public void ParseAtomElements(XElement parser, IAtomContainer molecule)
{
if (!Name_EL_ATOMSELEMENT.Equals(parser.Name))
{
return;
}
foreach (var elm in parser.Descendants())
{
if (Name_EL_ELEMENT.Equals(elm.Name))
{
var atomicNumber = int.Parse(elm.Value, NumberFormatInfo.InvariantInfo);
var element = factory.GetElement(atomicNumber);
if (element == null)
{
var atom = molecule.Builder.NewPseudoAtom();
molecule.Atoms.Add(atom);
}
else
{
var atom = molecule.Builder.NewAtom(element.Symbol);
atom.AtomicNumber = element.AtomicNumber;
molecule.Atoms.Add(atom);
}
}
}
}
public static void Main(string[] args)
{
{
#region
IsotopeFactory f = XMLIsotopeFactory.Instance;
ChemicalElement e1 = f.GetElement("C");
ChemicalElement e2 = f.GetElement(12);
#endregion
}
{
#region AtomicNumber
IAtom element = new Atom("C");
IsotopeFactory f = XMLIsotopeFactory.Instance;
f.Configure(element);
#endregion
}
}
/// <summary>
/// Gets the paulingElectronegativities attribute of the
/// InductivePartialCharges object.
/// </summary>
/// <param name="ac">AtomContainer</param>
/// <param name="modified">if true, some values are modified by following the reference</param>
/// <returns>The pauling electronegativities</returns>
public double[] GetPaulingElectronegativities(IAtomContainer ac, bool modified)
{
var paulingElectronegativities = new double[ac.Atoms.Count];
string symbol = null;
int atomicNumber = 0;
try
{
ifac = CDK.IsotopeFactory;
for (int i = 0; i < ac.Atoms.Count; i++)
{
var atom = ac.Atoms[i];
symbol = ac.Atoms[i].Symbol;
var element = ifac.GetElement(symbol);
atomicNumber = element.AtomicNumber;
if (modified)
{
switch (atom.AtomicNumber)
{
case AtomicNumbers.Cl:
paulingElectronegativities[i] = 3.28;
break;
case AtomicNumbers.Br:
paulingElectronegativities[i] = 3.13;
break;
case AtomicNumbers.I:
paulingElectronegativities[i] = 2.93;
break;
case AtomicNumbers.H:
paulingElectronegativities[i] = 2.10;
break;
case AtomicNumbers.C:
if (ac.GetMaximumBondOrder(atom) == BondOrder.Single)
{
// Csp3
paulingElectronegativities[i] = 2.20;
}
else if (ac.GetMaximumBondOrder(atom) == BondOrder.Double)
{
paulingElectronegativities[i] = 2.31;
}
else
{
paulingElectronegativities[i] = 3.15;
}
break;
case AtomicNumbers.O:
if (ac.GetMaximumBondOrder(atom) == BondOrder.Single)
{
// Osp3
paulingElectronegativities[i] = 3.20;
}
else if (ac.GetMaximumBondOrder(atom) != BondOrder.Single)
{
paulingElectronegativities[i] = 4.34;
}
break;
case AtomicNumbers.Si:
paulingElectronegativities[i] = 1.99;
break;
case AtomicNumbers.S:
paulingElectronegativities[i] = 2.74;
break;
case AtomicNumbers.N:
paulingElectronegativities[i] = 2.59;
break;
default:
paulingElectronegativities[i] = pauling[atomicNumber];
break;
}
}
else
{
paulingElectronegativities[i] = pauling[atomicNumber];
}
}
return(paulingElectronegativities);
}
catch (Exception ex1)
{
Debug.WriteLine(ex1);
throw new CDKException($"Problems with IsotopeFactory due to {ex1.Message}", ex1);
}
}
