleBond(6, 12);
mol.AddSingleBond(7, 13);
mol.AddSingleBond(8, 14);
mol.AddSingleBond(9, 10);
mol.AddSingleBond(9, 14);
mol.AddSingleBond(12, 17);
mol.AddSingleBond(13, 18);
mol.AddSingleBond(15, 16);
mol.AddSingleBond(15, 19);
mol.AddSingleBond(16, 17);
mol.AddSingleBond(18, 19);
mol.AddBond(0, 5, Molecule.BondOrder.Double);
mol.AddBond(1, 6, Molecule.BondOrder.Double);
mol.AddBond(2, 3, Molecule.BondOrder.Double);
mol.AddBond(4, 9, Molecule.BondOrder.Double);
mol.AddBond(7, 12, Molecule.BondOrder.Double);
mol.AddBond(8, 13, Molecule.BondOrder.Double);
mol.AddBond(10, 15, Molecule.BondOrder.Double);
mol.AddBond(11, 16, Molecule.BondOrder.Double);
mol.AddBond(17, 18, Molecule.BondOrder.Double);
mol.AddBond(14, 19, Molecule.BondOrder.Double);
for (int i = 0; i < 20; i++)
{
Assert.AreEqual(4, mol.GetTotalOrder(i), "Atom " + i + " has wrong order");
}
var mqg = new MoleculeQuotientGraph(mol);
Console.Out.WriteLine(mqg);
Assert.AreEqual(5, mqg.GetVertexCount());
Assert.AreEqual(9, mqg.GetEdgeCount());
Assert.AreEqual(3, mqg.NumberOfLoopEdges());
}
public void MultipleBondedFragmentTest()
{
Molecule molA = new Molecule();
molA.AddAtom("C");
molA.AddAtom("C");
molA.AddAtom("C");
molA.AddAtom("H");
molA.AddBond(0, 1, Molecule.BondOrder.Double);
molA.AddSingleBond(0, 2);
molA.AddSingleBond(0, 3);
MoleculeSignature molSig = new MoleculeSignature(molA);
string signatureFor0A = molSig.SignatureStringForVertex(0);
Console.Out.WriteLine(signatureFor0A);
Molecule molB = new Molecule();
molB.AddAtom("C");
molB.AddAtom("C");
molB.AddAtom("C");
molB.AddAtom("H");
molB.AddSingleBond(0, 1);
molB.AddBond(0, 2, Molecule.BondOrder.Double);
molB.AddSingleBond(0, 3);
molSig = new MoleculeSignature(molB);
string signatureFor0B = molSig.SignatureStringForVertex(0);
Console.Out.WriteLine(signatureFor0B);
Assert.AreEqual(signatureFor0A, signatureFor0B);
}
public void Cyclobut_2_ene()
{
Molecule mol = new Molecule();
for (int i = 0; i < 4; i++)
{
mol.AddAtom("C");
}
mol.AddSingleBond(0, 1);
mol.AddBond(0, 2, Molecule.BondOrder.Double);
mol.AddBond(1, 3, Molecule.BondOrder.Double);
mol.AddSingleBond(2, 3);
MoleculeSignature molSignature = new MoleculeSignature(mol);
Console.Out.WriteLine(molSignature.ToCanonicalString());
}
public void MinimalTest()
{
Molecule mol = new Molecule();
mol.AddAtom("C");
mol.AddAtom("O");
mol.AddAtom("N");
mol.AddSingleBond(0, 1);
mol.AddBond(0, 2, Molecule.BondOrder.Double);
// TODO : test this somehow...
// MoleculeWriter.WriteToStream(System.out, mol);
}
public void BenzeneTest()
{
Molecule mol = new Molecule();
for (int i = 0; i < 6; i++)
{
mol.AddAtom("C");
}
mol.AddSingleBond(0, 1);
mol.AddBond(1, 2, Molecule.BondOrder.Double);
mol.AddSingleBond(2, 3);
mol.AddBond(3, 4, Molecule.BondOrder.Double);
mol.AddSingleBond(4, 5);
mol.AddBond(5, 0, Molecule.BondOrder.Double);
MoleculeSignature molSig = new MoleculeSignature(mol);
string sigString0 = molSig.SignatureStringForVertex(0);
for (int i = 1; i < 6; i++)
{
string sigStringI = molSig.SignatureStringForVertex(i);
Assert.AreEqual(sigString0, sigStringI);
}
}
public void CocoTest()
{
Molecule moleculeA = new Molecule();
int chainLength = 6;
moleculeA.AddAtom("O");
moleculeA.AddAtom("C");
moleculeA.AddAtom("C");
moleculeA.AddAtom("O");
moleculeA.AddAtom("C");
moleculeA.AddAtom("O");
for (int i = 0; i < chainLength - 2; i++)
{
moleculeA.AddSingleBond(i, i + 1);
}
moleculeA.AddBond(chainLength - 2, chainLength - 1, Molecule.BondOrder.Double);
// moleculeA.AddBond(chainLength - 2, chainLength - 1, 1);
Molecule moleculeB = new Molecule();
moleculeB.AddAtom("O");
moleculeB.AddAtom("C");
moleculeB.AddAtom("C");
moleculeB.AddAtom("C");
moleculeB.AddAtom("O");
moleculeB.AddAtom("O");
moleculeB.AddSingleBond(0, 1);
moleculeB.AddSingleBond(1, 3);
moleculeB.AddSingleBond(2, 4);
moleculeB.AddBond(2, 5, Molecule.BondOrder.Double);
// moleculeB.AddBond(2, 5, 1);
moleculeB.AddSingleBond(3, 4);
MoleculeSignature molSigA = new MoleculeSignature(moleculeA);
string sigA = molSigA.SignatureStringForVertex(3);
Console.Out.WriteLine(sigA);
Console.Out.WriteLine("--------------------------------------");
MoleculeSignature molSigB = new MoleculeSignature(moleculeB);
string sigB = molSigB.SignatureStringForVertex(4);
Console.Out.WriteLine(sigB);
Assert.AreEqual(sigA, sigB);
}
public void AromaticTest()
{
Molecule benzene = new Molecule();
benzene.AddMultipleAtoms(6, "C");
benzene.AddBond(0, 1, Molecule.BondOrder.Aromatic);
benzene.AddBond(1, 2, Molecule.BondOrder.Aromatic);
benzene.AddBond(2, 3, Molecule.BondOrder.Aromatic);
benzene.AddBond(3, 4, Molecule.BondOrder.Aromatic);
benzene.AddBond(4, 5, Molecule.BondOrder.Aromatic);
benzene.AddBond(5, 0, Molecule.BondOrder.Aromatic);
MoleculeSignature molSig = new MoleculeSignature(benzene);
Console.Out.WriteLine(molSig.ToCanonicalString());
}
private static Molecule MakeMolecule(List <string> block)
{
Molecule molecule = new Molecule();
// counts are on the fourth line
string countLine = block[3];
int atomCount = int.Parse(countLine.Substring(0, 3).Trim(), NumberFormatInfo.InvariantInfo);
int bondCount = int.Parse(countLine.Substring(3, 3).Trim(), NumberFormatInfo.InvariantInfo);
// atom block starts on the fifth line (4th index)
int atomLineStart = 4;
int atomLineEnd = atomCount + atomLineStart;
for (int i = atomLineStart; i < atomLineEnd; i++)
{
string symbol = block[i].Substring(30, 33).Trim();
int atomIndex = i - atomLineStart;
molecule.AddAtom(atomIndex, symbol);
}
if (atomCount > 1)
{
// bond block starts right after the atom block
int bondLineStart = atomLineEnd;
int bondLineEnd = bondLineStart + bondCount;
for (int i = bondLineStart; i < bondLineEnd; i++)
{
string bondLine = block[i];
int atomNumberA =
int.Parse(bondLine.Substring(0, 3).Trim(), NumberFormatInfo.InvariantInfo);
int atomNumberB =
int.Parse(bondLine.Substring(3, 3).Trim(), NumberFormatInfo.InvariantInfo);
int order = int.Parse(bondLine.Substring(7, 3).Trim(), NumberFormatInfo.InvariantInfo);
var o = ConvertIntToBondOrder(order);
molecule.AddBond(atomNumberA - 1, atomNumberB - 1, o);
}
}
return(molecule);
}
