private static double GetBondEnergy(IBond bond, BondEnergies bondEnergy)
{
double energy = 0.0;
if ((bond.Atoms[0].IsPlaced == true && bond.Atoms[1].IsPlaced == false) ||
(bond.Atoms[0].IsPlaced == false && bond.Atoms[1].IsPlaced == true))
{
int val = bondEnergy.GetEnergies(bond.Atoms[0], bond.Atoms[1], bond.Order);
energy = val;
}
return(energy);
}
private static double GetEnergy(IAtomContainer educt, IAtomContainer product)
{
double eEnergy = 0.0;
BondEnergies bondEnergy = BondEnergies.Instance;
for (int i = 0; i < educt.Bonds.Count; i++)
{
IBond bond = educt.Bonds[i];
eEnergy += GetBondEnergy(bond, bondEnergy);
}
double pEnergy = 0.0;
for (int j = 0; j < product.Bonds.Count; j++)
{
IBond bond = product.Bonds[j];
pEnergy += GetBondEnergy(bond, bondEnergy);
}
return(eEnergy + pEnergy);
}
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!");
}
}
}