public void ElementContributingOneElectronRejectWhenNoDoubleBond()
{
int[] cycle = new int[] { 0, 1, 2, 3, 4, 5, 0 };
int[] contr = new int[] { 1, 1, 1, 1, 1, 1 };
int[] dbs = new int[] { 1, 0, 3, -1, 5, 4 };
Assert.IsFalse(MmffAromaticTypeMapping.IsAromaticRing(cycle, contr, dbs, new bool[contr.Length]));
}
public void IndexOfHetroAt4()
{
int[] cycle = new int[] { 3, 2, 1, 4, 5, 3 };
int[] contr = new int[] { 1, 1, 1, 1, 1, 1 };
contr[cycle[4]] = 2;
Assert.AreEqual(4, MmffAromaticTypeMapping.IndexOfHetro(cycle, contr));
}
public void ExocyclicDoubleBondsBreakAromaticity()
{
int[] cycle = new int[] { 0, 1, 2, 3, 4, 5, 0 };
int[] contr = new int[] { 1, 1, 1, 1, 1, 1, 1, 1 };
int[] dbs = new int[] { 1, 0, 6, 7, 5, 4 };
bool[] arom = new bool[contr.Length];
Assert.IsFalse(MmffAromaticTypeMapping.IsAromaticRing(cycle, contr, dbs, arom));
}
public void PyrroleIsAromatic()
{
int[] cycle = new int[] { 0, 1, 2, 3, 4, 0 };
int[] contr = new int[] { 2, 1, 1, 1, 1 };
int[] dbs = new int[] { -1, 2, 1, 4, 3 };
bool[] arom = new bool[contr.Length];
Assert.IsTrue(MmffAromaticTypeMapping.IsAromaticRing(cycle, contr, dbs, arom));
}
public void BenzeneIsAromatic()
{
int[] cycle = new int[] { 0, 1, 2, 3, 4, 5, 0 };
int[] contr = new int[] { 1, 1, 1, 1, 1, 1 };
int[] dbs = new int[] { 1, 0, 3, 2, 5, 4 };
bool[] arom = new bool[contr.Length];
Assert.IsTrue(MmffAromaticTypeMapping.IsAromaticRing(cycle, contr, dbs, arom));
}
public void NormaliseHetroAt2()
{
int[] cycle = new int[] { 3, 2, 1, 4, 5, 3 };
int[] contr = new int[] { 1, 1, 1, 1, 1, 1 };
contr[cycle[2]] = 2;
Assert.IsTrue(MmffAromaticTypeMapping.NormaliseCycle(cycle, contr));
Assert.IsTrue(Compares.AreDeepEqual(new int[] { 1, 4, 5, 3, 2, 1 }, cycle));
}
public void AnionCarbonTypesAreNeitherAlphaOrBeta()
{
var map = new Dictionary <string, string>()
{
{ "CB", "C5A" }
};
Assert.AreEqual("C5", MmffAromaticTypeMapping.GetAromaticType(map, 'A', "CB", false, true));
}
public void UpdateN2OXtoNPOX()
{
int[] cycle = new int[] { 2, 4, 3, 1, 0, 5, 2 };
string[] symbs = new string[10];
Arrays.Fill(symbs, "");
symbs[cycle[1]] = "N2OX";
MmffAromaticTypeMapping.UpdateAromaticTypesInSixMemberRing(cycle, symbs);
Assert.AreEqual("NPOX", symbs[cycle[1]]);
}
public void DelocaiIsedExocyclicDoubleBondsMaintainAromaticity()
{
int[] cycle = new int[] { 0, 1, 2, 3, 4, 5, 0 };
int[] contr = new int[] { 1, 1, 1, 1, 1, 1, 1, 1 };
int[] dbs = new int[] { 1, 0, 6, 7, 5, 4 };
bool[] arom = new bool[contr.Length];
arom[2] = arom[3] = arom[6] = arom[7] = true; // adjacent ring is aromatic
Assert.IsTrue(MmffAromaticTypeMapping.IsAromaticRing(cycle, contr, dbs, arom));
}
public void AnionNitrogensAreAlwaysN5M()
{
var map = new Dictionary <string, string>()
{
{ "N=C", "N5A" }
};
Assert.AreEqual("N5M", MmffAromaticTypeMapping.GetAromaticType(map, 'A', "N=C", false, true));
}
public void UseMappingWhenNeitherFlagIsRaised()
{
var map = new Dictionary <string, string>()
{
{ "N=C", "N5A" }
};
Assert.AreEqual("N5A", MmffAromaticTypeMapping.GetAromaticType(map, 'A', "N=C", false, false));
}
public void ImidazoleNitrogenTypesAreNeitherAlphaOrBeta()
{
var map = new Dictionary <string, string>()
{
{ "N=C", "N5A" }
};
Assert.AreEqual("N5", MmffAromaticTypeMapping.GetAromaticType(map, 'A', "N=C", true, false));
}
public void UpdateCStarToCB()
{
int[] cycle = new int[] { 2, 4, 3, 1, 0, 5, 2 };
string[] symbs = new string[10];
Arrays.Fill(symbs, "");
symbs[cycle[1]] = "C=C";
symbs[cycle[2]] = "C=N";
MmffAromaticTypeMapping.UpdateAromaticTypesInSixMemberRing(cycle, symbs);
Assert.AreEqual("CB", symbs[cycle[1]]);
Assert.AreEqual("CB", symbs[cycle[2]]);
}
public void UpdateToNPDPlus()
{
int[] cycle = new int[] { 2, 4, 3, 1, 0, 5, 2 };
string[] symbs = new string[10];
Arrays.Fill(symbs, "");
symbs[cycle[1]] = "NCN+";
symbs[cycle[2]] = "N+=C";
symbs[cycle[3]] = "N=+C";
MmffAromaticTypeMapping.UpdateAromaticTypesInSixMemberRing(cycle, symbs);
Assert.AreEqual("NPD+", symbs[cycle[1]]);
Assert.AreEqual("NPD+", symbs[cycle[2]]);
Assert.AreEqual("NPD+", symbs[cycle[3]]);
}
public void IntractableNumberOfCycles()
{
// to ensure intractable cycles are handled we create a complete graph
// where every vertex is attached to every other vertex. K8 is sufficient
// to trigger an abort when finding cycles
IAtomContainer container = new Mock <IAtomContainer>().Object;
int[][] graphK8 = Arrays.CreateJagged <int>(8, 7);
for (int i = 0; i < graphK8.Length; i++)
{
int n = 0;
for (int j = 0; j < graphK8.Length; j++)
{
if (i == j)
{
continue;
}
graphK8[i][n++] = j;
}
}
Assert.AreEqual(0, MmffAromaticTypeMapping.CyclesOfSizeFiveOrSix(container, graphK8).Length);
}
public void NormaliseNoHetro()
{
int[] cycle = new int[] { 3, 2, 1, 4, 5, 3 };
int[] contr = new int[] { 1, 1, 1, 1, 1, 1 };
Assert.IsFalse(MmffAromaticTypeMapping.NormaliseCycle(cycle, contr));
}
public void IndexOfNoHetroAtom()
{
int[] cycle = new int[] { 3, 2, 1, 4, 5, 3 };
int[] contr = new int[] { 1, 1, 1, 1, 1, 1 };
Assert.AreEqual(-1, MmffAromaticTypeMapping.IndexOfHetro(cycle, contr));
}
public void TrivalentBicoordinateNitrogenContributesOneElectron()
{
Assert.AreEqual(1, MmffAromaticTypeMapping.Contribution(7, 2, 3));
}
public void ContributionOfFiveValentNitrogen()
{
Assert.AreEqual(-1, MmffAromaticTypeMapping.Contribution(7, 3, 5));
}
public void ContributionOfThreeValentCarbon()
{
Assert.AreEqual(-1, MmffAromaticTypeMapping.Contribution(6, 3, 3));
}
public void BivalentBicoordinateNitrogenContributesTwoElectrons()
{
Assert.AreEqual(2, MmffAromaticTypeMapping.Contribution(7, 2, 2));
}
public void DivalentSulphurContributesTwoElectrons()
{
Assert.AreEqual(2, MmffAromaticTypeMapping.Contribution(16, 2, 2));
}
public void DivalentOxygenContributesTwoElectrons()
{
Assert.AreEqual(2, MmffAromaticTypeMapping.Contribution(8, 2, 2));
}
public void TetravalentCarbonContributesOneElectron()
{
Assert.AreEqual(1, MmffAromaticTypeMapping.Contribution(6, 3, 4));
}