private void SetupCustomizers()
{
if (customizers == null)
{
customizers = new Dictionary <string, ICMLCustomizer>();
}
try
{
Debug.WriteLine("Starting loading Customizers...");
var reader = new StreamReader(ResourceLoader.GetAsStream(this.GetType(), CUSTOMIZERS_LIST));
int customizerCount = 0;
string customizerName;
while ((customizerName = reader.ReadLine()) != null)
{
// load them one by one
customizerCount++;
if (customizers.ContainsKey(customizerName))
{
try
{
ICMLCustomizer customizer = (ICMLCustomizer)this.GetType().Assembly.CreateInstance(customizerName);
if (customizer == null)
{
Trace.TraceInformation("Could not find this Customizer: ", customizerName);
}
else
{
customizers[customizer.GetType().FullName] = customizer;
Trace.TraceInformation("Loaded Customizer: ", customizer.GetType().Name);
}
}
catch (IOException exception)
{
Trace.TraceWarning("Could not load this Customizer: ", customizerName);
Trace.TraceWarning(exception.Message);
Debug.WriteLine(exception);
}
catch (Exception exception)
{
Trace.TraceWarning(exception.Message);
Debug.WriteLine(exception);
}
}
else
{
Trace.TraceWarning("Duplicate attempt to register a customizer");
}
}
Trace.TraceInformation("Number of loaded customizers: ", customizerCount);
}
catch (Exception exception)
{
Trace.TraceError($"Could not load this list: {CUSTOMIZERS_LIST}");
Debug.WriteLine(exception);
}
}
public void RegisterCustomizer(ICMLCustomizer customizer)
{
if (customizers == null)
{
customizers = new List <ICMLCustomizer>();
}
customizers.Add(customizer);
Trace.TraceInformation("Loaded Customizer: ", customizer.GetType().Name);
}
public void RegisterCustomizer(ICMLCustomizer customizer)
{
if (customizers == null)
{
customizers = new Dictionary <string, ICMLCustomizer>();
}
if (!customizers.ContainsKey(customizer.GetType().Name))
{
customizers[customizer.GetType().Name] = customizer;
Trace.TraceInformation("Loaded Customizer: ", customizer.GetType().Name);
}
else
{
Trace.TraceWarning("Duplicate attempt to register a customizer");
}
}
public CMLBond CDKJBondToCMLBond(IBond cdkBond)
{
CMLBond cmlBond = new CMLBond();
this.CheckPrefix(cmlBond);
if (string.IsNullOrEmpty(cdkBond.Id))
{
cmlBond.Id = "b" + cdkBond.GetHashCode();
}
else
{
cmlBond.Id = cdkBond.Id;
}
string[] atomRefArray = new string[cdkBond.Atoms.Count];
for (int i = 0; i < cdkBond.Atoms.Count; i++)
{
string 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;
}
BondOrder 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:
CMLScalar 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)
{
CMLBondType bType = new CMLBondType {
DictRef = "cdk:aromaticBond"
};
cmlBond.Add(bType);
}
switch (cdkBond.Stereo)
{
case BondStereo.Up:
case BondStereo.Down:
CMLBondStereo 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)
{
ICMLCustomizer 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);
}
public CMLAtom CDKAtomToCMLAtom(IAtomContainer container, IAtom cdkAtom)
{
CMLAtom cmlAtom = new CMLAtom();
this.CheckPrefix(cmlAtom);
AddAtomID(cdkAtom, cmlAtom);
AddDictRef(cdkAtom, cmlAtom);
cmlAtom.ElementType = cdkAtom.Symbol;
if (cdkAtom is IPseudoAtom)
{
string label = ((IPseudoAtom)cdkAtom).Label;
if (label != null)
{
cmlAtom.Title = label;
}
cmlAtom.ElementType = "Du";
}
Map2DCoordsToCML(cmlAtom, cdkAtom);
Map3DCoordsToCML(cmlAtom, cdkAtom);
MapFractionalCoordsToCML(cmlAtom, cdkAtom);
int?formalCharge = cdkAtom.FormalCharge;
if (formalCharge != null)
{
cmlAtom.FormalCharge = formalCharge.Value;
}
// CML's hydrogen count consists of the sum of implicit and explicit
// hydrogens (see bug #1655045).
int?totalHydrogen = cdkAtom.ImplicitHydrogenCount;
if (totalHydrogen != null)
{
if (container != null)
{
foreach (var bond in container.GetConnectedBonds(cdkAtom))
{
foreach (var atom in bond.Atoms)
{
if (AtomicNumbers.H.Equals(atom.AtomicNumber) && atom != cdkAtom)
{
totalHydrogen++;
}
}
}
} // else: it is the implicit hydrogen count
cmlAtom.HydrogenCount = totalHydrogen.Value;
} // else: don't report it, people can count the explicit Hs themselves
int?massNumber = cdkAtom.MassNumber;
if (!(cdkAtom is IPseudoAtom))
{
if (massNumber != null)
{
cmlAtom.IsotopeNumber = massNumber.Value;
}
}
if (cdkAtom.Charge != null)
{
CMLScalar scalar = new CMLScalar();
this.CheckPrefix(scalar);
scalar.DictRef = "cdk:partialCharge";
scalar.SetValue(cdkAtom.Charge.Value);
cmlAtom.Add(scalar);
}
WriteProperties(cdkAtom, cmlAtom);
if (cdkAtom.IsAromatic)
{
CMLScalar aromAtom = new CMLScalar {
DictRef = "cdk:aromaticAtom"
};
cmlAtom.Add(aromAtom);
}
foreach (var element in customizers.Keys)
{
ICMLCustomizer customizer = customizers[element];
try
{
customizer.Customize(cdkAtom, cmlAtom);
}
catch (Exception exception)
{
Trace.TraceError("Error while customizing CML output with customizer: ", customizer.GetType().Name);
Debug.WriteLine(exception);
}
}
return(cmlAtom);
}
