public virtual void TestInitiate_IAtomContainerSet_IAtomContainerSet()
{
EntryReact entry = (EntryReact)dictionary[entryString.ToLowerInvariant()];
var xmlList = entry.ExampleReactions;
Assert.IsTrue(xmlList.Count != 0, "The representation entry for [" + entryString
+ "] must contain at least one example of reaction.");
Assert.IsTrue(xmlList.Count > 0, "The representation entry for [" + entryString
+ "] must contain at least one example of reaction.");
foreach (var xml in xmlList)
{
CMLReader reader = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(xml)));
var chemFile = (IChemFile)reader.Read(builder.NewChemFile());
IReaction reactionDict = chemFile[0][0].ReactionSet[0];
var reactants = reactionDict.Reactants;
var agents = reactionDict.Agents;
var products = reactionDict.Products;
if (agents.Count == 0)
{
agents = null;
}
IReactionSet reactions = reaction.Initiate(reactants, agents);
Assert.IsTrue(reactions.Count > 0, "The products for [" + entryString + "] reaction is at least one reaction expected.");
Assert.AreEqual(products[0].Atoms.Count,
reactions[0].Products[0].Atoms.Count,
"The products for [" + entryString + "] reaction is not the expected.");
}
}
/// <summary>
/// Creates a map with the name and type of the parameters.
/// </summary>
private void InitiateParameterMap2(EntryReact entry)
{
var paramDic = entry.ParameterClass;
this.ParameterList = new List <IParameterReaction>();
foreach (var param in paramDic)
{
string paramName = "NCDK.Reactions.Types.Parameters." + param[0];
try
{
var ipc = (IParameterReaction)this.GetType().Assembly.GetType(paramName).GetConstructor(Type.EmptyTypes).Invoke(Array.Empty <object>());
ipc.IsSetParameter = bool.Parse(param[1]);
ipc.Value = param[2];
Trace.TraceInformation("Loaded parameter class: ", paramName);
ParameterList.Add(ipc);
}
catch (ArgumentException exception)
{
Trace.TraceError($"Could not find this IParameterReact: {paramName}");
Debug.WriteLine(exception);
}
catch (Exception exception)
{
Trace.TraceError($"Could not load this IParameterReact: {paramName}");
Debug.WriteLine(exception);
}
}
}
public void TestGetEntryRepresentation()
{
EntryReact entry = (EntryReact)dictionary[entryString.ToLowerInvariant()];
Assert.AreNotSame(0, entry.Representations.Count, "The representation entry for [" + entryString
+ "] must contain at least one representation.");
}
public void TestGetParameterList()
{
var paramObj = reaction.ParameterList;
EntryReact entry = (EntryReact)dictionary[entryString.ToLowerInvariant()];
var paramDic = entry.ParameterClass;
Assert.IsNotNull(paramObj, "The parameters entry for [" + entryString + "] must contain at least one parameter.");
Assert.IsNotNull(paramDic, "The parameters entry for [" + entryString + "] must contain at least one parameter.");
Assert.AreEqual(paramObj.Count, paramDic.Count, "The parameters entry for [" + entryString
+ "] must contain the same lenght as the reaction object.");
}
/// <summary>
/// Constructor of the ReactionEngine object.
/// </summary>
public ReactionEngine()
{
try
{
IReactionProcess reaction = (IReactionProcess)this;
EntryReact entry = InitiateDictionary("reaction-processes", (IReactionProcess)reaction);
InitiateParameterMap2(entry);
reaction.ParameterList = ParameterList;
// extract mechanism dependence, if there is one
if (!string.IsNullOrEmpty(entry.Mechanism))
{
ExtractMechanism(entry);
}
}
catch (Exception e)
{
Console.Error.WriteLine(e.StackTrace);
}
}
/// <summary>
/// Extract the mechanism necessary for this reaction.
/// </summary>
/// <param name="entry">The EntryReact object</param>
private void ExtractMechanism(EntryReact entry)
{
string mechanismName = "NCDK.Reactions.Mechanisms." + entry.Mechanism;
try
{
Mechanism = (IReactionMechanism)this.GetType().Assembly.GetType(mechanismName).GetConstructor(Type.EmptyTypes).Invoke(Array.Empty <object>());
Trace.TraceInformation("Loaded mechanism: ", mechanismName);
}
catch (ArgumentException exception)
{
Trace.TraceError($"Could not find this IReactionMechanism: {mechanismName}");
Debug.WriteLine(exception);
}
catch (Exception exception)
{
Trace.TraceError($"Could not load this IReactionMechanism: {mechanismName}");
Debug.WriteLine(exception);
}
}
public void TestGetEntryDescription()
{
EntryReact entry = (EntryReact)dictionary[entryString.ToLowerInvariant()];
Assert.IsNotNull(entry.Description, "The description entry for [" + entryString + "] must not be null.");
}
public void TestGetDictionaryEntry()
{
EntryReact entry = (EntryReact)dictionary[entryString.ToLowerInvariant()];
Assert.IsNotNull(entry, "The Entry [" + entryString + "] doesn't exist in OWL Dictionary.");
}
