private void UpdateElectronCount(BondOrder order)
{
if (order == BondOrder.Unset)
{
return;
}
this.ElectronCount = order.Numeric() * 2;
}
/// <summary>
/// Get the single bond equivalent (SBE) of a list of bonds, given an iterator to the list.
/// </summary>
/// <param name="bonds">An iterator to the list of bonds</param>
/// <returns>The SBE sum</returns>
public static int GetSingleBondEquivalentSum(IEnumerable <IBond> bonds)
{
int sum = 0;
foreach (var bond in bonds)
{
BondOrder order = bond.Order;
if (!order.IsUnset())
{
sum += order.Numeric();
}
}
return(sum);
}
private void SetTargetSingleAtomMap(bool removeHydrogen)
{
int counter = 0;
BondEnergies be = BondEnergies.Instance;
foreach (var targetAtom in target.Atoms)
{
if ((removeHydrogen && !targetAtom.AtomicNumber.Equals(AtomicNumbers.H)) || (!removeHydrogen))
{
foreach (var sourceAtoms in source.Atoms)
{
var mapAtoms = new Dictionary <IAtom, IAtom>();
if (string.Equals(targetAtom.Symbol, sourceAtoms.Symbol, StringComparison.OrdinalIgnoreCase))
{
mapAtoms[sourceAtoms] = targetAtom;
var bonds = source.GetConnectedBonds(sourceAtoms);
double totalOrder = 0;
foreach (var bond in bonds)
{
BondOrder order = bond.Order;
totalOrder += order.Numeric() + BondEnergies.GetEnergies(bond);
}
if (sourceAtoms.FormalCharge != targetAtom.FormalCharge)
{
totalOrder += 0.5;
}
connectedBondOrder[counter] = totalOrder;
mappings.Insert(counter++, mapAtoms);
}
}
}
else
{
Console.Error.WriteLine("Skipping Hydrogen mapping or This is not a single mapping case!");
}
}
}
private void SetSourceSingleAtomMap(IQueryAtomContainer source, bool removeHydrogen)
{
int counter = 0;
BondEnergies be = BondEnergies.Instance;
foreach (var sourceAtom in source.Atoms)
{
var smartAtom = (IQueryAtom)sourceAtom;
if ((removeHydrogen && !smartAtom.AtomicNumber.Equals(AtomicNumbers.H)) || (!removeHydrogen))
{
foreach (var targetAtom in target.Atoms)
{
var mapAtoms = new Dictionary <IAtom, IAtom>();
if (smartAtom.Matches(targetAtom))
{
mapAtoms[sourceAtom] = targetAtom;
var bonds = target.GetConnectedBonds(targetAtom);
double totalOrder = 0;
foreach (var bond in bonds)
{
BondOrder order = bond.Order;
totalOrder += order.Numeric() + BondEnergies.GetEnergies(bond);
}
if (targetAtom.FormalCharge != sourceAtom.FormalCharge)
{
totalOrder += 0.5;
}
connectedBondOrder[counter] = totalOrder;
mappings.Insert(counter++, mapAtoms);
}
}
}
else
{
Console.Error.WriteLine("Skipping Hydrogen mapping or This is not a single mapping case!");
}
}
}
/// <summary>
/// Returns the number of times the side chain should end up as the CIP-expanded ligand list. The CIP
/// rules prescribe that a double bonded oxygen should be represented twice in the list.
/// </summary>
/// <param name="order"><see cref="BondOrder"/> of the bond</param>
/// <returns>int reflecting the duplication number</returns>
private static int GetDuplication(BondOrder order)
{
return(order.Numeric());
}
public static double[] GetAtomWeights(IAtomContainer atomContainer)
{
IAtom atom, headAtom, endAtom;
int headAtomPosition, endAtomPosition;
//int k = 0;
double[] weightArray = new double[atomContainer.Atoms.Count];
double[][] adjaMatrix = ConnectionMatrix.GetMatrix(atomContainer);
int[][] apspMatrix = PathTools.ComputeFloydAPSP(adjaMatrix);
int[] atomLayers = GetAtomLayers(apspMatrix);
int[] valenceSum;
int[] interLayerBondSum;
Debug.WriteLine("adjacency matrix: ");
DisplayMatrix(adjaMatrix);
Debug.WriteLine("all-pairs-shortest-path matrix: ");
DisplayMatrix(apspMatrix);
Debug.WriteLine("atom layers: ");
DisplayArray(atomLayers);
for (int i = 0; i < atomContainer.Atoms.Count; i++)
{
atom = atomContainer.Atoms[i];
valenceSum = new int[atomLayers[i]];
for (int v = 0; v < valenceSum.Length; v++)
{
valenceSum[v] = 0;
}
interLayerBondSum = new int[atomLayers[i] - 1];
for (int v = 0; v < interLayerBondSum.Length; v++)
{
interLayerBondSum[v] = 0;
}
//weightArray[k] = atom.GetValenceElectronsCount() - atom.GetHydrogenCount(); // method unfinished
if (AtomicNumbers.O.Equals(atom.AtomicNumber))
{
weightArray[i] = 6 - atom.ImplicitHydrogenCount.Value;
}
else
{
weightArray[i] = 4 - atom.ImplicitHydrogenCount.Value;
}
for (int j = 0; j < apspMatrix.Length; j++)
{
if (string.Equals("O", atomContainer.Atoms[j].Symbol, StringComparison.Ordinal))
{
valenceSum[apspMatrix[j][i]] += 6 - atomContainer.Atoms[j].ImplicitHydrogenCount.Value;
}
else
{
valenceSum[apspMatrix[j][i]] += 4 - atomContainer.Atoms[j].ImplicitHydrogenCount.Value;
}
}
var bonds = atomContainer.Bonds;
foreach (var bond in bonds)
{
headAtom = bond.Begin;
endAtom = bond.End;
headAtomPosition = atomContainer.Atoms.IndexOf(headAtom);
endAtomPosition = atomContainer.Atoms.IndexOf(endAtom);
if (Math.Abs(apspMatrix[i][headAtomPosition] - apspMatrix[i][endAtomPosition]) == 1)
{
int min = Math.Min(apspMatrix[i][headAtomPosition], apspMatrix[i][endAtomPosition]);
BondOrder order = bond.Order;
interLayerBondSum[min] += order.IsUnset() ? 0 : order.Numeric();
}
}
for (int j = 0; j < interLayerBondSum.Length; j++)
{
weightArray[i] += interLayerBondSum[j] * valenceSum[j + 1] * Math.Pow(10, -(j + 1));
}
Debug.WriteLine("valence sum: ");
DisplayArray(valenceSum);
Debug.WriteLine("inter-layer bond sum: ");
DisplayArray(interLayerBondSum);
}
Debug.WriteLine("weight array: ");
DisplayArray(weightArray);
return(weightArray);
}
public static double DestroyBondOrder(BondOrder bondOrder)
{
return(bondOrder.Numeric());
}