/// <summary>
/// gets the chemical element from the cmlElement CML
/// </summary>
/// <param name="cmlElement">XElement containing CML</param>
/// <returns></returns>
private ElementBase GetChemicalElement(XElement cmlElement, out string message)
{
message = "";
XAttribute xa = cmlElement.Attribute("elementType");
if (xa != null)
{
string symbol = xa.Value;
//try to return a chemical element from the Periodic Table
if (Globals.PeriodicTable.HasElement(symbol))
{
return(Globals.PeriodicTable.Elements[symbol]);
}
//if that fails, see if it's a functional group
// ReSharper disable once InconsistentNaming
FunctionalGroup newFG;
if (FunctionalGroups.TryParse(symbol, out newFG))
{
return(newFG);
}
//if we got here then it went very wrong
message = $"Unrecognised element '{symbol}' in {cmlElement}";
}
else
{
message = $"cml attribute 'elementType' missing from {cmlElement}";
}
return(null);
}
/// <summary>
/// Initialization method for when EDI data string is known
/// and the segment seperator if the interchange is known
/// </summary>
private void Parse(string value, FormattingOptions options)
{
var segmentStringValueCollection = value.Split(options.SegmentTerminator.AsSplitDelimiter(), StringSplitOptions.None);
var functionalGroupStringArray = new List <System.Text.StringBuilder>();
foreach (var segment in segmentStringValueCollection)
{
var segmentStringInstance = segment;
segmentStringInstance = RemoveCharacterFromString(segmentStringInstance, "\r", options);
segmentStringInstance = RemoveCharacterFromString(segmentStringInstance, "\n", options);
if (segmentStringInstance.Length < 3)
{
continue;
}
switch (segmentStringInstance.Substring(0, 3))
{
case InterchangeControlHeader.ElementName:
Header = new InterchangeControlHeader(segmentStringInstance, options);
break;
case InterchangeControlTrailer.ElementName:
Trailer = new InterchangeControlTrailer(segmentStringInstance, options);
break;
default:
if (segmentStringInstance.Substring(0, 2).Equals(FunctionalGroupHeader.ElementName))
{
functionalGroupStringArray.Add(new System.Text.StringBuilder());
}
functionalGroupStringArray[functionalGroupStringArray.Count - 1].Append(segmentStringInstance);
functionalGroupStringArray[functionalGroupStringArray.Count - 1].Append(options.SegmentTerminator);
break;
}
}
foreach (var functionalGroupString in functionalGroupStringArray)
{
var fg = new FunctionalGroup.FunctionalGroup(functionalGroupString.ToString(), FormattingOptions);
FunctionalGroups.Add(fg);
}
FunctionalGroups.TrimExcess();
}
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);
}
/// <summary>
/// gets the chemical element from the cmlElement CML
/// </summary>
/// <param name="cmlElement">XElement containing CML</param>
/// <returns></returns>
private ElementBase GetChemicalElement(XElement cmlElement)
{
string symbol = cmlElement.Attribute("elementType").Value;
//try to return a chemical element from the Periodic Table
if (Globals.PeriodicTable.HasElement(symbol))
{
return(Globals.PeriodicTable.Elements[symbol]);
}
//if that fails, see if it's a functional group
// ReSharper disable once InconsistentNaming
FunctionalGroup newFG;
if (FunctionalGroups.TryParse(symbol, out newFG))
{
return(newFG);
}
//if we got here then it went very wrong
throw new ArgumentOutOfRangeException($"Unrecognised element '{symbol}'.");
}
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);
}
