private XElement GetXElement(Atom atom)
{
var elementType = "";
if (atom.Element is Element element)
{
elementType = element.Symbol;
}
if (atom.Element is FunctionalGroup functionalGroup)
{
elementType = FunctionalGroups.GetKey(functionalGroup);
}
XElement result = new XElement(CMLNamespaces.cml + CMLConstants.TagAtom,
new XAttribute(CMLConstants.AttributeId, atom.Id),
new XAttribute(CMLConstants.AttributeElementType, elementType),
new XAttribute(CMLConstants.AttributeX2, atom.Position.X.ToString("0.####", CultureInfo.InvariantCulture)),
new XAttribute(CMLConstants.AttributeY2, atom.Position.Y.ToString("0.####", CultureInfo.InvariantCulture))
);
if (atom.FormalCharge != null && atom.FormalCharge.Value != 0)
{
result.Add(new XAttribute(CMLConstants.AttributeFormalCharge, atom.FormalCharge.Value));
}
if (atom.IsotopeNumber != null && atom.IsotopeNumber.Value != 0)
{
result.Add(new XAttribute(CMLConstants.AttributeIsotopeNumber, atom.IsotopeNumber.Value));
}
if (atom.Element is Element element2)
{
if (element2 == Globals.PeriodicTable.C && atom.ShowSymbol != null)
{
result.Add(new XAttribute(CMLNamespaces.c4w + CMLConstants.AttributeExplicit, atom.ShowSymbol));
}
}
return(result);
}
private string FormatAtomSymbol(Atom atom)
{
var elementType = "";
if (atom.Element is Element element)
{
elementType = element.Symbol;
}
// Bit of a bodge, but it ensures that it can be re-loaded without exploding
if (atom.Element is FunctionalGroup functionalGroup)
{
elementType = FunctionalGroups.GetKey(functionalGroup);
if (elementType.Length > 3)
{
elementType = "*";
}
}
// Add three spaces the trim back to three characters
return($"{elementType} ".Substring(0, 3));
}
private static MolJSON ExportMol(Molecule m1)
{
MolJSON mj = new MolJSON();
mj.a = new AtomJSON[m1.Atoms.Count];
Dictionary <Atom, int> indexLookup = new Dictionary <Atom, int>();
int iAtom = 0;
foreach (Atom a in m1.Atoms.Values)
{
string elem = null;
if (a.Element.Symbol != "C")
{
if (a.Element is Element element)
{
elem = element.Symbol;
}
if (a.Element is FunctionalGroup functionalGroup)
{
elem = FunctionalGroups.GetKey(functionalGroup);
}
}
mj.a[iAtom] = new AtomJSON()
{
i = a.Id,
x = a.Position.X,
y = a.Position.Y,
l = elem
};
if (a.FormalCharge != null)
{
mj.a[iAtom].c = a.FormalCharge.Value;
}
indexLookup[a] = iAtom;
iAtom++;
}
int iBond = 0;
if (m1.Bonds.Any())
{
mj.b = new BondJSON[m1.Bonds.Count];
foreach (Bond bond in m1.Bonds)
{
mj.b[iBond] = new BondJSON()
{
i = bond.Id,
b = indexLookup[bond.StartAtom],
e = indexLookup[bond.EndAtom]
};
if (bond.Stereo == Globals.BondStereo.Wedge)
{
mj.b[iBond].s = Protruding;
}
else if (bond.Stereo == Globals.BondStereo.Hatch)
{
mj.b[iBond].s = Recessed;
}
else if (bond.Stereo == Globals.BondStereo.Indeterminate)
{
mj.b[iBond].s = Ambiguous;
}
if (bond.Order != Globals.OrderSingle)
{
mj.b[iBond].o = bond.OrderValue;
}
iBond++;
}
}
return(mj);
}
