public Dictionary <string, TbData> RetrieveAdi(ITbBasket target, Dictionary <string, string> Modelinfo)
{
Dictionary <string, TbData> Adidictionary = new Dictionary <string, TbData>();
string tag = this.Modelinfo["tag"];
var setup = new BridgeSetup(false);
//setup.AddAllJarsClassPath(@"B:\ToolboxAddinExamples\lib");
setup.AddAllJarsClassPath(System.IO.Path.GetDirectoryName(System.Reflection.Assembly.GetExecutingAssembly().Location));
Bridge.CreateJVM(setup);
Bridge.RegisterAssembly(typeof(AdiArray).Assembly);
java.util.List list = AdiArray.getADI(tag, target.Chemical.Smiles);
if (list.size() == 0)
{
return(Adidictionary);
}
//create the iterator
for (int i = 0; i < list.size(); i++)
{
AdiArray adicomponent = (AdiArray)list.get(i);
Adidictionary.Add(adicomponent.AdiName, new TbData(new TbUnit(TbScale.EmptyRatioScale.Name, string.Empty), adicomponent.AdiValue));
}
return(Adidictionary);
}
public ITbPrediction Predict(ITbBasket target)
{
target.WorkTask.TbToken.ThrowIfCancellationRequested();
//understand how to pass scalar predictions
TbData predictedTbData = (TbData)Calculate(target);
// var predictedTbData = new TbData(predictedScalarData.Unit, predictedScalarData.Value);
//var targetLogKow =
// target.WorkTask.CalcService.CalculateParameter(_logKowDescriptor.Descriptor, null, target);
//mock descriptor
Dictionary <string, string> ModelPred = this.RetrieveModelPreD(target, Modelinfo);
TbData Mockdescriptordata = new TbData(new TbUnit(TbScale.EmptyRatioScale.FamilyGroup, TbScale.EmptyRatioScale.BaseUnit), new double?());
//TODO pack additional metadata into an unique object and then predicton probably will be faster
Dictionary <string, string> AdditionalMetadata = new Dictionary <string, string>()
{
{
"Guide name",
this.Modelinfo["GuideUrl"]
}
};
if (ModelPred.ContainsKey("assessment"))
{
AdditionalMetadata.Add("Assessment", ModelPred["assessment"]);
}
if (ModelPred.ContainsKey("assessment_verbose"))
{
AdditionalMetadata.Add("Brief Explanation", ModelPred["assessment_verbose"]);
}
if (ModelPred.ContainsKey("Similar_molecules_smiles"))
{
AdditionalMetadata.Add("Analogues' SMILES", ModelPred["Similar_molecules_smiles"]);
}
//if (Modelinfo.ContainsKey("QMRFlink"))
// AdditionalMetadata.Add("QMRF", Modelinfo["QMRFlink"]);
//if (Modelinfo.ContainsKey("Lambda"))
//{
// AdditionalMetadata.Add("Lambda", double.Parse(this.Modelinfo["Lambda"], CultureInfo.InvariantCulture).ToString());
//}
Dictionary <TbObjectId, TbData> matrixdescriptorvalues = new Dictionary <TbObjectId, TbData>()
{
{
this.objectId,
Mockdescriptordata
}
};
//run method Retrieve ADI, to retrieve all adi indexes
Dictionary <string, TbData> ADImetadata = this.RetrieveAdi(target, Modelinfo);
TbMetadata metadata = new TbMetadata((IReadOnlyDictionary <string, string>)AdditionalMetadata, (IReadOnlyDictionary <string, TbData>)ADImetadata);
//return new PredictionAddin(predictedTbData, predictionDescription, xData);
return(new PredictionAddin(predictedTbData, metadata, matrixdescriptorvalues, null));
}
public bool IsDisconnected(ITbBasket target)
{
string smiles = target.Chemical.Smiles;
Regex regex = new Regex(@"\.");
//Doesn't work, don't ask why
if (regex.IsMatch(smiles))
{
return(true);
}
return(false);
}
public bool IsRelevantToChemical(ITbBasket target, out string reason)
{
Dictionary <string, string> ModelPred = RetrieveModelPreD(target, Modelinfo);
if (ModelPred.ContainsKey("error"))
{
reason = ModelPred["error"];
return(false);
}
reason = (string)null;
return(true);
}
public TbScalarData Calculate(ITbBasket target)
{
Dictionary <string, string> ModelPred = this.RetrieveModelPreD(target, Modelinfo);
if (ModelPred.ContainsKey("error"))
{
throw new Exception(ModelPred["error"]);
}
return(Utilities.ConvertData(ModelPred["prediction"], this.ScaleDeclaration, Modelinfo));
}
public TbDomainStatus CheckDomain(ITbBasket target)
{
Dictionary <string, string> ModelPred = RetrieveModelPreD(target, Modelinfo);
if (ModelPred.ContainsKey("error"))
{
return(TbDomainStatus.Undefined);
}
//double ADI;
//try
//{
// ADI = DoubleParser(ModelPred["ADI"]);
//}
//catch
//{
// return TbDomainStatus.Undefined;
//}
//return ADI > 0.7 ? TbDomainStatus.InDomain : TbDomainStatus.OutOfDomain;
Regex regex = new Regex(@".*low reliability.*");
return(regex.IsMatch(ModelPred["assessment"]) ? TbDomainStatus.OutOfDomain : TbDomainStatus.InDomain);
}
//public string runmodel(ITbBasket target, string output, Dictionary<string, string> Modelinfo)
//{
// string tag = this.Modelinfo["tag"];
// var setup = new BridgeSetup(false);
// //setup.AddAllJarsClassPath(@"B:\ToolboxAddinExamples\lib");
// setup.AddAllJarsClassPath(System.IO.Path.GetDirectoryName(System.Reflection.Assembly.GetExecutingAssembly().Location));
// Bridge.CreateJVM(setup);
// Bridge.RegisterAssembly(typeof(VegaDockInterface).Assembly);
// java.lang.String stdout = VegaDockInterface.@getValues(tag, output, target.Chemical.Smiles);
// return stdout;
//}
public Dictionary <string, string> RetrieveModelPreD(ITbBasket target, Dictionary <string, string> Modelinfo)
{
Dictionary <string, string> ModelPred = new Dictionary <string, string>();
if (IsDisconnected(target))
{
ModelPred.Add("error", "Unable to run the model. SMILES provided is a Disconnected Structure");
return(ModelPred);
}
string tag = this.Modelinfo["tag"];
var setup = new BridgeSetup(false);
//setup.AddAllJarsClassPath(@"B:\ToolboxAddinExamples\lib");
setup.AddAllJarsClassPath(System.IO.Path.GetDirectoryName(System.Reflection.Assembly.GetExecutingAssembly().Location));
Bridge.CreateJVM(setup);
Bridge.RegisterAssembly(typeof(VegaDockObject).Assembly);
VegaDockObject vdo = new VegaDockObject();
vdo.run(tag, target.Chemical.Smiles);
if (VegaDockObject.error.length() != 0)
{
ModelPred.Add("error", VegaDockObject.error);
return(ModelPred);
}
ModelPred.Add("prediction", VegaDockObject.prediction);
ModelPred.Add("assessment", VegaDockObject.assessment);
ModelPred.Add("assessment_verbose", VegaDockObject.assessment_verbose);
ModelPred.Add("Experimental", VegaDockObject.Experimental);
ModelPred.Add("ADI", VegaDockObject.ADI);
ModelPred.Add("Similar_molecules_index", VegaDockObject.Similar_molecules_index);
ModelPred.Add("Similar_molecules_smiles", VegaDockObject.Similar_molecules_smiles);
return(ModelPred);
}
