public void TestPropellane()
{
IAtomContainer propellane = AbstractSignatureTest.MakePropellane();
SignatureQuotientGraph qGraph = new SignatureQuotientGraph(propellane);
CheckParameters(qGraph, 2, 2, 1);
}
public void TestTwistane()
{
IAtomContainer twistane = AbstractSignatureTest.MakeTwistane();
SignatureQuotientGraph qGraph = new SignatureQuotientGraph(twistane);
CheckParameters(qGraph, 3, 4, 2);
}
public void TestCuneaneAtHeight2()
{
IAtomContainer cuneane = AbstractSignatureTest.MakeCuneane();
SignatureQuotientGraph qGraph = new SignatureQuotientGraph(cuneane, 2);
CheckParameters(qGraph, 3, 5, 3);
}
public void TestCubane()
{
string expected = "[C]([C]([C,3]([C,2])[C,1]([C,2]))[C]([C,3][C,0]" + "([C,2]))[C]([C,0][C,1]))";
IAtomContainer mol = AbstractSignatureTest.MakeCubane();
Assert.AreEqual(expected, this.CanonicalStringFromMolecule(mol));
}
public void TestAromatic()
{
IAtomContainer benzene = AbstractSignatureTest.MakeBenzene();
SignatureQuotientGraph qGraph = new SignatureQuotientGraph(benzene);
CheckParameters(qGraph, 1, 1, 1);
}
public void TestCubane()
{
IAtomContainer cubane = AbstractSignatureTest.MakeCubane();
SignatureQuotientGraph qGraph = new SignatureQuotientGraph(cubane);
CheckParameters(qGraph, 1, 1, 1);
}
public void MethyleneCyclopropeneTest()
{
IAtomContainer mol = builder.NewAtomContainer();
AbstractSignatureTest.AddCarbons(mol, 4);
AbstractSignatureTest.AddHydrogens(mol, 1, 2);
AbstractSignatureTest.AddHydrogens(mol, 2, 1);
AbstractSignatureTest.AddHydrogens(mol, 3, 1);
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Double);
mol.AddBond(mol.Atoms[0], mol.Atoms[2], BondOrder.Single);
mol.AddBond(mol.Atoms[0], mol.Atoms[3], BondOrder.Single);
mol.AddBond(mol.Atoms[2], mol.Atoms[3], BondOrder.Double);
MoleculeSignature molSig = new MoleculeSignature(mol);
string sigFor2Height1 = molSig.SignatureStringForVertex(2, 1);
string sigFor3Height1 = molSig.SignatureStringForVertex(3, 1);
Assert.IsTrue(
sigFor2Height1.Equals(sigFor3Height1),
"Height 1 signatures for atoms 2 and 3" + " should be the same");
string sigFor2Height2 = molSig.SignatureStringForVertex(2, 1);
string sigFor3Height2 = molSig.SignatureStringForVertex(3, 1);
Assert.IsTrue(
sigFor2Height2.Equals(sigFor3Height2),
"Height 2 signatures for atoms 2 and 3" + " should be the same");
}
public static IAtomContainer MakePropellane()
{
IAtomContainer mol = AbstractSignatureTest.MakePseudoPropellane();
mol.AddBond(mol.Atoms[0], mol.Atoms[4], BondOrder.Single);
return(mol);
}
public static IAtomContainer MakeBridgedCyclobutane()
{
IAtomContainer mol = AbstractSignatureTest.MakeCyclobutane();
mol.AddBond(mol.Atoms[0], mol.Atoms[2], BondOrder.Single);
return(mol);
}
public static IAtomContainer MakeSandwich(int ringSize, bool hasMethyl)
{
IAtomContainer mol = builder.NewAtomContainer();
AbstractSignatureTest.AddCarbons(mol, (ringSize * 2));
mol.Atoms.Add(builder.NewAtom("Fe"));
int center = ringSize * 2;
// face A
for (int i = 0; i < ringSize - 1; i++)
{
mol.AddBond(mol.Atoms[i], mol.Atoms[i + 1], BondOrder.Single);
mol.AddBond(mol.Atoms[i], mol.Atoms[center], BondOrder.Single);
}
mol.AddBond(mol.Atoms[ringSize - 1], mol.Atoms[0], BondOrder.Single);
mol.AddBond(mol.Atoms[ringSize - 1], mol.Atoms[center], BondOrder.Single);
// // face B
for (int i = 0; i < ringSize - 1; i++)
{
mol.AddBond(mol.Atoms[ringSize + 1], mol.Atoms[i + ringSize + 1], BondOrder.Single);
mol.AddBond(mol.Atoms[ringSize + 1], mol.Atoms[center], BondOrder.Single);
}
mol.AddBond(mol.Atoms[(2 * ringSize) - 1], mol.Atoms[ringSize], BondOrder.Single);
mol.AddBond(mol.Atoms[(2 * ringSize) - 1], mol.Atoms[center], BondOrder.Single);
if (hasMethyl)
{
mol.Atoms.Add(builder.NewAtom("C"));
mol.AddBond(mol.Atoms[0], mol.Atoms.Last(), BondOrder.Single);
}
return(mol);
}
public void TestBenzeneWithDoubleBonds()
{
IAtomContainer benzene = builder.NewAtomContainer();
AbstractSignatureTest.AddCarbons(benzene, 6);
for (int i = 0; i < 6; i++)
{
AbstractSignatureTest.AddHydrogens(benzene, i, 1);
}
benzene.AddBond(benzene.Atoms[0], benzene.Atoms[1], BondOrder.Single);
benzene.AddBond(benzene.Atoms[1], benzene.Atoms[2], BondOrder.Double);
benzene.AddBond(benzene.Atoms[2], benzene.Atoms[3], BondOrder.Single);
benzene.AddBond(benzene.Atoms[3], benzene.Atoms[4], BondOrder.Double);
benzene.AddBond(benzene.Atoms[4], benzene.Atoms[5], BondOrder.Single);
benzene.AddBond(benzene.Atoms[5], benzene.Atoms[0], BondOrder.Double);
MoleculeSignature signature = new MoleculeSignature(benzene);
string carbonSignature = signature.SignatureStringForVertex(0);
for (int i = 1; i < 6; i++)
{
string carbonSignatureI = signature.SignatureStringForVertex(i);
Assert.AreEqual(carbonSignature, carbonSignatureI);
}
}
public void TestBridgedCycloButane()
{
string expected = "[C]([C]([C,0])[C]([C,0])[C,0])";
IAtomContainer mol = AbstractSignatureTest.MakeBridgedCyclobutane();
string signature = this.CanonicalStringFromMolecule(mol);
Assert.AreEqual(expected, signature);
}
public void CycleWheelTest()
{
IAtomContainer mol = AbstractSignatureTest.MakeCycleWheel(3, 3);
string expected = "[C]([C]([C]([C,2])[C,2])" + "[C]([C]([C,1])[C,1])" + "[C]([C]([C,0])[C,0]))";
MoleculeSignature molSig = new MoleculeSignature(mol);
string centralSignature = molSig.SignatureStringForVertex(0);
Assert.AreEqual(expected, centralSignature);
}
public static IAtomContainer MakeCycleWheel(int ringSize, int ringCount)
{
IAtomContainer mol = builder.NewAtomContainer();
mol.Atoms.Add(builder.NewAtom("C"));
for (int r = 0; r < ringCount; r++)
{
AbstractSignatureTest.AddRing(0, ringSize, mol);
}
return(mol);
}
public void CuneaneCubaneHeightTest()
{
IAtomContainer cuneane = AbstractSignatureTest.MakeCuneane();
IAtomContainer cubane = AbstractSignatureTest.MakeCubane();
int height = 1;
AtomSignature cuneaneSignature = new AtomSignature(0, height, cuneane);
AtomSignature cubaneSignature = new AtomSignature(0, height, cubane);
string cuneaneSigString = cuneaneSignature.ToCanonicalString();
string cubaneSigString = cubaneSignature.ToCanonicalString();
Assert.AreEqual(cuneaneSigString, cubaneSigString);
}
public void DodecahedraneHeightTest()
{
IAtomContainer dodecahedrane = AbstractSignatureTest.MakeDodecahedrane();
MoleculeIsCarbon3Regular(dodecahedrane);
int diameter = 5;
for (int height = 0; height <= diameter; height++)
{
AllEqualAtHeightTest(dodecahedrane, height);
}
}
public void TestPropellane()
{
string expectedA = "[C]([C]([C,0])[C]([C,0])[C]([C,0])[C,0])";
string expectedB = "[C]([C]([C,2][C,1][C,0])[C,2]([C,1][C,0]))";
IAtomContainer mol = AbstractSignatureTest.MakePropellane();
string signature = this.CanonicalStringFromMolecule(mol);
Assert.AreEqual(expectedA, signature);
string fullExpected = "2" + expectedA + " + 3" + expectedB;
string fullSignature = FullStringFromMolecule(mol);
Assert.AreEqual(fullExpected, fullSignature);
}
public void TestC7H16Isomers()
{
IAtomContainer c7H16A = AbstractSignatureTest.MakeC7H16A();
IAtomContainer c7H16B = AbstractSignatureTest.MakeC7H16B();
IAtomContainer c7H16C = AbstractSignatureTest.MakeC7H16C();
SignatureQuotientGraph qGraphA = new SignatureQuotientGraph(c7H16A, 1);
SignatureQuotientGraph qGraphB = new SignatureQuotientGraph(c7H16B, 1);
SignatureQuotientGraph qGraphC = new SignatureQuotientGraph(c7H16C, 1);
CheckParameters(qGraphA, 4, 7, 1);
CheckParameters(qGraphB, 4, 5, 0);
CheckParameters(qGraphC, 4, 7, 1);
}
public void TtprTest()
{
string expected = "[Rh]([P]([C]([C]([C]([C,6]))" + "[C]([C]([C,6])))[C]([C]([C]([C,3]))"
+ "[C]([C]([C,3])))[C]([C]([C]([C,2]))" + "[C]([C]([C,2]))))[P]([C]([C]([C]([C,7]))"
+ "[C]([C]([C,7])))[C]([C]([C]([C,4]))" + "[C]([C]([C,4])))[C]([C]([C]([C,1]))"
+ "[C]([C]([C,1]))))[P]([C]([C]([C]([C,8]))" + "[C]([C]([C,8])))[C]([C]([C]([C,5]))"
+ "[C]([C]([C,5])))[C]([C]([C]([C,0]))" + "[C]([C]([C,0])))))";
int phosphateCount = 3;
int ringCount = 3;
IAtomContainer ttpr = AbstractSignatureTest.MakeRhLikeStructure(phosphateCount, ringCount);
MoleculeSignature molSig = new MoleculeSignature(ttpr);
string centralSignature = molSig.SignatureStringForVertex(0);
Assert.AreEqual(expected, centralSignature);
}
public void TestCage()
{
string expectedA = "[C]([C]([C]([C,4][C,3]([C,1]))[C]([C,5][C,3]))"
+ "[C]([C,4]([C]([C,2][C,1]))[C]([C,2]([C,0])[C,6]))" + "[C]([C,5]([C]([C,0][C,1]))[C,6]([C,0])))";
string expectedB = "[C]([C]([C]([C]([C,1]([C,0])[C,4])[C,5])[C,7]"
+ "([C,4]([C,3])))[C]([C]([C,3]([C,0])[C,6])[C,7])" + "[C]([C,5]([C]([C,2][C,1]))[C,6]([C,2]([C,0]))))";
IAtomContainer mol = AbstractSignatureTest.MakeCage();
string signature = this.CanonicalStringFromMolecule(mol);
Assert.AreEqual(expectedA, signature);
string fullSignature = FullStringFromMolecule(mol);
string fullExpected = "8" + expectedA + " + 8" + expectedB;
Assert.AreEqual(fullExpected, fullSignature);
}
public void CyclobuteneTest()
{
string expectedA = "[C]([C]([C,0])=[C]([C,0]))";
string expectedB = "[C]([C]([C,0])[C](=[C,0]))";
IAtomContainer cyclobutene = builder.NewAtomContainer();
AbstractSignatureTest.AddCarbons(cyclobutene, 4);
cyclobutene.AddBond(cyclobutene.Atoms[0], cyclobutene.Atoms[1], BondOrder.Single);
cyclobutene.AddBond(cyclobutene.Atoms[0], cyclobutene.Atoms[2], BondOrder.Single);
cyclobutene.AddBond(cyclobutene.Atoms[1], cyclobutene.Atoms[3], BondOrder.Double);
cyclobutene.AddBond(cyclobutene.Atoms[2], cyclobutene.Atoms[3], BondOrder.Single);
Assert.AreEqual(expectedA, CanonicalStringFromMolecule(cyclobutene));
string expectedFullString = "2" + expectedA + " + 2" + expectedB;
string actualFullString = FullStringFromMolecule(cyclobutene);
Assert.AreEqual(expectedFullString, actualFullString);
}
public void FusedSquareMultipleBondTest()
{
IAtomContainer mol = builder.NewAtomContainer();
string expected = "[C]([C]([C,1])[C]([C,0])[C](=[C,1])[C](=[C,0]))";
AbstractSignatureTest.AddCarbons(mol, 7);
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Single);
mol.AddBond(mol.Atoms[0], mol.Atoms[2], BondOrder.Single);
mol.AddBond(mol.Atoms[0], mol.Atoms[3], BondOrder.Single);
mol.AddBond(mol.Atoms[0], mol.Atoms[4], BondOrder.Single);
mol.AddBond(mol.Atoms[1], mol.Atoms[5], BondOrder.Double);
mol.AddBond(mol.Atoms[2], mol.Atoms[5], BondOrder.Single);
mol.AddBond(mol.Atoms[3], mol.Atoms[6], BondOrder.Single);
mol.AddBond(mol.Atoms[4], mol.Atoms[6], BondOrder.Double);
MoleculeSignature molSig = new MoleculeSignature(mol);
string sigFor0 = molSig.SignatureStringForVertex(0);
Assert.AreEqual(expected, sigFor0);
}
public static IAtomContainer MakeC7H16C()
{
IAtomContainer mol = builder.NewAtomContainer();
AbstractSignatureTest.AddCarbons(mol, 7);
mol.AddBond(mol.Atoms[0], mol.Atoms[2], BondOrder.Single);
mol.AddBond(mol.Atoms[1], mol.Atoms[2], BondOrder.Single);
mol.AddBond(mol.Atoms[2], mol.Atoms[3], BondOrder.Single);
mol.AddBond(mol.Atoms[3], mol.Atoms[4], BondOrder.Single);
mol.AddBond(mol.Atoms[4], mol.Atoms[5], BondOrder.Single);
mol.AddBond(mol.Atoms[5], mol.Atoms[6], BondOrder.Single);
AbstractSignatureTest.AddHydrogens(mol, 0, 3);
AbstractSignatureTest.AddHydrogens(mol, 1, 3);
AbstractSignatureTest.AddHydrogens(mol, 2, 1);
AbstractSignatureTest.AddHydrogens(mol, 3, 2);
AbstractSignatureTest.AddHydrogens(mol, 4, 2);
AbstractSignatureTest.AddHydrogens(mol, 5, 2);
AbstractSignatureTest.AddHydrogens(mol, 6, 3);
return(mol);
}
public static IAtomContainer MakeRhLikeStructure(int pCount, int ringCount)
{
IAtomContainer ttpr = builder.NewAtomContainer();
ttpr.Atoms.Add(builder.NewAtom("Rh"));
for (int i = 1; i <= pCount; i++)
{
ttpr.Atoms.Add(builder.NewAtom("P"));
ttpr.AddBond(ttpr.Atoms[0], ttpr.Atoms[i], BondOrder.Single);
}
for (int j = 1; j <= pCount; j++)
{
for (int k = 0; k < ringCount; k++)
{
AbstractSignatureTest.AddRing(j, 6, ttpr);
}
}
return(ttpr);
}
