public void Add(CMLBond bond)
{
var aa = this.Element(XName_CML_bondArray);
if (aa == null)
{
aa = new CMLBondArray();
this.Add(aa);
}
aa.Add(bond);
}
public void TestCdkBondToCMLBond_Hatch()
{
IChemObjectBuilder builder = ChemObjectBuilder.Instance;
IBond bond = builder.NewBond();
bond.Order = BondOrder.Single;
bond.Stereo = BondStereo.Down;
Convertor convertor = new Convertor(true, null);
CMLBond cmlBond = convertor.CDKJBondToCMLBond(bond);
var writer = new StringWriter();
var d = new XDocument(cmlBond);
d.Save(writer);
string expected = "<bondStereo dictRef=\"cml:H\">H</bondStereo>";
string actual = writer.ToString();
Assert.IsTrue(actual.Contains(expected));
}
public CMLBond CDKJBondToCMLBond(IBond cdkBond)
{
var cmlBond = new CMLBond();
this.CheckPrefix(cmlBond);
if (string.IsNullOrEmpty(cdkBond.Id))
{
cmlBond.Id = "b" + cdkBond.GetHashCode();
}
else
{
cmlBond.Id = cdkBond.Id;
}
var atomRefArray = new string[cdkBond.Atoms.Count];
for (int i = 0; i < cdkBond.Atoms.Count; i++)
{
var atomID = cdkBond.Atoms[i].Id;
if (string.IsNullOrEmpty(atomID))
{
atomRefArray[i] = "a" + cdkBond.Atoms[i].GetHashCode().ToString(NumberFormatInfo.InvariantInfo);
}
else
{
atomRefArray[i] = atomID;
}
}
if (atomRefArray.Length == 2)
{
cmlBond.AtomRefs2 = atomRefArray;
}
else
{
cmlBond.AtomRefs = atomRefArray;
}
var border = cdkBond.Order;
switch (border)
{
case BondOrder.Single:
cmlBond.Order = "S";
break;
case BondOrder.Double:
cmlBond.Order = "D";
break;
case BondOrder.Triple:
cmlBond.Order = "T";
break;
default:
var scalar = new CMLScalar();
this.CheckPrefix(scalar);
scalar.DictRef = "cdk:bondOrder";
scalar.Title = "order";
scalar.SetValue(cdkBond.Order.Numeric());
cmlBond.Add(scalar);
break;
}
if (cdkBond.IsAromatic)
{
var bType = new CMLBondType {
DictRef = "cdk:aromaticBond"
};
cmlBond.Add(bType);
}
switch (cdkBond.Stereo)
{
case BondStereo.Up:
case BondStereo.Down:
var bondStereo = new CMLBondStereo();
this.CheckPrefix(bondStereo);
if (cdkBond.Stereo == BondStereo.Up)
{
bondStereo.DictRef = "cml:W";
bondStereo.Value = "W";
}
else
{
bondStereo.DictRef = "cml:H";
bondStereo.Value = "H";
}
cmlBond.Add(bondStereo);
break;
}
if (cdkBond.GetProperties().Count > 0)
{
WriteProperties(cdkBond, cmlBond);
}
foreach (var element in customizers.Keys)
{
var customizer = customizers[element];
try
{
customizer.Customize(cdkBond, cmlBond);
}
catch (Exception exception)
{
Trace.TraceError("Error while customizing CML output with customizer: ", customizer.GetType().Name);
Debug.WriteLine(exception);
}
}
return(cmlBond);
}
private CMLMolecule CDKAtomContainerToCMLMolecule(IAtomContainer structure, bool setIDs, bool isRef)
{
CMLMolecule 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)
{
CMLIdentifier 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++)
{
IAtom cdkAtom = structure.Atoms[i];
CMLAtom 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++)
{
CMLBond 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);
}