protected override void Context()
{
base.Context();
_project = new MoBiProject();
var molecule = new MoleculeBuilder().WithName(_moleculeName);
var moleculeParameter = new Parameter().WithName(_moleculeParameterName);
molecule.Add(moleculeParameter);
var molecules = new MoleculeBuildingBlock()
{
molecule
};
_project.AddBuildingBlock(molecules);
var parameter = new Parameter().WithName(_parameterName);
var root = new Container().WithName("Root");
root.Add(parameter);
var spatialStructure = new MoBiSpatialStructure().WithTopContainer(root);
_project.AddBuildingBlock(spatialStructure);
var reactionBuilder = new ReactionBuilder().WithName(_reactionName);
var reactions = new MoBiReactionBuildingBlock()
{
reactionBuilder
};
_project.AddBuildingBlock(reactions);
A.CallTo(() => _context.CurrentProject).Returns(_project);
}
private static MoleculeBuilder createMoleculeBuilder(string moleculeName)
{
var drug = new MoleculeBuilder().WithName(moleculeName);
drug.AddParameter(new Parameter().WithName("MoleculeProperty").WithFormula(new ConstantFormula(1)).WithMode(ParameterBuildMode.Global));
return(drug);
}
protected override void Context()
{
base.Context();
var moleculeBuildingBlock1 = new MoleculeBuildingBlock().WithName("Tada");
var moleculeBuilderA = new MoleculeBuilder().WithName("MSVa");
var moleculeBuilderB = new MoleculeBuilder().WithName("MSVb");
moleculeBuildingBlock1.Add(moleculeBuilderA);
moleculeBuildingBlock1.Add(moleculeBuilderB);
var moleculeBuildingBlock2 = new MoleculeBuildingBlock().WithName("Toto");
moleculeBuilderA = new MoleculeBuilder().WithName("MSVa");
moleculeBuilderB = new MoleculeBuilder().WithName("MSVb");
moleculeBuildingBlock2.Add(moleculeBuilderA);
moleculeBuildingBlock2.Add(moleculeBuilderB);
_object1 = moleculeBuildingBlock1;
_object2 = moleculeBuildingBlock2;
_comparerSettings.OnlyComputingRelevant = false;
}
protected override void Context()
{
_quantity = A.Fake <IParameter>().WithName("P");
base.Context();
_parameter.Name = "P";
var moleculeBuilder1 = new MoleculeBuilder().WithName("Mol1");
var moleculeBuilder2 = new MoleculeBuilder().WithName("Mol2");
var transporterMolecule1 = new TransporterMoleculeContainer {
TransportName = "TRANSPORT", Name = "TRANSPORTER"
};
var molecule1 = new Container().WithName("Mol1");
molecule1.Add(transporterMolecule1);
var molecule2 = new Container().WithName("Mol2");
var transporterMolecule2 = new TransporterMoleculeContainer {
TransportName = "TRANSPORT", Name = "TRANSPORTER"
};
molecule2.Add(transporterMolecule2);
moleculeBuilder1.AddTransporterMoleculeContainer(transporterMolecule1);
moleculeBuilder2.AddTransporterMoleculeContainer(transporterMolecule2);
var moleculeBuildingBlock = new MoleculeBuildingBlock {
moleculeBuilder1, moleculeBuilder2
};
_buildingBlockInfo.UntypedBuildingBlock = moleculeBuildingBlock;
transporterMolecule1.AddParameter(_parameter);
_quantity.ParentContainer.Name = transporterMolecule1.TransportName;
_quantity.ParentContainer.ParentContainer.Name = moleculeBuilder1.Name;
}
protected override void Context()
{
base.Context();
var container = new Container {
Mode = ContainerMode.Physical, Name = "containerName"
};
var subContainer = new Container {
Mode = ContainerMode.Physical, Name = "subContainerName"
};
subContainer.Add(new Parameter {
Name = "containerParameter"
});
container.Add(subContainer);
_spatialStructure.AddTopContainer(container);
var builder = new MoleculeBuilder {
Name = "C1"
};
builder.AddParameter(new Parameter {
BuildMode = ParameterBuildMode.Local, Name = "localParameter"
});
_moleculeBuildingBlock.Add(builder);
}
protected override void Context()
{
base.Context();
A.CallTo(() => _reactionDimensionRetriever.SelectedDimensionMode).Returns(ReactionDimensionMode.ConcentrationBased);
_moleculeBuilder = new MoleculeBuilder {
DefaultStartFormula = new ConstantFormula(0), Dimension = DomainHelperForSpecs.AmountDimension
};
}
protected override void Context()
{
base.Context();
_moleculeParameter = new Parameter().WithName("RP");
var moleculeBuilder = new MoleculeBuilder();
moleculeBuilder.Add(_moleculeParameter);
}
protected override void Context()
{
base.Context();
_explicitFormula = new ExplicitFormula("A+B");
A.CallTo(() => _reactionDimensionRetriever.SelectedDimensionMode).Returns(ReactionDimensionMode.ConcentrationBased);
_moleculeBuilder = new MoleculeBuilder {
DefaultStartFormula = _explicitFormula, Dimension = DomainHelperForSpecs.AmountDimension
};
A.CallTo(() => _amoutToConcentrationFormulaMapper.HasMappingFor(_explicitFormula)).Returns(false);
}
protected override void Context()
{
base.Context();
var builder = new MoleculeBuilder {
Name = "C1"
};
builder.AddParameter(new Parameter {
BuildMode = ParameterBuildMode.Local, Name = "localParameter"
});
_moleculeBuildingBlock.Add(builder);
}
protected override void Context()
{
base.Context();
var molecule = new MoleculeBuilder {
Name = "Mol", Dimension = Constants.Dimension.NO_DIMENSION
};
var nanStartValue = new MoleculeStartValue {
Name = molecule.Name, StartValue = null, Dimension = Constants.Dimension.NO_DIMENSION
};
_moleculeStartValueBuildingBlock.Add(nanStartValue);
A.CallTo(_moleculeResolver).WithReturnType <IMoleculeBuilder>().Returns(molecule);
}
protected override void Context()
{
base.Context();
_dimension = DimensionFactoryForSpecs.Factory.Dimension(DimensionFactoryForSpecs.DimensionNames.Mass);
_moleculeStartValue = new MoleculeStartValue {
Dimension = _dimension, Name = _name, Formula = null
};
_builder = new MoleculeBuilder
{
Name = _name,
Dimension = _dimension
};
}
public void TestSerialization()
{
MoleculeBuilder x1 = CreateObject <MoleculeBuilder>().WithName("Monica.Builder");
x1.IsFloating = true;
x1.QuantityType = QuantityType.Metabolite;
x1.DefaultStartFormula = CreateObject <ConstantFormula>().WithDimension(DimensionLength).WithValue(23.4);
TransportBuilder t1 = CreateObject <TransportBuilder>().WithName("Passive Transport");
IFormula consFormula = CreateObject <ConstantFormula>().WithDimension(DimensionLength).WithValue(5);
IParameter transporterParameter = CreateObject <Parameter>().WithName("Passive Transport Param").WithFormula(consFormula).WithMode(ParameterBuildMode.Property)
.WithDimension(DimensionLength);
t1.AddParameter(transporterParameter);
IFormula f1 = CreateObject <ExplicitFormula>().WithDimension(DimensionLength).WithFormulaString("3*Patty");
IFormulaUsablePath fup = new FormulaUsablePath(new[] { "Patricia" }).WithAlias("Patty").WithDimension(DimensionLength);
f1.AddObjectPath(fup);
IParameter p1 = CreateObject <Parameter>().WithName("Patricia").WithFormula(f1).WithValue(3.1).WithMode(ParameterBuildMode.Property);
IParameter p2 = CreateObject <Parameter>().WithName("Pascal").WithFormula(f1).WithValue(3.2).WithMode(ParameterBuildMode.Local);
IParameter p3 = CreateObject <Parameter>().WithName("Paul").WithFormula(f1).WithValue(3.3);
x1.AddParameter(p1);
x1.AddParameter(p2);
var atbc1 = CreateObject <TransporterMoleculeContainer>().WithName("Tranquilo");
ITransportBuilder atb1 = CreateObject <TransportBuilder>();
atb1.Formula = CreateObject <ConstantFormula>().WithDimension(DimensionLength).WithValue(2.5);
atb1.AddParameter(p3);
atb1.Name = "Tranquilo";
atbc1.AddActiveTransportRealization(atb1);
var atbc2 = CreateObject <TransporterMoleculeContainer>().WithName("Tranquilo2");
ITransportBuilder atb2 = CreateObject <TransportBuilder>();
atb2.Formula = f1;
atb2.Name = "Tranquilo2";
atbc2.AddActiveTransportRealization(atb2);
x1.AddTransporterMoleculeContainer(atbc1);
x1.AddTransporterMoleculeContainer(atbc2);
x1.IsXenobiotic = !x1.IsXenobiotic;
var interactionContainer = CreateObject <InteractionContainer>().WithName("Interactions");
x1.AddInteractionContainer(interactionContainer);
var x2 = SerializeAndDeserialize(x1);
AssertForSpecs.AreEqualMoleculeBuilder(x1, x2);
}
protected override void Context()
{
base.Context();
var builder = new MoleculeBuilder {
Name = "molecule", Dimension = Constants.Dimension.NO_DIMENSION, DefaultStartFormula = new ExplicitFormula("50")
};
var startValue = new MoleculeStartValue {
Name = builder.Name, StartValue = 45, Dimension = Constants.Dimension.NO_DIMENSION, Formula = null
};
_moleculeStartValueBuildingBlock.Add(startValue);
A.CallTo(() => _cloneManagerForBuildingBlock.Clone(builder.DefaultStartFormula, _moleculeStartValueBuildingBlock.FormulaCache)).Returns(new ExplicitFormula("M/V"));
A.CallTo(_moleculeResolver).WithReturnType <IMoleculeBuilder>().Returns(builder);
}
public static MoleculeReference AddSideChain(this MoleculeReference moleculeReference, params ElementName[] sideChainElements)
{
if (!moleculeReference.IsInitialized)
{
throw new InvalidOperationException("Cannot add atoms. Molecule reference is not initialized");
}
var sideChainBuilder = new MoleculeBuilder();
var sideChainReference = sideChainBuilder.Start.Add(sideChainElements);
moleculeReference.Molecule.AddMolecule(sideChainReference,
moleculeReference.FirstAtomId,
moleculeReference.LastAtomId);
return(moleculeReference);
}
protected override void Context()
{
_quantity = _parameter;
base.Context();
var moleculeBuilder = new MoleculeBuilder();
moleculeBuilder.AddParameter(_parameter);
var moleculeBuildingBlock = new MoleculeBuildingBlock {
moleculeBuilder
};
_buildingBlockInfo.UntypedBuildingBlock = moleculeBuildingBlock;
}
protected override void Context()
{
base.Context();
var moleculeBuilder1 = new MoleculeBuilder().WithName("Drug");
moleculeBuilder1.DefaultStartFormula = new ConstantFormula(0);
var moleculeBuilder2 = new MoleculeBuilder().WithName("Drug");
moleculeBuilder2.DefaultStartFormula = new ConstantFormula(1.1);
_object1 = moleculeBuilder1;
_object2 = moleculeBuilder2;
}
protected override void Context()
{
base.Context();
var moleculeBuindingBlock = new MoleculeBuildingBlock();
var molecule = new MoleculeBuilder {
Name = "Mol", Dimension = Constants.Dimension.NO_DIMENSION
};
moleculeBuindingBlock.Add(molecule);
_nullStartValue = new MoleculeStartValue {
Name = molecule.Name, StartValue = 1, Dimension = Constants.Dimension.NO_DIMENSION
};
_moleculeStartValueBuildingBlock.Add(_nullStartValue);
A.CallTo(_context.Context).WithReturnType <IMoleculeBuildingBlock>().Returns(moleculeBuindingBlock);
}
protected override void Context()
{
base.Context();
_parameter = new Parameter()
.WithName("P")
.WithMode(_parameterBuildMode)
.WithParentContainer(new Container().WithName("Drug"));
var moleculeBuilder = new MoleculeBuilder().WithName("Drug");
var parameterBuilder = new Parameter()
.WithName(_parameter.Name)
.WithMode(_parameterBuildMode);
moleculeBuilder.AddParameter(parameterBuilder);
_moleculeBuidingBlock.Add(moleculeBuilder);
}
/// <summary>
/// Add values to the NodeType Properties of a Node.
/// </summary>
/// <param name="Node">The Node whose properties are being filled in.</param>
/// <param name="CurrentIndex">The current index in the ProductSize array in a CswC3Product object. This is ONLY needed for Size Nodes.</param>
public void addNodeTypeProps(CswNbtNode Node, int CurrentIndex = 0)
{
CswNbtMetaDataNodeType NodeType = _CswNbtResources.MetaData.getNodeType(Node.NodeTypeId);
foreach (CswNbtMetaDataNodeTypeProp NTP in NodeType.getNodeTypeProps())
{
if (null != Node.Properties[NTP] && _Mappings.ContainsKey(NTP.PropName))
{
C3Mapping C3Mapping = _Mappings[NTP.PropName];
switch (Node.Properties[NTP].getFieldTypeValue())
{
case CswEnumNbtFieldType.MOL:
if (false == string.IsNullOrEmpty(C3Mapping.C3ProductPropertyValue))
{
string propAttr = new CswPropIdAttr(Node, NTP).ToString();
string molData = C3Mapping.C3ProductPropertyValue;
CswNbtSdBlobData SdBlobData = new CswNbtSdBlobData(_CswNbtResources);
MolecularGraph Mol = MoleculeBuilder.CreateMolFromString(molData);
if (false == Mol.ContainsInvalidAtom())
{
string Href;
string FormattedMolString;
string errorMsg;
SdBlobData.saveMol(molData, propAttr, out Href, out FormattedMolString, out errorMsg, Node: Node);
}
else
{
_CswNbtResources.logMessage("Failed to save the MOL file for product with ProductId " + _ProductToImport.ProductId + " during the C3 import process because it contained an invalid atom.");
}
}
break;
default:
CswNbtSubField SubField = NTP.getFieldTypeRule().SubFields[(CswEnumNbtPropColumn)C3Mapping.NBTSubFieldPropColName];
if (null != SubField)
{
Node.Properties[NTP].SetSubFieldValue(SubField, C3Mapping.C3ProductPropertyValue);
}
break;
}
} //if( null != Node.Properties[NTP] && _Mappings.ContainsKey( NTP.PropName ) )
} //foreach( CswNbtMetaDataNodeTypeProp NTP in NodeType.getNodeTypeProps() )
} //addNodeTypeProps()
protected override void Context()
{
base.Context();
var moleculeBuilder1 = new MoleculeBuilder().WithName("Drug");
var formula1 = new ExplicitFormula("A+B");
formula1.AddObjectPath(new FormulaUsablePath("Sim1", "A", "B", "C").WithAlias("Same"));
moleculeBuilder1.DefaultStartFormula = formula1;
var moleculeBuilder2 = new MoleculeBuilder().WithName("Drug");
var formula2 = new ExplicitFormula("A+B");
formula2.AddObjectPath(new FormulaUsablePath("Sim2", "A", "B", "C").WithAlias("Same"));
moleculeBuilder2.DefaultStartFormula = formula2;
_object1 = moleculeBuilder1;
_object2 = moleculeBuilder2;
}
protected override void Context()
{
base.Context();
var moleculeBuilder1 = new MoleculeBuilder().WithName("Drug");
moleculeBuilder1.DefaultStartFormula = new ConstantFormula(0);
moleculeBuilder1.AddUsedCalculationMethod(new UsedCalculationMethod("Cat1", "CM1"));
moleculeBuilder1.AddUsedCalculationMethod(new UsedCalculationMethod("Cat2", "CM2"));
var moleculeBuilder2 = new MoleculeBuilder().WithName("Drug");
moleculeBuilder2.DefaultStartFormula = new ConstantFormula(0);
moleculeBuilder2.AddUsedCalculationMethod(new UsedCalculationMethod("Cat1", "CM1"));
moleculeBuilder2.AddUsedCalculationMethod(new UsedCalculationMethod("Cat2", "CM3"));
_object1 = moleculeBuilder1;
_object2 = moleculeBuilder2;
}
protected override void Context()
{
base.Context();
_comparerSettings.OnlyComputingRelevant = false;
var moleculeBuilder1 = new MoleculeBuilder().WithName("Drug");
moleculeBuilder1.DefaultStartFormula = new ConstantFormula(0);
moleculeBuilder1.IsFloating = false;
moleculeBuilder1.QuantityType = QuantityType.Drug;
var moleculeBuilder2 = new MoleculeBuilder().WithName("Drug");
moleculeBuilder2.DefaultStartFormula = new ConstantFormula(0);
moleculeBuilder2.IsFloating = true;
moleculeBuilder2.QuantityType = QuantityType.Metabolite;
_object1 = moleculeBuilder1;
_object2 = moleculeBuilder2;
}
protected override void Context()
{
base.Context();
var moleculeBuilder1 = new MoleculeBuilder().WithName("Drug");
var formula1 = new SumFormula();
formula1.Criteria = Create.Criteria(x => x.With("A").And.Not("B"));
formula1.Variable = "X";
moleculeBuilder1.DefaultStartFormula = formula1;
var moleculeBuilder2 = new MoleculeBuilder().WithName("Drug");
var formula2 = new SumFormula();
formula2.Criteria = Create.Criteria(x => x.With("A").And.With("B"));
formula2.Variable = "Y";
moleculeBuilder2.DefaultStartFormula = formula2;
_object1 = moleculeBuilder1;
_object2 = moleculeBuilder2;
}
protected override void Context()
{
base.Context();
_project = new MoBiProject();
var molecule = new MoleculeBuilder().WithName(_moleculeName);
var moleculeParameter = new Parameter().WithName(_moleculeParameterName);
molecule.Add(moleculeParameter);
var molecules = new MoleculeBuildingBlock()
{
molecule
};
_project.AddBuildingBlock(molecules);
var parameter = new Parameter().WithName(_parameterName);
var root = new Container().WithName(_topContainerName);
root.Add(parameter);
var spatialStructure = new MoBiSpatialStructure().WithTopContainer(root);
spatialStructure.GlobalMoleculeDependentProperties = new Container().WithName(Constants.MOLECULE_PROPERTIES);
spatialStructure.NeighborhoodsContainer = new Container().WithName(Constants.NEIGHBORHOODS);
_project.AddBuildingBlock(spatialStructure);
var reactionBuilder = new ReactionBuilder().WithName(_reactionName);
var reactions = new MoBiReactionBuildingBlock()
{
reactionBuilder
};
_project.AddBuildingBlock(reactions);
_project.AddSimulation(new MoBiSimulation().WithName(_simulationName));
var eventGroupBuilder = new EventGroupBuilder().WithName(_eventGroupName);
var eventGroupBuildingBlock = new EventGroupBuildingBlock();
eventGroupBuildingBlock.Add(eventGroupBuilder);
_project.AddBuildingBlock(eventGroupBuildingBlock);
A.CallTo(() => _context.CurrentProject).Returns(_project);
}
protected override void Context()
{
base.Context();
sut.SelectionPredicate = p => true;
var id = "mp";
var physical = new Container().WithName("PHYS").WithMode(ContainerMode.Physical);
var moleculeProperties = new Container().WithName(Constants.MOLECULE_PROPERTIES).WithParentContainer(physical);
var p1 = new Parameter().WithName("P1");
moleculeProperties.Add(p1);
var moleculeName = "Drug";
_moleculePropertiesDTO =
new DummyMoleculeContainerDTO()
{
MoleculePropertiesContainer = new ObjectBaseDTO().WithId(id)
}.WithId("ANY")
.WithName(moleculeName);
A.CallTo(() => _context.Get <IContainer>(id)).Returns(moleculeProperties);
var objectBaseRepository = A.Fake <IWithIdRepository>();
A.CallTo(() => _context.ObjectRepository).Returns(objectBaseRepository);
A.CallTo(() => objectBaseRepository.ContainsObjectWithId(id)).Returns(true);
A.CallTo(() => _parameterMapper.MapFrom(p1, A <IContainer> ._, A <IObjectBaseDTO> ._)).Returns(_dtoP1);
var project = A.Fake <IMoBiProject>();
var moleculeBuildingBlock = new MoleculeBuildingBlock();
var molecule = new MoleculeBuilder().WithName(moleculeName);
var localP = new Parameter().WithName("local").WithMode(ParameterBuildMode.Local).WithParentContainer(molecule);
var globalP =
new Parameter().WithName("global").WithMode(ParameterBuildMode.Global).WithParentContainer(molecule);
moleculeBuildingBlock.Add(molecule);
A.CallTo(() => project.MoleculeBlockCollection).Returns(new[] { moleculeBuildingBlock });
A.CallTo(() => _parameterMapper.MapFrom(localP, A <IContainer> ._, A <IObjectBaseDTO> ._)).Returns(_dtoPlocal);
A.CallTo(() => _parameterMapper.MapFrom(globalP, A <IContainer> ._, A <IObjectBaseDTO> ._)).Returns(_dtoPglobal);
A.CallTo(() => _context.CurrentProject).Returns(project);
}
protected override void Context()
{
base.Context();
var moleculeBuildingBlock1 = new MoleculeBuildingBlock().WithName("Tada");
var moleculeBuilderA = new MoleculeBuilder().WithName("DrugA");
var moleculeBuilderB = new MoleculeBuilder().WithName("DrugB");
moleculeBuildingBlock1.Add(moleculeBuilderA);
moleculeBuildingBlock1.Add(moleculeBuilderB);
var moleculeBuildingBlock2 = new MoleculeBuildingBlock().WithName("Tada");
moleculeBuilderA = new MoleculeBuilder().WithName("DrugA");
moleculeBuilderB = new MoleculeBuilder().WithName("DrugC");
moleculeBuildingBlock2.Add(moleculeBuilderA);
moleculeBuildingBlock2.Add(moleculeBuilderB);
_object1 = moleculeBuildingBlock1;
_object2 = moleculeBuildingBlock2;
}
protected override void Context()
{
base.Context();
_passiveTransports2 = new PassiveTransportBuildingBlock();
_project.AddBuildingBlock(_passiveTransports);
_project.AddBuildingBlock(_passiveTransports2);
_project.AddBuildingBlock(_molecules);
var anotherMoleculeWithPassiveTransport = new MoleculeBuilder().WithName("MOLECULE");
var molecules2 = new MoleculeBuildingBlock {
anotherMoleculeWithPassiveTransport
}.WithName("MBB2");
var samePassiveTransport = new TransportBuilder().WithName("PASSIVE TRANSPORT").WithFormula(A.Fake <IFormula>());
anotherMoleculeWithPassiveTransport.Add(samePassiveTransport);
A.CallTo(() => _formulaTask.FormulasAreTheSame(_passiveTransportKinetic, samePassiveTransport.Formula)).Returns(true);
A.CallTo(() => _cloneManagerForModel.Clone <ITransportBuilder>(_passiveTransport)).ReturnsLazily(x => new TransportBuilder().WithFormula(_passiveTransportKinetic));
A.CallTo(() => _containerTask.CreateUniqueName(_passiveTransports, A <string> ._, true)).ReturnsLazily(x => x.Arguments[1].ConvertedTo <string>());
_project.AddBuildingBlock(molecules2);
}
public void saveMol(string MolString, string PropId, out string Href, out string FormattedMolString, out string errorMsg, bool PostChanges = true, CswNbtNode Node = null)
{
CswPropIdAttr PropIdAttr = new CswPropIdAttr(PropId);
CswNbtMetaDataNodeTypeProp MetaDataProp = _CswNbtResources.MetaData.getNodeTypeProp(PropIdAttr.NodeTypePropId);
//Case 29769 - enforce correct mol file format
FormattedMolString = MoleculeBuilder.FormatMolFile(MolString);
errorMsg = string.Empty;
Href = string.Empty;
if (null == Node)
{
Node = _CswNbtResources.Nodes[PropIdAttr.NodeId];
}
if (null != Node)
{
CswNbtNodePropMol molProp = Node.Properties[MetaDataProp];
if (null != molProp)
{
molProp.setMol(FormattedMolString);
//If DirectStructureSearch is enabled, use the new code to generate an image. Otherwise, use the legacy code.
byte[] molImage =
(_CswNbtResources.Modules.IsModuleEnabled(CswEnumNbtModuleName.DirectStructureSearch) ?
_CswNbtResources.AcclDirect.GetImage(FormattedMolString) :
CswStructureSearch.GetImage(FormattedMolString));
CswNbtSdBlobData SdBlobData = new CswNbtSdBlobData(_CswNbtResources);
Href = CswNbtNodePropMol.getLink(molProp.JctNodePropId, Node.NodeId);
//Save the mol image to blob_data
SdBlobData.saveFile(PropId, molImage, CswNbtNodePropMol.MolImgFileContentType, CswNbtNodePropMol.MolImgFileName, out Href, Int32.MinValue, PostChanges, Node: Node);
//case 28364 - calculate fingerprint and save it
_CswNbtResources.StructureSearchManager.InsertFingerprintRecord(PropIdAttr.NodeId.PrimaryKey, FormattedMolString, out errorMsg);
}
}
}
protected override void Context()
{
base.Context();
_reactionBuildingBlock = new MoBiReactionBuildingBlock
{
DiagramModel = new DiagramModel(),
DiagramManager = new MoBiReactionDiagramManager()
};
_moBiReactionDiagramManager = _reactionBuildingBlock.DiagramManager.DowncastTo <IReactionDiagramManager <IMoBiReactionBuildingBlock> >();
_moBiReactionDiagramManager.InitializeWith(_reactionBuildingBlock, A.Fake <IDiagramOptions>());
_molecule = new MoleculeBuilder().WithId("moleculeId").WithName("moleculeName");
_reaction = new ReactionBuilder().WithId("reactionId");
_reaction.AddEduct(new ReactionPartnerBuilder(_molecule.Name, 1.0));
_reactionBuildingBlock.Add(_reaction);
_moBiReactionDiagramManager.AddObjectBase(_reaction);
_moBiReactionDiagramManager.AddMolecule(_reaction, "moleculeName");
_moleculeNode = _moBiReactionDiagramManager.GetMoleculeNodes("moleculeName").FirstOrDefault();
_reactionNode = _moBiReactionDiagramManager.PkModel.DiagramModel.GetAllChildren <ReactionNode>().FirstOrDefault();
_interactionTask = A.Fake <IInteractionTasksForChildren <IMoBiReactionBuildingBlock, IReactionBuilder> >();
_activeSubjectRetriever = A.Fake <IActiveSubjectRetriever>();
var reactionLink = new ReactionLink();
reactionLink.Initialize(ReactionLinkType.Educt, _reactionNode, _moleculeNode);
sut.Edit(_reactionBuildingBlock);
var removeReactionCommand = new RemoveCommandFor <IMoBiReactionBuildingBlock, IReactionBuilder>(_interactionTask, _moBiContext, _activeSubjectRetriever);
A.CallTo(() => _moBiContext.Get <IReactionBuilder>(_reaction.Id)).Returns(_reaction);
A.CallTo(() => _moBiContext.Resolve <RemoveCommandFor <IMoBiReactionBuildingBlock, IReactionBuilder> >()).Returns(removeReactionCommand);
A.CallTo(() => _activeSubjectRetriever.Active <IBuildingBlock>()).Returns(_reactionBuildingBlock);
A.CallTo(() => _interactionTask.Remove(_reaction, _reactionBuildingBlock, _reactionBuildingBlock, A <bool> ._)).Invokes(x => _reactionBuildingBlock.Remove(_reaction));
}
protected override void Context()
{
base.Context();
_moleculeStartValues = new MoleculeStartValuesBuildingBlock();
_moleculeStartValues.Add(new MoleculeStartValue {
Name = "drug", IsPresent = true
});
_moleculeStartValues.Add(new MoleculeStartValue {
Name = "molecule", IsPresent = true
});
_moleculeStartValues.Add(new MoleculeStartValue {
Name = "moleculeThatDoesNotExist", IsPresent = true
});
_moleculeStartValues.Add(new MoleculeStartValue {
Name = "moleculeThatDoesExistButNotPresent", IsPresent = false
});
_drug = new MoleculeBuilder().WithName("drug");
sut.Add(_drug);
_molecule = new MoleculeBuilder().WithName("molecule");
sut.Add(_molecule);
sut.Add(new MoleculeBuilder().WithName("moleculeThatDoesExistButNotPresent"));
}
