Examples with MembraneMapping cbit.vcell.mapping.MembraneMapping used on opensource projects

Example 6 with MembraneMapping

use of cbit.vcell.mapping.MembraneMapping in project vcell by virtualcell.

the class ElectricalCircuitGraph method getCircuitGraph.

/**
 * Insert the method's description here.
 * Creation date: (2/19/2002 11:24:04 AM)
 * @return cbit.vcell.mapping.potential.Graph
 * @param simContext cbit.vcell.mapping.SimulationContext
 */
public static Graph getCircuitGraph(SimulationContext simContext, AbstractMathMapping mathMapping) throws ExpressionException {
    Graph graph = new Graph();
    Model model = simContext.getModel();
    // 
    // add nodes to the graph (one for each Feature)
    // 
    Structure[] structures = model.getStructures();
    for (int i = 0; i < structures.length; i++) {
        if (structures[i] instanceof Feature) {
            graph.addNode(new Node(structures[i].getName(), structures[i]));
        }
    }
    // 
    // add edges for all current clamp electrodes (always have dependent voltages)
    // 
    ElectricalStimulus[] stimuli = simContext.getElectricalStimuli();
    Electrode groundElectrode = simContext.getGroundElectrode();
    for (int i = 0; i < stimuli.length; i++) {
        ElectricalStimulus stimulus = stimuli[i];
        // 
        // get electrodes
        // 
        Electrode probeElectrode = stimulus.getElectrode();
        if (probeElectrode == null) {
            throw new RuntimeException("null electrode for electrical stimulus");
        }
        if (groundElectrode == null) {
            throw new RuntimeException("null ground electrode for electrical stimulus");
        }
        // if (!membraneMapping.getResolved()){
        Node groundNode = graph.getNode(groundElectrode.getFeature().getName());
        Node probeNode = graph.getNode(probeElectrode.getFeature().getName());
        if (stimulus instanceof CurrentDensityClampStimulus) {
            CurrentDensityClampStimulus ccStimulus = (CurrentDensityClampStimulus) stimulus;
            ElectricalDevice device = new CurrentClampElectricalDevice(ccStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        } else if (stimulus instanceof TotalCurrentClampStimulus) {
            TotalCurrentClampStimulus ccStimulus = (TotalCurrentClampStimulus) stimulus;
            ElectricalDevice device = new CurrentClampElectricalDevice(ccStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        }
    // }
    }
    // 
    // add edges for all membranes
    // 
    ElectricalTopology electricalTopology = simContext.getModel().getElectricalTopology();
    for (int i = 0; i < structures.length; i++) {
        if (structures[i] instanceof Membrane) {
            Membrane membrane = (Membrane) structures[i];
            MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membrane);
            Feature positiveFeature = electricalTopology.getPositiveFeature(membrane);
            Feature negativeFeature = electricalTopology.getNegativeFeature(membrane);
            if (positiveFeature != null && negativeFeature != null) {
                Node insideNode = graph.getNode(positiveFeature.getName());
                Node outsideNode = graph.getNode(negativeFeature.getName());
                // 
                // getTotalMembraneCurrent() already converts to "outwardCurrent" so that same convention as voltage
                // 
                Expression currentSource = getTotalMembraneCurrent(simContext, membrane, mathMapping);
                MembraneElectricalDevice device = new MembraneElectricalDevice(membraneMapping, mathMapping);
                device.getParameterFromRole(ElectricalDevice.ROLE_TransmembraneCurrent).setExpression(currentSource);
                Edge edge = new Edge(insideNode, outsideNode, device);
                graph.addEdge(edge);
            }
        }
    }
    // 
    for (int i = 0; i < stimuli.length; i++) {
        ElectricalStimulus stimulus = stimuli[i];
        // 
        // get electrodes
        // 
        Electrode probeElectrode = stimulus.getElectrode();
        if (probeElectrode == null) {
            throw new RuntimeException("null electrode for electrical stimulus");
        }
        if (groundElectrode == null) {
            throw new RuntimeException("null ground electrode for electrical stimulus");
        }
        // if (!membraneMapping.getResolved()){
        Node groundNode = graph.getNode(groundElectrode.getFeature().getName());
        Node probeNode = graph.getNode(probeElectrode.getFeature().getName());
        if (stimulus instanceof VoltageClampStimulus) {
            VoltageClampStimulus vcStimulus = (VoltageClampStimulus) stimulus;
            ElectricalDevice device = new VoltageClampElectricalDevice(vcStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        }
    // }
    }
    // System.out.println(graph);
    return graph;
}

Example 7 with MembraneMapping

use of cbit.vcell.mapping.MembraneMapping in project vcell by virtualcell.

the class MathMapping_4_8 method getResidualVolumeFraction.

public Expression getResidualVolumeFraction(FeatureMapping featureMapping) throws ExpressionException {
    Expression exp = new Expression(1.0);
    Structure[] structures = simContext.getGeometryContext().getModel().getStructures();
    StructureTopology structTopology = simContext.getModel().getStructureTopology();
    for (int i = 0; i < structures.length; i++) {
        // 
        // for each membrane that is distributed within this feature, subtract that volume fraction
        // ????? beware, 1 - v1 - v2 ... can result in a negative number if we're not careful.
        // 
        Structure struct = structures[i];
        if (struct instanceof Membrane) {
            if ((structTopology.getOutsideFeature((Membrane) struct)) == featureMapping.getFeature()) {
                MembraneMapping mm = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(struct);
                if (getResolved(mm) == false) {
                    exp = Expression.add(exp, Expression.negate(new Expression(mm.getVolumeFractionParameter(), simContext.getNameScope())));
                }
            }
        }
    }
    return exp;
}

Example 8 with MembraneMapping

use of cbit.vcell.mapping.MembraneMapping in project vcell by virtualcell.

the class MathMapping_4_8 method refreshKFluxParameters.

/**
 * Insert the method's description here.
 * Creation date: (6/13/2004 8:10:34 AM)
 */
private void refreshKFluxParameters() throws ExpressionException {
    MathMapping_4_8.MathMappingParameter[] newMathMappingParameters = (MathMappingParameter[]) fieldMathMappingParameters.clone();
    // 
    for (int i = 0; i < newMathMappingParameters.length; i++) {
        if (newMathMappingParameters[i].getRole() == PARAMETER_ROLE_KFLUX) {
            newMathMappingParameters = (MathMappingParameter[]) BeanUtils.removeElement(newMathMappingParameters, newMathMappingParameters[i]);
        }
    }
    // 
    // Add new KFlux Parameters
    // 
    StructureMapping[] structureMappings = simContext.getGeometryContext().getStructureMappings();
    StructureTopology structTopology = simContext.getModel().getStructureTopology();
    VCUnitDefinition lengthInverseUnit = simContext.getModel().getX().getUnitDefinition().getInverse();
    for (int i = 0; i < structureMappings.length; i++) {
        if (structureMappings[i] instanceof MembraneMapping && !getResolved(structureMappings[i])) {
            MembraneMapping membraneMapping = (MembraneMapping) structureMappings[i];
            // 
            // add "inside" flux correction
            // 
            Expression insideCorrectionExp = getInsideFluxCorrectionExpression(membraneMapping);
            insideCorrectionExp.bindExpression(this);
            Membrane memMappingMembrane = membraneMapping.getMembrane();
            Feature insideFeature = structTopology.getInsideFeature(memMappingMembrane);
            String membraneNameWithScope = membraneMapping.getNameScope().getName();
            String insideName = "KFlux_" + membraneNameWithScope + "_" + insideFeature.getNameScope().getName();
            KFluxParameter insideKFluxParameter = new KFluxParameter(insideName, insideCorrectionExp, lengthInverseUnit, membraneMapping, insideFeature);
            newMathMappingParameters = (MathMappingParameter[]) BeanUtils.addElement(newMathMappingParameters, insideKFluxParameter);
            // 
            // add "outside" flux correction
            // 
            Expression outsideCorrectionExp = getOutsideFluxCorrectionExpression(simContext, membraneMapping);
            outsideCorrectionExp.bindExpression(this);
            Feature outsideFeature = structTopology.getOutsideFeature(memMappingMembrane);
            String outsideName = "KFlux_" + membraneNameWithScope + "_" + outsideFeature.getNameScope().getName();
            KFluxParameter outsideKFluxParameter = new KFluxParameter(outsideName, outsideCorrectionExp, lengthInverseUnit, membraneMapping, outsideFeature);
            newMathMappingParameters = (MathMappingParameter[]) BeanUtils.addElement(newMathMappingParameters, outsideKFluxParameter);
        }
    }
    try {
        setMathMapppingParameters(newMathMappingParameters);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage());
    }
}

Example 9 with MembraneMapping

use of cbit.vcell.mapping.MembraneMapping in project vcell by virtualcell.

the class MathMapping_4_8 method getStructures.

public Structure[] getStructures(SubVolume subVolume) {
    ArrayList<Structure> list = new ArrayList<Structure>();
    StructureMapping[] structureMappings = simContext.getGeometryContext().getStructureMappings();
    // 
    for (int i = 0; i < structureMappings.length; i++) {
        StructureMapping sm = structureMappings[i];
        if (sm instanceof FeatureMapping && ((FeatureMapping) sm).getGeometryClass() == subVolume) {
            list.add(sm.getStructure());
        }
    }
    // 
    for (int i = 0; i < structureMappings.length; i++) {
        StructureMapping sm = structureMappings[i];
        if (sm instanceof MembraneMapping) {
            Membrane membrane = ((MembraneMapping) sm).getMembrane();
            if (list.contains(simContext.getModel().getStructureTopology().getInsideFeature(membrane))) {
                list.add(membrane);
            }
        }
    }
    if (list.size() > 0) {
        return list.toArray(new Structure[list.size()]);
    } else {
        return null;
    }
}

Example 10 with MembraneMapping

use of cbit.vcell.mapping.MembraneMapping in project vcell by virtualcell.

the class MathMapping_4_8 method getMathSymbol0.

/**
 * Substitutes appropriate variables for speciesContext bindings
 *
 * @return cbit.vcell.parser.Expression
 * @param origExp cbit.vcell.parser.Expression
 * @param structureMapping cbit.vcell.mapping.StructureMapping
 */
private String getMathSymbol0(SymbolTableEntry ste, StructureMapping structureMapping) throws MappingException {
    String steName = ste.getName();
    if (ste instanceof Kinetics.KineticsParameter) {
        Integer count = localNameCountHash.get(steName);
        if (count == null) {
            throw new MappingException("KineticsParameter " + steName + " not found in local name count");
        }
        if (count > 1 || steName.equals("J")) {
            return steName + "_" + ste.getNameScope().getName();
        // return getNameScope().getSymbolName(ste);
        } else {
            return steName;
        }
    }
    if (ste instanceof MathMapping_4_8.ProbabilityParameter) {
        // be careful here, to see if we need mangle the reaction name
        MathMapping_4_8.ProbabilityParameter probParm = (MathMapping_4_8.ProbabilityParameter) ste;
        return probParm.getName();
    }
    if (ste instanceof MathMapping_4_8.SpeciesConcentrationParameter) {
        MathMapping_4_8.SpeciesConcentrationParameter concParm = (MathMapping_4_8.SpeciesConcentrationParameter) ste;
        return concParm.getSpeciesContextSpec().getSpeciesContext().getName() + MATH_FUNC_SUFFIX_SPECIES_CONCENTRATION;
    }
    if (ste instanceof MathMapping_4_8.SpeciesCountParameter) {
        MathMapping_4_8.SpeciesCountParameter countParm = (MathMapping_4_8.SpeciesCountParameter) ste;
        return countParm.getSpeciesContextSpec().getSpeciesContext().getName() + MATH_VAR_SUFFIX_SPECIES_COUNT;
    }
    if (ste instanceof MathMapping_4_8.EventAssignmentInitParameter) {
        MathMapping_4_8.EventAssignmentInitParameter eventInitParm = (MathMapping_4_8.EventAssignmentInitParameter) ste;
        return eventInitParm.getName() + MATH_FUNC_SUFFIX_EVENTASSIGN_INIT;
    }
    if (ste instanceof Model.ReservedSymbol) {
        return steName;
    }
    if (ste instanceof Membrane.MembraneVoltage) {
        return steName;
    }
    if (ste instanceof Structure.StructureSize) {
        Structure structure = ((Structure.StructureSize) ste).getStructure();
        StructureMapping.StructureMappingParameter sizeParameter = simContext.getGeometryContext().getStructureMapping(structure).getSizeParameter();
        return getMathSymbol(sizeParameter, structureMapping);
    }
    if (ste instanceof ProxyParameter) {
        ProxyParameter pp = (ProxyParameter) ste;
        return getMathSymbol0(pp.getTarget(), structureMapping);
    }
    // 
    Model model = simContext.getModel();
    if (ste instanceof ModelParameter) {
        ModelParameter mp = (ModelParameter) ste;
        if (simContext.getGeometry().getDimension() == 0) {
            return mp.getName();
        } else {
            if (mp.getExpression().getSymbols() == null) {
                return mp.getName();
            }
            // check if global param variant name exists in globalVarsHash. If so, return it, else, throw exception.
            Hashtable<String, Expression> smVariantsHash = globalParamVariantsHash.get(mp);
            String variantName = mp.getName() + "_" + TokenMangler.fixTokenStrict(structureMapping.getStructure().getName());
            if (smVariantsHash.get(variantName) != null) {
                return variantName;
            } else {
                // global param variant doesn't exist in the hash, so get the substituted expression for global param and
                // gather all symbols (speciesContexts) that do not match with arg 'structureMapping' to display a proper error message.
                Expression expr = null;
                try {
                    expr = substituteGlobalParameters(mp.getExpression());
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException("Could not substitute expression for global parameter '" + mp.getName() + "' with expression '" + "'" + e.getMessage());
                }
                // find symbols (typically speciesContexts) in 'exp' that do not match with the arg 'structureMapping'
                String[] symbols = expr.getSymbols();
                String msg = "";
                if (symbols != null) {
                    Vector<String> spContextNamesVector = new Vector<String>();
                    for (int j = 0; j < symbols.length; j++) {
                        SpeciesContext sc = model.getSpeciesContext(symbols[j]);
                        if (sc != null) {
                            if (!sc.getStructure().compareEqual(structureMapping.getStructure())) {
                                spContextNamesVector.addElement(sc.getName());
                            }
                        }
                    }
                    for (int i = 0; (spContextNamesVector != null && i < spContextNamesVector.size()); i++) {
                        if (i == 0) {
                            msg += "'" + spContextNamesVector.elementAt(i) + ", ";
                        } else if (i == spContextNamesVector.size() - 1) {
                            msg += spContextNamesVector.elementAt(i) + "'";
                        } else {
                            msg += spContextNamesVector.elementAt(i) + ", ";
                        }
                    }
                }
                throw new RuntimeException("Global parameter '" + mp.getName() + "' is not defined in compartment '" + structureMapping.getStructure().getName() + "', but was referenced in that compartment." + "\n\nExpression '" + mp.getExpression().infix() + "' for global parameter '" + mp.getName() + "' expands to '" + expr.infix() + "' " + "and contains species " + msg + " that is/are not in adjacent compartments.");
            }
        // return (mp.getName()+"_"+TokenMangler.fixTokenStrict(structureMapping.getStructure().getName()));
        }
    }
    if (ste instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
        SpeciesContextSpec.SpeciesContextSpecParameter scsParm = (SpeciesContextSpec.SpeciesContextSpecParameter) ste;
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_InitialConcentration) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + MATH_FUNC_SUFFIX_SPECIES_INIT_CONCENTRATION;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_InitialCount) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + MATH_FUNC_SUFFIX_SPECIES_INIT_COUNT;
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_DiffusionRate) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_diffusionRate";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueXm) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryXm";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueXp) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryXp";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueYm) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryYm";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueYp) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryYp";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueZm) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryZm";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_BoundaryValueZp) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_boundaryZp";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityX) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_velocityX";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityY) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_velocityY";
        }
        if (scsParm.getRole() == SpeciesContextSpec.ROLE_VelocityZ) {
            return ((SpeciesContextSpec) (scsParm.getNameScope().getScopedSymbolTable())).getSpeciesContext().getName() + "_velocityZ";
        }
    }
    if (ste instanceof ElectricalDevice.ElectricalDeviceParameter) {
        ElectricalDevice.ElectricalDeviceParameter edParm = (ElectricalDevice.ElectricalDeviceParameter) ste;
        ElectricalDevice electricalDevice = (ElectricalDevice) edParm.getNameScope().getScopedSymbolTable();
        if (electricalDevice instanceof MembraneElectricalDevice) {
            String nameWithScope = ((MembraneElectricalDevice) electricalDevice).getMembraneMapping().getMembrane().getNameScope().getName();
            if (edParm.getRole() == ElectricalDevice.ROLE_TotalCurrent) {
                return "I_" + nameWithScope;
            }
            if (edParm.getRole() == ElectricalDevice.ROLE_TransmembraneCurrent) {
                return "F_" + nameWithScope;
            }
        // }else if (electricalDevice instanceof CurrentClampElectricalDevice) {
        // if (edParm.getRole()==ElectricalDevice.ROLE_TotalCurrentDensity){
        // return "I_"+((CurrentClampElectricalDevice)electricalDevice).getCurrentClampStimulus().getNameScope().getName();
        // }
        // if (edParm.getRole()==ElectricalDevice.ROLE_TransmembraneCurrentDensity){
        // return "F_"+((CurrentClampElectricalDevice)electricalDevice).getCurrentClampStimulus().getNameScope().getName();
        // }
        // }else if (electricalDevice instanceof VoltageClampElectricalDevice) {
        // if (edParm.getRole()==ElectricalDevice.ROLE_TotalCurrentDensity){
        // return "I_"+((VoltageClampElectricalDevice)electricalDevice).getVoltageClampStimulus().getNameScope().getName();
        // }
        // if (edParm.getRole()==ElectricalDevice.ROLE_TransmembraneCurrentDensity){
        // return "F_"+((VoltageClampElectricalDevice)electricalDevice).getVoltageClampStimulus().getNameScope().getName();
        // }
        }
    }
    if (ste instanceof LocalParameter && ((LocalParameter) ste).getNameScope() instanceof ElectricalStimulus.ElectricalStimulusNameScope) {
        LocalParameter esParm = (LocalParameter) ste;
        String nameWithScope = esParm.getNameScope().getName();
        if (esParm.getRole() == ElectricalStimulusParameterType.TotalCurrent) {
            return "I_" + nameWithScope;
        } else if (esParm.getRole() == ElectricalStimulusParameterType.Voltage) {
            return "V_" + nameWithScope;
        }
    }
    StructureTopology structTopology = model.getStructureTopology();
    if (ste instanceof StructureMapping.StructureMappingParameter) {
        StructureMapping.StructureMappingParameter smParm = (StructureMapping.StructureMappingParameter) ste;
        Structure structure = ((StructureMapping) (smParm.getNameScope().getScopedSymbolTable())).getStructure();
        int role = smParm.getRole();
        if (role == StructureMapping.ROLE_VolumeFraction) {
            return "VolFract_" + (structTopology.getInsideFeature((Membrane) structure)).getNameScope().getName();
        } else {
            String nameWithScope = structure.getNameScope().getName();
            if (role == StructureMapping.ROLE_SurfaceToVolumeRatio) {
                return "SurfToVol_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_InitialVoltage) {
                return smParm.getName();
            } else if (role == StructureMapping.ROLE_SpecificCapacitance) {
                return "C_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_AreaPerUnitArea) {
                return "AreaPerUnitArea_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_AreaPerUnitVolume) {
                return "AreaPerUnitVolume_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_VolumePerUnitArea) {
                return "VolumePerUnitArea_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_VolumePerUnitVolume) {
                return "VolumePerUnitVolume_" + nameWithScope;
            } else if (role == StructureMapping.ROLE_Size) {
                if (simContext.getGeometry().getDimension() == 0) {
                    // if geometry is compartmental, make sure compartment sizes are set if referenced in model.
                    if (smParm.getExpression() == null || smParm.getExpression().isZero()) {
                        throw new MappingException("\nIn non-spatial application '" + getSimulationContext().getName() + "', " + "size of structure '" + structure.getName() + "' must be assigned a " + "positive value if referenced in the model.\n\nPlease go to 'Structure Mapping' tab to check the size.");
                    }
                }
                return "Size_" + nameWithScope;
            }
        }
    }
    // 
    if (ste instanceof SpeciesContext) {
        SpeciesContext sc = (SpeciesContext) ste;
        SpeciesContextMapping scm = getSpeciesContextMapping(sc);
        // 
        if (structureMapping instanceof FeatureMapping) {
            // 
            if (scm.getVariable() != null && !scm.getVariable().getName().equals(steName)) {
                return scm.getVariable().getName();
            }
        // 
        // for reactions within a spatially resolved membrane, may need "_INSIDE" or "_OUTSIDE" for jump condition
        // 
        // if the membrane is distributed, then always use the plain variable.
        // 
        } else if (structureMapping instanceof MembraneMapping) {
            Membrane membrane = ((MembraneMapping) structureMapping).getMembrane();
            // 
            if (sc.getStructure() instanceof Membrane || getResolved(structureMapping) == false) {
                if (scm.getVariable() != null && !(scm.getVariable().getName().equals(steName))) {
                    return scm.getVariable().getName();
                }
            // 
            // if the speciesContext is outside the membrane
            // 
            } else {
                SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
                if (sc.getStructure() == structTopology.getInsideFeature(membrane) || sc.getStructure() == structTopology.getOutsideFeature(membrane)) {
                    if (getResolved(structureMapping) && !scs.isConstant()) {
                        if (!scs.isDiffusing()) {
                            throw new MappingException("Enable diffusion in Application '" + simContext.getName() + "'. This must be done for any species (e.g '" + sc.getName() + "') in flux reactions.\n\n" + "To save or run simulations, set the diffusion rate to a non-zero " + "value in Initial Conditions or disable those reactions in Specifications->Reactions.");
                        }
                        return scm.getVariable().getName() + (sc.getStructure() == structTopology.getInsideFeature(membrane) ? "_INSIDE" : "_OUTSIDE");
                    } else {
                        return scm.getSpeciesContext().getName();
                    }
                } else {
                    throw new MappingException(sc.getName() + " shouldn't be involved with structure " + structureMapping.getStructure().getName());
                }
            }
        }
    }
    return getNameScope().getSymbolName(ste);
}