public void TestCalculatePiElectronegativity_IAtomContainer_IAtom_Int_Int()
{
PiElectronegativity pe = new PiElectronegativity();
IAtomContainer molecule = builder.NewAtomContainer();
molecule.Atoms.Add(builder.NewAtom("F"));
molecule.Atoms.Add(builder.NewAtom("C"));
molecule.AddBond(molecule.Atoms[0], molecule.Atoms[1], BondOrder.Single);
AddExplicitHydrogens(molecule);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
CDK.LonePairElectronChecker.Saturate(molecule);
for (int i = 0; i < molecule.Atoms.Count; i++)
{
if (i == 0)
{
Assert.AreNotSame(0.0, pe.CalculatePiElectronegativity(molecule, molecule.Atoms[i], 6, 50));
}
else
{
Assert.AreEqual(0.0, pe.CalculatePiElectronegativity(molecule, molecule.Atoms[i], 6, 50), 0.001);
}
}
}
public void TestSetMaxResonStruc_Int()
{
PiElectronegativity pe = new PiElectronegativity();
int maxRes = 10;
pe.MaxResonanceStructures = maxRes;
Assert.AreEqual(maxRes, pe.MaxResonanceStructures);
}
public void TestSetMaxIterations_Int()
{
PiElectronegativity pe = new PiElectronegativity();
int maxIter = 10;
pe.MaxIterations = maxIter;
Assert.AreEqual(maxIter, pe.MaxIterations);
}
/// <summary>
/// calculate the stabilization of orbitals when they contain deficiency of charge.
/// </summary>
/// <param name="atomContainer">the molecule to be considered</param>
/// <param name="atom">IAtom for which effective atom StabilizationCharges factor should be calculated</param>
/// <returns>stabilizationValue</returns>
public static double CalculatePositive(IAtomContainer atomContainer, IAtom atom)
{
/* restrictions */
// if(atomContainer.GetConnectedSingleElectronsCount(atom) > 0 || atom.FormalCharge != 1){
if (atom.FormalCharge != 1)
{
return(0.0);
}
// only must be generated all structures which stabilize the atom in question.
StructureResonanceGenerator gRI = new StructureResonanceGenerator();
var reactionList = gRI.Reactions.ToList();
reactionList.Add(new HyperconjugationReaction());
gRI.Reactions = reactionList;
var resonanceS = gRI.GetStructures(atomContainer);
var containerS = gRI.GetContainers(atomContainer);
if (resonanceS.Count < 2) // meaning it was not find any resonance structure
{
return(0.0);
}
int positionStart = atomContainer.Atoms.IndexOf(atom);
var result1 = new List <double>();
var distance1 = new List <int>();
resonanceS.RemoveAt(0);// the first is the initial structure
foreach (var resonance in resonanceS)
{
if (resonance.Atoms.Count < 2) // resonance with only one atom donnot have resonance
{
continue;
}
ShortestPaths shortestPaths = new ShortestPaths(resonance, resonance.Atoms[positionStart]);
/* search positive charge */
PiElectronegativity electronegativity = new PiElectronegativity();
foreach (var atomP in resonance.Atoms)
{
IAtom atomR = atomContainer.Atoms[resonance.Atoms.IndexOf(atomP)];
if (containerS[0].Contains(atomR))
{
electronegativity.MaxIterations = 6;
double result = electronegativity.CalculatePiElectronegativity(resonance, atomP);
result1.Add(result);
int dis = shortestPaths.GetDistanceTo(atomP);
distance1.Add(dis);
}
}
}
/* logarithm */
double value = 0.0;
double sum = 0.0;
var itDist = distance1.GetEnumerator();
foreach (var ee in result1)
{
double suM = ee;
if (suM < 0)
{
suM = -1 * suM;
}
itDist.MoveNext();
sum += suM * Math.Pow(0.67, itDist.Current);
}
value = sum;
return(value);
}
public void TestGetMaxResonStruc()
{
PiElectronegativity pe = new PiElectronegativity();
Assert.AreEqual(50, pe.MaxResonanceStructures);
}
public void TestGetMaxIterations()
{
PiElectronegativity pe = new PiElectronegativity();
Assert.AreEqual(6, pe.MaxIterations);
}
