private CMLMolecule CDKAtomContainerToCMLMolecule(IAtomContainer structure, bool setIDs, bool isRef)
{
var cmlMolecule = new CMLMolecule();
if (useCMLIDs && setIDs)
{
IDCreator.CreateIDs(structure);
}
this.CheckPrefix(cmlMolecule);
if (!string.IsNullOrEmpty(structure.Id))
{
if (!isRef)
{
cmlMolecule.Id = structure.Id;
}
else
{
cmlMolecule.Ref = structure.Id;
}
}
if (structure.Title != null)
{
cmlMolecule.Title = structure.Title;
}
if (structure.GetProperty <string>(CDKPropertyName.InChI) != null)
{
var ident = new CMLIdentifier
{
Convention = "iupac:inchi"
};
ident.SetAttributeValue(CMLElement.Attribute_value, structure.GetProperty <string>(CDKPropertyName.InChI));
cmlMolecule.Add(ident);
}
if (!isRef)
{
for (int i = 0; i < structure.Atoms.Count; i++)
{
var cdkAtom = structure.Atoms[i];
var cmlAtom = CDKAtomToCMLAtom(structure, cdkAtom);
if (structure.GetConnectedSingleElectrons(cdkAtom).Count() > 0)
{
cmlAtom.SpinMultiplicity = structure.GetConnectedSingleElectrons(cdkAtom).Count() + 1;
}
cmlMolecule.Add(cmlAtom);
}
for (int i = 0; i < structure.Bonds.Count; i++)
{
var cmlBond = CDKJBondToCMLBond(structure.Bonds[i]);
cmlMolecule.Add(cmlBond);
}
}
// ok, output molecular properties, but not TITLE, INCHI, or DictRef's
var props = structure.GetProperties();
foreach (var propKey in props.Keys)
{
if (propKey is string key)
{
// but only if a string
if (!isRef)
{
object value = props[key];
switch (key)
{
case CDKPropertyName.Title:
case CDKPropertyName.InChI:
break;
default:
// ok, should output this
var scalar = new CMLScalar();
this.CheckPrefix(scalar);
scalar.DictRef = "cdk:molecularProperty";
scalar.Title = (string)key;
scalar.SetValue(value.ToString());
cmlMolecule.Add(scalar);
break;
}
}
// FIXME: At the moment the order writing the formula is into properties
// but it should be that IMolecularFormula is a extension of IAtomContainer
if (!isRef && string.Equals(key, CDKPropertyName.Formula, StringComparison.Ordinal))
{
switch (props[key])
{
case IMolecularFormula cdkFormula:
{
var cmlFormula = new CMLFormula();
var isotopesList = MolecularFormulaManipulator.PutInOrder(MolecularFormulaManipulator.OrderEle, cdkFormula);
foreach (var isotope in isotopesList)
{
cmlFormula.Add(isotope.Symbol, cdkFormula.GetCount(isotope));
}
cmlMolecule.Add(cmlFormula);
}
break;
case IMolecularFormulaSet cdkFormulaSet:
foreach (var cdkFormula in cdkFormulaSet)
{
var isotopesList = MolecularFormulaManipulator.PutInOrder(MolecularFormulaManipulator.OrderEle, cdkFormula);
var cmlFormula = new CMLFormula {
DictRef = "cdk:possibleMachts"
};
foreach (var isotope in isotopesList)
{
cmlFormula.Add(isotope.Symbol, cdkFormula.GetCount(isotope));
}
cmlMolecule.Add(cmlFormula);
}
break;
}
}
}
}
foreach (var element in customizers.Keys)
{
var customizer = customizers[element];
try
{
customizer.Customize(structure, cmlMolecule);
}
catch (Exception exception)
{
Trace.TraceError($"Error while customizing CML output with customizer: {customizer.GetType().Name}");
Debug.WriteLine(exception);
}
}
return(cmlMolecule);
}