/// <summary>
/// Main method which assigns MMFF94 partial charges
/// </summary>
/// <param name="ac">AtomContainer</param>
/// <returns>AtomContainer with MMFF94 partial charges as atom properties</returns>
public IAtomContainer AssignMMFF94PartialCharges(IAtomContainer ac)
{
if (!mmff.AssignAtomTypes(ac))
{
throw new CDKException("Molecule had an atom of unknown MMFF type");
}
mmff.PartialCharges(ac);
mmff.ClearProps(ac);
foreach (var atom in ac.Atoms)
{
atom.SetProperty(Key, atom.Charge);
}
return(ac);
}
public PartialTChargeMMFF94Descriptor(IAtomContainer container)
{
foreach (var atom in container.Atoms)
{
if (atom.ImplicitHydrogenCount == null || atom.ImplicitHydrogenCount != 0)
{
throw new CDKException("Hydrogens must be explicit for MMFF charge calculation");
}
}
clonedContainer = (IAtomContainer)container.Clone();
var mmff = new Mmff();
if (!mmff.AssignAtomTypes(clonedContainer))
{
Trace.TraceWarning("One or more atoms could not be assigned an MMFF atom type");
}
mmff.PartialCharges(clonedContainer);
mmff.ClearProps(clonedContainer);
this.container = container;
}