/// <summary>
/// RemovePseudoAtoms
/// </summary>
/// <param name="mol"></param>
/// <returns>Pseudo atom count</returns>
public static int RemovePseudoAtoms(IAtomContainer mol)
{
List <IAtom> pseudoAtoms = new List <IAtom>();
for (int ai = 0; ai < mol.Atoms.Count; ai++)
{
IAtom atom = mol.Atoms[ai];
if (atom is IPseudoAtom)
{
pseudoAtoms.Add(atom);
}
}
if (pseudoAtoms.Count == 0)
{
return(0);
}
foreach (IAtom atom in pseudoAtoms)
{
mol.RemoveAtom(atom);
}
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
mol = AtomContainerManipulator.SuppressHydrogens(mol);
GetHydrogenAdder().AddImplicitHydrogens(mol);
return(pseudoAtoms.Count);
}
public static void RemoveAtomAndConnectedElectronContainers(IReaction reaction, IAtom atom)
{
var reactants = reaction.Reactants;
for (int i = 0; i < reactants.Count; i++)
{
IAtomContainer mol = reactants[i];
if (mol.Contains(atom))
{
mol.RemoveAtom(atom);
}
}
var agents = reaction.Reactants;
for (int i = 0; i < agents.Count; i++)
{
var mol = agents[i];
if (mol.Contains(atom))
{
mol.RemoveAtom(atom);
}
}
var products = reaction.Products;
for (int i = 0; i < products.Count; i++)
{
var mol = products[i];
if (mol.Contains(atom))
{
mol.RemoveAtom(atom);
}
}
}
public static void FixSulphurH(IAtomContainer m)
{
// removes extra H's attached to sulphurs
for (int i = 0; i <= m.Atoms.Count - 1; i++)
{
var a = m.Atoms[i];
if (a.AtomicNumber.Equals(AtomicNumbers.S))
{
var connectedAtoms = m.GetConnectedAtoms(a);
int bondOrderSum = 0;
foreach (var conAtom in connectedAtoms)
{
if (!conAtom.AtomicNumber.Equals(AtomicNumbers.H))
{
IBond bond = m.GetBond(a, conAtom);
if (bond.Order == BondOrder.Single)
{
bondOrderSum += 1;
}
else if (bond.Order == BondOrder.Double)
{
bondOrderSum += 2;
}
else if (bond.Order == BondOrder.Triple)
{
bondOrderSum += 3;
}
else if (bond.Order == BondOrder.Quadruple)
{
bondOrderSum += 4;
}
}
}
if (bondOrderSum > 1)
{
foreach (var conAtom in connectedAtoms)
{
if (conAtom.AtomicNumber.Equals(AtomicNumbers.H))
{
m.RemoveAtom(conAtom);
}
}
}
}
}
}
private static void RemoveHydrogens(IAtomContainer ac)
{
IAtom atom = null;
int f = ac.Atoms.Count - 1;
do
{
atom = ac.Atoms[f];
switch (atom.AtomicNumber)
{
case AtomicNumbers.H:
ac.RemoveAtom(atom);
break;
}
f--;
} while (f >= 0);
}
