/// <summary>
/// </summary>
/// <param name="set">The collection of IAtomContainer objects</param>
/// <returns>The summed formal charges of all atoms in this set.</returns>
public static double GetTotalFormalCharge(IChemObjectSet <IAtomContainer> set)
{
int charge = 0;
for (int i = 0; i < set.Count; i++)
{
int thisCharge = AtomContainerManipulator.GetTotalFormalCharge(set[i]);
double stoich = set.GetMultiplier(i).Value;
charge += (int)(stoich * thisCharge);
}
return(charge);
}
public override void Write(IChemObject arg0)
{
CustomizeJob();
if (arg0 is IAtomContainer)
{
try
{
IAtomContainer container = (IAtomContainer)arg0;
writer.Write(mopacCommands.Setting);
int formalCharge = AtomContainerManipulator.GetTotalFormalCharge(container);
if (formalCharge != 0)
{
writer.Write(" CHARGE=" + formalCharge);
}
writer.Write('\n');
//if (container.GetProperty("Names") != null) writer.Write(container.GetProperty("Names").ToString());
writer.Write('\n');
writer.Write(Title);
writer.Write('\n');
for (int i = 0; i < container.Atoms.Count; i++)
{
IAtom atom = container.Atoms[i];
if (atom.Point3D != null)
{
Vector3 point = atom.Point3D.Value;
WriteAtom(atom, point.X, point.Y, point.Z, optimize.IsSet ? 1 : 0);
}
else if (atom.Point2D != null)
{
Vector2 point = atom.Point2D.Value;
WriteAtom(atom, point.X, point.Y, 0, optimize.IsSet ? 1 : 0);
}
else
{
WriteAtom(atom, 0, 0, 0, 1);
}
}
writer.Write("0");
writer.Write('\n');
}
catch (IOException ioException)
{
Trace.TraceError(ioException.Message);
throw new CDKException(ioException.Message, ioException);
}
}
else
{
throw new CDKException("Unsupported object!\t" + arg0.GetType().Name);
}
}
