Examples with SpeciesContext cbit.vcell.model.SpeciesContext used on opensource projects

Example 96 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class MembraneStructureAnalyzer method refreshResolvedFluxes.

/**
 * This method was created in VisualAge.
 */
void refreshResolvedFluxes() throws Exception {
    // System.out.println("MembraneStructureAnalyzer.refreshResolvedFluxes()");
    GeometryContext geoContext = mathMapping_4_8.getSimulationContext().getGeometryContext();
    StructureTopology structTopology = mathMapping_4_8.getSimulationContext().getModel().getStructureTopology();
    Vector<ResolvedFlux> resolvedFluxList = new Vector<ResolvedFlux>();
    // 
    // for each reaction, get all fluxReactions associated with this membrane
    // 
    Vector<ReactionStep> fluxList = new Vector<ReactionStep>();
    ReactionSpec[] reactionSpecs = mathMapping_4_8.getSimulationContext().getReactionContext().getReactionSpecs();
    for (int j = 0; j < reactionSpecs.length; j++) {
        if (reactionSpecs[j].isExcluded()) {
            continue;
        }
        ReactionStep rs = reactionSpecs[j].getReactionStep();
        if (rs.getStructure() == getMembrane()) {
            if (rs instanceof FluxReaction) {
                fluxList.addElement(rs);
            }
        }
    }
    // 
    for (int i = 0; i < fluxList.size(); i++) {
        FluxReaction fr = (FluxReaction) fluxList.elementAt(i);
        Species fluxCarrier = null;
        for (ReactionParticipant rp : fr.getReactionParticipants()) {
            if (rp instanceof Reactant || rp instanceof Product) {
                if (fluxCarrier == null) {
                    fluxCarrier = rp.getSpecies();
                } else {
                    if (fluxCarrier != rp.getSpecies()) {
                        throw new Exception("Flux reaction '" + fr.getName() + "' with multiple species not allowed in VCell 4.8.");
                    }
                }
            }
        }
        if (fluxCarrier == null) {
            continue;
        }
        ResolvedFlux rf = null;
        for (int j = 0; j < resolvedFluxList.size(); j++) {
            ResolvedFlux rf_tmp = (ResolvedFlux) resolvedFluxList.elementAt(j);
            if (rf_tmp.getSpecies() == fluxCarrier) {
                rf = rf_tmp;
            }
        }
        // 
        // if "inside" speciesContext is not "fixed", add flux to ResolvedFlux
        // 
        SpeciesContext insideSpeciesContext = mathMapping_4_8.getSimulationContext().getModel().getSpeciesContext(fluxCarrier, structTopology.getInsideFeature(getMembrane()));
        SpeciesContextSpec insideSpeciesContextSpec = mathMapping_4_8.getSimulationContext().getReactionContext().getSpeciesContextSpec(insideSpeciesContext);
        // if (!insideSpeciesContextSpec.isConstant()){
        if (bNoFluxIfFixed || !insideSpeciesContextSpec.isConstant()) {
            if (bNoFluxIfFixed && insideSpeciesContextSpec.isConstant()) {
                bNoFluxIfFixedExercised = true;
            }
            if (rf == null) {
                rf = new ResolvedFlux(fluxCarrier, fr.getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate).getUnitDefinition());
                resolvedFluxList.addElement(rf);
            }
            FeatureMapping insideFeatureMapping = (FeatureMapping) geoContext.getStructureMapping((structTopology.getInsideFeature((Membrane) fr.getStructure())));
            Expression residualVolumeFraction = mathMapping_4_8.getResidualVolumeFraction(insideFeatureMapping).renameBoundSymbols(mathMapping_4_8.getNameScope());
            Expression insideFluxCorrection = Expression.invert(residualVolumeFraction);
            // 
            if (bResolvedFluxCorrectionBug && !residualVolumeFraction.compareEqual(new Expression(1.0))) {
                bResolvedFluxCorrectionBugExercised = true;
                System.out.println("MembraneStructureAnalyzer.refreshResolvedFluxes() ... 'ResolvedFluxCorrection' bug compatability mode");
                insideFluxCorrection = new Expression(1.0);
            }
            // 
            if (fr.getKinetics() instanceof DistributedKinetics) {
                Expression reactionRateParameter = new Expression(((DistributedKinetics) fr.getKinetics()).getReactionRateParameter(), mathMapping_4_8.getNameScope());
                if (rf.inFluxExpression.isZero()) {
                    rf.inFluxExpression = Expression.mult(reactionRateParameter, insideFluxCorrection).flatten();
                } else {
                    rf.inFluxExpression = Expression.add(rf.inFluxExpression, Expression.mult(reactionRateParameter, insideFluxCorrection).flatten());
                }
            } else if (fr.getKinetics() instanceof LumpedKinetics) {
                throw new RuntimeException("Lumped Kinetics for fluxes not yet supported");
            } else {
                throw new RuntimeException("unexpected Kinetic type in MembraneStructureAnalyzer.refreshResolvedFluxes()");
            }
        // rf.inFlux.bindExpression(mathMapping);
        }
        SpeciesContext outsideSpeciesContext = mathMapping_4_8.getSimulationContext().getModel().getSpeciesContext(fluxCarrier, structTopology.getOutsideFeature(getMembrane()));
        SpeciesContextSpec outsideSpeciesContextSpec = mathMapping_4_8.getSimulationContext().getReactionContext().getSpeciesContextSpec(outsideSpeciesContext);
        // if (!outsideSpeciesContextSpec.isConstant()){
        if (bNoFluxIfFixed || !outsideSpeciesContextSpec.isConstant()) {
            if (bNoFluxIfFixed && outsideSpeciesContextSpec.isConstant()) {
                bNoFluxIfFixedExercised = true;
            }
            if (rf == null) {
                rf = new ResolvedFlux(fluxCarrier, fr.getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate).getUnitDefinition());
                resolvedFluxList.addElement(rf);
            }
            FeatureMapping outsideFeatureMapping = (FeatureMapping) geoContext.getStructureMapping(structTopology.getOutsideFeature((Membrane) fr.getStructure()));
            Expression residualVolumeFraction = mathMapping_4_8.getResidualVolumeFraction(outsideFeatureMapping).renameBoundSymbols(mathMapping_4_8.getNameScope());
            Expression outsideFluxCorrection = Expression.invert(residualVolumeFraction);
            // 
            if (bResolvedFluxCorrectionBug && !residualVolumeFraction.compareEqual(new Expression(1.0))) {
                bResolvedFluxCorrectionBugExercised = true;
                System.out.println("MembraneStructureAnalyzer.refreshResolvedFluxes() ... 'ResolvedFluxCorrection' bug compatability mode");
                outsideFluxCorrection = new Expression(1.0);
            }
            // 
            if (fr.getKinetics() instanceof DistributedKinetics) {
                Expression reactionRateParameter = new Expression(((DistributedKinetics) fr.getKinetics()).getReactionRateParameter(), mathMapping_4_8.getNameScope());
                if (rf.outFluxExpression.isZero()) {
                    rf.outFluxExpression = Expression.mult(Expression.negate(reactionRateParameter), outsideFluxCorrection).flatten();
                } else {
                    rf.outFluxExpression = Expression.add(rf.outFluxExpression, Expression.mult(Expression.negate(reactionRateParameter), outsideFluxCorrection).flatten());
                }
            } else if (fr.getKinetics() instanceof LumpedKinetics) {
                throw new RuntimeException("Lumped Kinetics not yet supported for Flux Reaction: " + fr.getName());
            } else {
                throw new RuntimeException("unexpected Kinetics type for Flux Reaction " + fr.getName());
            }
        // rf.outFlux.bindExpression(mathMapping);
        }
    }
    // 
    // for each reaction, incorporate all reactionSteps involving binding with volumetric species
    // 
    double kMoleValue = 1 / 602.0;
    for (int i = 0; i < reactionSpecs.length; i++) {
        if (reactionSpecs[i].isExcluded()) {
            continue;
        }
        ReactionStep rs = reactionSpecs[i].getReactionStep();
        if (rs.getStructure() == getMembrane()) {
            if (rs instanceof SimpleReaction) {
                SimpleReaction sr = (SimpleReaction) rs;
                ReactionParticipant[] rp_Array = sr.getReactionParticipants();
                for (int k = 0; k < rp_Array.length; k++) {
                    if (rp_Array[k] instanceof Reactant || rp_Array[k] instanceof Product) {
                        SpeciesContextSpec scs = mathMapping_4_8.getSimulationContext().getReactionContext().getSpeciesContextSpec(rp_Array[k].getSpeciesContext());
                        // if (rp_Array[k].getStructure() instanceof Feature && !scs.isConstant()){
                        if (rp_Array[k].getStructure() instanceof Feature && (bNoFluxIfFixed || !scs.isConstant())) {
                            if (bNoFluxIfFixed && scs.isConstant()) {
                                bNoFluxIfFixedExercised = true;
                            }
                            // 
                            // for each Reactant or Product binding to this membrane...
                            // 
                            // 
                            // get ResolvedFlux for this species
                            // 
                            ResolvedFlux rf = null;
                            for (int j = 0; j < resolvedFluxList.size(); j++) {
                                ResolvedFlux rf_tmp = (ResolvedFlux) resolvedFluxList.elementAt(j);
                                if (rf_tmp.getSpecies() == rp_Array[k].getSpecies()) {
                                    rf = rf_tmp;
                                }
                            }
                            if (rf == null) {
                                rf = new ResolvedFlux(rp_Array[k].getSpecies(), sr.getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate).getUnitDefinition());
                                resolvedFluxList.addElement(rf);
                            }
                            Expression reactionRateExpression = getReactionRateExpression(sr, rp_Array[k]).renameBoundSymbols(mathMapping_4_8.getNameScope());
                            if (rp_Array[k].getStructure() == structTopology.getInsideFeature(getMembrane())) {
                                // 
                                // for binding on inside, add to ResolvedFlux.inFlux
                                // 
                                FeatureMapping insideFeatureMapping = (FeatureMapping) geoContext.getStructureMapping(structTopology.getInsideFeature(getMembrane()));
                                Expression residualVolumeFraction = mathMapping_4_8.getResidualVolumeFraction(insideFeatureMapping).renameBoundSymbols(mathMapping_4_8.getNameScope());
                                Expression insideFluxCorrection = Expression.div(new Expression(kMoleValue), residualVolumeFraction).flatten();
                                // 
                                if (bResolvedFluxCorrectionBug && !residualVolumeFraction.compareEqual(new Expression(1.0))) {
                                    bResolvedFluxCorrectionBugExercised = true;
                                    System.out.println("MembraneStructureAnalyzer.refreshResolvedFluxes() ... 'ResolvedFluxCorrection' bug compatability mode");
                                    insideFluxCorrection = new Expression(kMoleValue);
                                }
                                if (rf.inFluxExpression.isZero()) {
                                    rf.inFluxExpression = Expression.mult(insideFluxCorrection, reactionRateExpression);
                                } else {
                                    rf.inFluxExpression = Expression.add(rf.inFluxExpression, Expression.mult(insideFluxCorrection, reactionRateExpression));
                                }
                            // rf.inFlux.bindExpression(mathMapping);
                            } else if (rp_Array[k].getStructure() == structTopology.getOutsideFeature(getMembrane())) {
                                // 
                                // for binding on outside, add to ResolvedFlux.outFlux
                                // 
                                FeatureMapping outsideFeatureMapping = (FeatureMapping) geoContext.getStructureMapping(structTopology.getOutsideFeature(getMembrane()));
                                Expression residualVolumeFraction = mathMapping_4_8.getResidualVolumeFraction(outsideFeatureMapping).renameBoundSymbols(mathMapping_4_8.getNameScope());
                                Expression outsideFluxCorrection = Expression.div(new Expression(kMoleValue), residualVolumeFraction).flatten();
                                // 
                                if (bResolvedFluxCorrectionBug && !residualVolumeFraction.compareEqual(new Expression(1.0))) {
                                    bResolvedFluxCorrectionBugExercised = true;
                                    System.out.println("MembraneStructureAnalyzer.refreshResolvedFluxes() ... 'ResolvedFluxCorrection' bug compatability mode");
                                    outsideFluxCorrection = new Expression(kMoleValue);
                                }
                                if (rf.outFluxExpression.isZero()) {
                                    rf.outFluxExpression = Expression.mult(outsideFluxCorrection, reactionRateExpression);
                                } else {
                                    rf.outFluxExpression = Expression.add(rf.outFluxExpression, Expression.mult(outsideFluxCorrection, reactionRateExpression));
                                }
                            // rf.outFlux.bindExpression(mathMapping);
                            } else {
                                throw new Exception("SpeciesContext " + rp_Array[k].getSpeciesContext().getName() + " doesn't border membrane " + getMembrane().getName() + " but reacts there");
                            }
                        }
                    }
                }
            }
        }
    }
    // 
    if (resolvedFluxList.size() > 0) {
        resolvedFluxes = new ResolvedFlux[resolvedFluxList.size()];
        resolvedFluxList.copyInto(resolvedFluxes);
    } else {
        resolvedFluxes = null;
    }
}

Example 97 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class StochMathMapping_4_8 method getSubstitutedExpr.

/**
 * @param expr
 * @param bConcentration
 * @return
 * @throws ExpressionException
 */
private Expression getSubstitutedExpr(Expression expr, boolean bConcentration, boolean bIsInitialCondn) throws ExpressionException {
    expr = new Expression(expr);
    String[] symbols = expr.getSymbols();
    // Check if 'expr' has other speciesContexts in its expression, need to replace it with 'spContext_init'
    for (int j = 0; symbols != null && j < symbols.length; j++) {
        // if symbol is a speciesContext, replacing it with a reference to initial condition for that speciesContext.
        SpeciesContext spC = null;
        SymbolTableEntry ste = expr.getSymbolBinding(symbols[j]);
        if (ste instanceof ProxyParameter) {
            // if expression is for speciesContextSpec or Kinetics, ste will be a ProxyParameter instance.
            ProxyParameter spspp = (ProxyParameter) ste;
            if (spspp.getTarget() instanceof SpeciesContext) {
                spC = (SpeciesContext) spspp.getTarget();
            }
        } else if (ste instanceof SpeciesContext) {
            // if expression is for a global parameter, ste will be a SpeciesContext instance.
            spC = (SpeciesContext) ste;
        }
        if (spC != null) {
            SpeciesContextSpec spcspec = getSimulationContext().getReactionContext().getSpeciesContextSpec(spC);
            Parameter spCParm = null;
            if (bConcentration && bIsInitialCondn) {
                // speciesContext has initConcentration set, so need to replace 'spContext' in 'expr' 'spContext_init'
                spCParm = spcspec.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
            } else if (!bConcentration && bIsInitialCondn) {
                // speciesContext has initCount set, so need to replace 'spContext' in 'expr' 'spContext_initCount'
                spCParm = spcspec.getParameterFromRole(SpeciesContextSpec.ROLE_InitialCount);
            } else if (bConcentration && !bIsInitialCondn) {
                // need to replace 'spContext' in 'expr' 'spContext_Conc'
                spCParm = getSpeciesConcentrationParameter(spC);
            } else if (!bConcentration && !bIsInitialCondn) {
                // need to replace 'spContext' in 'expr' 'spContext_Count'
                spCParm = getSpeciesCountParameter(spC);
            }
            // need to get init condn expression, but can't get it from getMathSymbol() (mapping between bio and math), hence get it as below.
            Expression scsInitExpr = new Expression(spCParm, getNameScope());
            // scsInitExpr.bindExpression(this);
            expr.substituteInPlace(new Expression(spC.getName()), scsInitExpr);
        }
    }
    return expr;
}

Example 98 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class StochMathMapping_4_8 method refreshMathDescription.

/**
 * set up a math description based on current simulationContext.
 */
private void refreshMathDescription() throws MappingException, MatrixException, MathException, ExpressionException, ModelException {
    // use local variable instead of using getter all the time.
    SimulationContext simContext = getSimulationContext();
    // local structure mapping list
    StructureMapping[] structureMappings = simContext.getGeometryContext().getStructureMappings();
    // We have to check if all the reactions are able to tranform to stochastic jump processes before generating the math.
    String stochChkMsg = simContext.getModel().isValidForStochApp();
    if (!(stochChkMsg.equals(""))) {
        throw new ModelException("Problem updating math description: " + simContext.getName() + "\n" + stochChkMsg);
    }
    // All sizes must be set for new ODE models and ratios must be set for old ones.
    simContext.checkValidity();
    // 
    // verify that all structures are mapped to subvolumes and all subvolumes are mapped to a structure
    // 
    Structure[] structures = simContext.getGeometryContext().getModel().getStructures();
    for (int i = 0; i < structures.length; i++) {
        StructureMapping sm = simContext.getGeometryContext().getStructureMapping(structures[i]);
        if (sm == null || (sm instanceof FeatureMapping && getSubVolume(((FeatureMapping) sm)) == null)) {
            throw new MappingException("model structure '" + structures[i].getName() + "' not mapped to a geometry subVolume");
        }
        if (sm != null && (sm instanceof MembraneMapping) && ((MembraneMapping) sm).getVolumeFractionParameter() != null) {
            Expression volFractExp = ((MembraneMapping) sm).getVolumeFractionParameter().getExpression();
            try {
                if (volFractExp != null) {
                    double volFract = volFractExp.evaluateConstant();
                    if (volFract >= 1.0) {
                        throw new MappingException("model structure '" + (getSimulationContext().getModel().getStructureTopology().getInsideFeature(((MembraneMapping) sm).getMembrane()).getName() + "' has volume fraction >= 1.0"));
                    }
                }
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
            }
        }
    }
    SubVolume[] subVolumes = simContext.getGeometryContext().getGeometry().getGeometrySpec().getSubVolumes();
    for (int i = 0; i < subVolumes.length; i++) {
        if (getStructures(subVolumes[i]) == null || getStructures(subVolumes[i]).length == 0) {
            throw new MappingException("geometry subVolume '" + subVolumes[i].getName() + "' not mapped from a model structure");
        }
    }
    // 
    // gather only those reactionSteps that are not "excluded"
    // 
    ReactionSpec[] reactionSpecs = simContext.getReactionContext().getReactionSpecs();
    Vector<ReactionStep> rsList = new Vector<ReactionStep>();
    for (int i = 0; i < reactionSpecs.length; i++) {
        if (reactionSpecs[i].isExcluded() == false) {
            rsList.add(reactionSpecs[i].getReactionStep());
        }
    }
    ReactionStep[] reactionSteps = new ReactionStep[rsList.size()];
    rsList.copyInto(reactionSteps);
    // 
    for (int i = 0; i < reactionSteps.length; i++) {
        Kinetics.UnresolvedParameter[] unresolvedParameters = reactionSteps[i].getKinetics().getUnresolvedParameters();
        if (unresolvedParameters != null && unresolvedParameters.length > 0) {
            StringBuffer buffer = new StringBuffer();
            for (int j = 0; j < unresolvedParameters.length; j++) {
                if (j > 0) {
                    buffer.append(", ");
                }
                buffer.append(unresolvedParameters[j].getName());
            }
            throw new MappingException(reactionSteps[i].getDisplayType() + " '" + reactionSteps[i].getName() + "' contains unresolved identifier(s): " + buffer);
        }
    }
    // 
    // create new MathDescription (based on simContext's previous MathDescription if possible)
    // 
    MathDescription oldMathDesc = simContext.getMathDescription();
    mathDesc = null;
    if (oldMathDesc != null) {
        if (oldMathDesc.getVersion() != null) {
            mathDesc = new MathDescription(oldMathDesc.getVersion());
        } else {
            mathDesc = new MathDescription(oldMathDesc.getName());
        }
    } else {
        mathDesc = new MathDescription(simContext.getName() + "_generated");
    }
    // 
    // temporarily place all variables in a hashtable (before binding) and discarding duplicates
    // 
    VariableHash varHash = new VariableHash();
    // 
    // conversion factors
    // 
    Model model = simContext.getModel();
    ModelUnitSystem modelUnitSystem = model.getUnitSystem();
    varHash.addVariable(new Constant(getMathSymbol(model.getKMOLE(), null), getIdentifierSubstitutions(model.getKMOLE().getExpression(), model.getKMOLE().getUnitDefinition(), null)));
    varHash.addVariable(new Constant(getMathSymbol(model.getN_PMOLE(), null), getIdentifierSubstitutions(model.getN_PMOLE().getExpression(), model.getN_PMOLE().getUnitDefinition(), null)));
    varHash.addVariable(new Constant(getMathSymbol(model.getFARADAY_CONSTANT(), null), getIdentifierSubstitutions(model.getFARADAY_CONSTANT().getExpression(), model.getFARADAY_CONSTANT().getUnitDefinition(), null)));
    varHash.addVariable(new Constant(getMathSymbol(model.getFARADAY_CONSTANT_NMOLE(), null), getIdentifierSubstitutions(model.getFARADAY_CONSTANT_NMOLE().getExpression(), model.getFARADAY_CONSTANT_NMOLE().getUnitDefinition(), null)));
    varHash.addVariable(new Constant(getMathSymbol(model.getGAS_CONSTANT(), null), getIdentifierSubstitutions(model.getGAS_CONSTANT().getExpression(), model.getGAS_CONSTANT().getUnitDefinition(), null)));
    varHash.addVariable(new Constant(getMathSymbol(model.getTEMPERATURE(), null), getIdentifierSubstitutions(new Expression(simContext.getTemperatureKelvin()), model.getTEMPERATURE().getUnitDefinition(), null)));
    Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        if (scm.getVariable() instanceof StochVolVariable) {
            varHash.addVariable(scm.getVariable());
        }
    }
    // 
    // add rate term for all reactions
    // add current source terms for each reaction step in a membrane
    // 
    /*for (int i = 0; i < reactionSteps.length; i++){
			boolean bAllReactionParticipantsFixed = true;
			ReactionParticipant rp_Array[] = reactionSteps[i].getReactionParticipants();
			for (int j = 0; j < rp_Array.length; j++) {
				SpeciesContextSpec scs = getSimulationContext().getReactionContext().getSpeciesContextSpec(rp_Array[j].getSpeciesContext());
				if (!(rp_Array[j] instanceof Catalyst) && !scs.isConstant()){
					bAllReactionParticipantsFixed = false;  // found at least one reactionParticipant that is not fixed and needs this rate
				}
			}
			StructureMapping sm = simContext.getGeometryContext().getStructureMapping(reactionSteps[i].getStructure());
		}---don't think it's useful, isn't it?*/
    // deals with model parameters
    ModelParameter[] modelParameters = simContext.getModel().getModelParameters();
    for (int j = 0; j < modelParameters.length; j++) {
        Expression expr = getSubstitutedExpr(modelParameters[j].getExpression(), true, false);
        expr = getIdentifierSubstitutions(expr, modelParameters[j].getUnitDefinition(), null);
        varHash.addVariable(newFunctionOrConstant(getMathSymbol(modelParameters[j], null), expr));
    }
    // added July 2009, ElectricalStimulusParameter electric mapping tab
    ElectricalStimulus[] elecStimulus = simContext.getElectricalStimuli();
    if (elecStimulus.length > 0) {
        throw new MappingException("Modles with electrophysiology are not supported for stochastic applications.");
    }
    for (int j = 0; j < structureMappings.length; j++) {
        if (structureMappings[j] instanceof MembraneMapping) {
            MembraneMapping memMapping = (MembraneMapping) structureMappings[j];
            Parameter initialVoltageParm = memMapping.getInitialVoltageParameter();
            try {
                Expression exp = initialVoltageParm.getExpression();
                exp.evaluateConstant();
                varHash.addVariable(newFunctionOrConstant(getMathSymbol(memMapping.getMembrane().getMembraneVoltage(), memMapping), getIdentifierSubstitutions(memMapping.getInitialVoltageParameter().getExpression(), memMapping.getInitialVoltageParameter().getUnitDefinition(), memMapping)));
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new MappingException("Membrane initial voltage: " + initialVoltageParm.getName() + " cannot be evaluated as constant.");
            }
        }
    }
    // 
    for (int j = 0; j < reactionSteps.length; j++) {
        ReactionStep rs = reactionSteps[j];
        if (simContext.getReactionContext().getReactionSpec(rs).isExcluded()) {
            continue;
        }
        if (rs.getKinetics() instanceof LumpedKinetics) {
            throw new RuntimeException("Lumped Kinetics not yet supported for Stochastic Math Generation");
        }
        Kinetics.KineticsParameter[] parameters = rs.getKinetics().getKineticsParameters();
        StructureMapping sm = simContext.getGeometryContext().getStructureMapping(rs.getStructure());
        if (parameters != null) {
            for (int i = 0; i < parameters.length; i++) {
                if ((parameters[i].getRole() == Kinetics.ROLE_CurrentDensity) && (parameters[i].getExpression() == null || parameters[i].getExpression().isZero())) {
                    continue;
                }
                // don't add rate, we'll do it later when creating the jump processes
                if (parameters[i].getRole() != Kinetics.ROLE_ReactionRate) {
                    Expression expr = getSubstitutedExpr(parameters[i].getExpression(), true, false);
                    varHash.addVariable(newFunctionOrConstant(getMathSymbol(parameters[i], sm), getIdentifierSubstitutions(expr, parameters[i].getUnitDefinition(), sm)));
                }
            }
        }
    }
    // the parameter "Size" is already put into mathsymbolmapping in refreshSpeciesContextMapping()
    for (int i = 0; i < structureMappings.length; i++) {
        StructureMapping sm = structureMappings[i];
        StructureMapping.StructureMappingParameter parm = sm.getParameterFromRole(StructureMapping.ROLE_Size);
        if (parm.getExpression() != null) {
            try {
                double value = parm.getExpression().evaluateConstant();
                varHash.addVariable(new Constant(getMathSymbol(parm, sm), new Expression(value)));
            } catch (ExpressionException e) {
                // varHash.addVariable(new Function(getMathSymbol0(parm,sm),getIdentifierSubstitutions(parm.getExpression(),parm.getUnitDefinition(),sm)));
                e.printStackTrace(System.out);
                throw new MappingException("Size of structure:" + sm.getNameScope().getName() + " cannot be evaluated as constant.");
            }
        }
    }
    // 
    // species initial values (either function or constant)
    // 
    SpeciesContextSpec[] speciesContextSpecs = simContext.getReactionContext().getSpeciesContextSpecs();
    for (int i = 0; i < speciesContextSpecs.length; i++) {
        // can be concentration or amount
        SpeciesContextSpec.SpeciesContextSpecParameter initParam = null;
        Expression iniExp = null;
        StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
        if (speciesContextSpecs[i].getInitialConcentrationParameter() != null && speciesContextSpecs[i].getInitialConcentrationParameter().getExpression() != null) {
            // use concentration, need to set up amount functions
            initParam = speciesContextSpecs[i].getInitialConcentrationParameter();
            iniExp = initParam.getExpression();
            iniExp = getSubstitutedExpr(iniExp, true, !speciesContextSpecs[i].isConstant());
            // now create the appropriate function or Constant for the speciesContextSpec.
            varHash.addVariable(newFunctionOrConstant(getMathSymbol(initParam, sm), getIdentifierSubstitutions(iniExp, initParam.getUnitDefinition(), sm)));
            // add function for initial amount
            SpeciesContextSpec.SpeciesContextSpecParameter initAmountParam = speciesContextSpecs[i].getInitialCountParameter();
            Expression iniAmountExp = getExpressionConcToAmt(new Expression(initParam, getNameScope()), speciesContextSpecs[i].getSpeciesContext());
            // iniAmountExp.bindExpression(this);
            varHash.addVariable(new Function(getMathSymbol(initAmountParam, sm), getIdentifierSubstitutions(iniAmountExp, initAmountParam.getUnitDefinition(), sm), nullDomain));
        } else if (speciesContextSpecs[i].getInitialCountParameter() != null && speciesContextSpecs[i].getInitialCountParameter().getExpression() != null) {
            // use amount
            initParam = speciesContextSpecs[i].getInitialCountParameter();
            iniExp = initParam.getExpression();
            iniExp = getSubstitutedExpr(iniExp, false, !speciesContextSpecs[i].isConstant());
            // now create the appropriate function or Constant for the speciesContextSpec.
            varHash.addVariable(newFunctionOrConstant(getMathSymbol(initParam, sm), getIdentifierSubstitutions(iniExp, initParam.getUnitDefinition(), sm)));
        }
        // add spConcentration (concentration of species) to varHash as function or constant
        SpeciesConcentrationParameter spConcParam = getSpeciesConcentrationParameter(speciesContextSpecs[i].getSpeciesContext());
        varHash.addVariable(newFunctionOrConstant(getMathSymbol(spConcParam, sm), getIdentifierSubstitutions(spConcParam.getExpression(), spConcParam.getUnitDefinition(), sm)));
    }
    // 
    // constant species (either function or constant)
    // 
    enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
        if (scm.getVariable() instanceof Constant) {
            varHash.addVariable(scm.getVariable());
        }
    }
    // 
    if (simContext.getGeometryContext().getGeometry() != null) {
        try {
            mathDesc.setGeometry(simContext.getGeometryContext().getGeometry());
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace(System.out);
            throw new MappingException("failure setting geometry " + e.getMessage());
        }
    } else {
        throw new MappingException("geometry must be defined");
    }
    // 
    // functions: species which is not a variable, but has dependency expression
    // 
    enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
        if (scm.getVariable() == null && scm.getDependencyExpression() != null) {
            StructureMapping sm = simContext.getGeometryContext().getStructureMapping(scm.getSpeciesContext().getStructure());
            Expression exp = scm.getDependencyExpression();
            exp.bindExpression(this);
            SpeciesCountParameter spCountParam = getSpeciesCountParameter(scm.getSpeciesContext());
            varHash.addVariable(new Function(getMathSymbol(spCountParam, sm), getIdentifierSubstitutions(exp, spCountParam.getUnitDefinition(), sm), nullDomain));
        }
    }
    // 
    // create subDomains
    // 
    SubDomain subDomain = null;
    subVolumes = simContext.getGeometryContext().getGeometry().getGeometrySpec().getSubVolumes();
    for (int j = 0; j < subVolumes.length; j++) {
        SubVolume subVolume = (SubVolume) subVolumes[j];
        // 
        // get priority of subDomain
        // 
        int priority;
        Feature spatialFeature = getResolvedFeature(subVolume);
        if (spatialFeature == null) {
            if (simContext.getGeometryContext().getGeometry().getDimension() > 0) {
                throw new MappingException("no compartment (in Physiology) is mapped to subdomain '" + subVolume.getName() + "' (in Geometry)");
            } else {
                priority = CompartmentSubDomain.NON_SPATIAL_PRIORITY;
            }
        } else {
            // now does not have to match spatial feature, *BUT* needs to be unique
            priority = j;
        }
        subDomain = new CompartmentSubDomain(subVolume.getName(), priority);
        mathDesc.addSubDomain(subDomain);
    }
    // ReactionSpec[] reactionSpecs = simContext.getReactionContext().getReactionSpecs();---need to take a look here!
    for (int i = 0; i < reactionSpecs.length; i++) {
        if (reactionSpecs[i].isExcluded()) {
            continue;
        }
        // get the reaction
        ReactionStep reactionStep = reactionSpecs[i].getReactionStep();
        Kinetics kinetics = reactionStep.getKinetics();
        // the structure where reaction happens
        StructureMapping sm = simContext.getGeometryContext().getStructureMapping(reactionStep.getStructure());
        // create symbol table for jump process based on reactionStep and structure mapping
        // final ReactionStep finalRS = reactionStep;
        // final StructureMapping finalSM = sm;
        // SymbolTable symTable = new SymbolTable(){
        // public SymbolTableEntry getEntry(String identifierString) throws ExpressionBindingException {
        // SymbolTableEntry ste = finalRS.getEntry(identifierString);
        // if(ste == null)
        // {
        // ste = finalSM.getEntry(identifierString);
        // }
        // return ste;
        // }
        // };
        // Different ways to deal with simple reactions and flux reactions
        // probability parameter from modelUnitSystem
        VCUnitDefinition probabilityParamUnit = modelUnitSystem.getStochasticSubstanceUnit().divideBy(modelUnitSystem.getTimeUnit());
        if (// simple reactions
        reactionStep instanceof SimpleReaction) {
            // check the reaction rate law to see if we need to decompose a reaction(reversible) into two jump processes.
            // rate constants are important in calculating the probability rate.
            // for Mass Action, we use KForward and KReverse,
            // for General Kinetics we parse reaction rate J to see if it is in Mass Action form.
            Expression forwardRate = null;
            Expression reverseRate = null;
            if (kinetics.getKineticsDescription().equals(KineticsDescription.MassAction)) {
                forwardRate = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KForward).getExpression();
                reverseRate = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KReverse).getExpression();
            } else if (kinetics.getKineticsDescription().equals(KineticsDescription.General)) {
                Expression rateExp = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate).getExpression();
                MassActionSolver.MassActionFunction maFunc = MassActionSolver.solveMassAction(null, null, rateExp, reactionStep);
                if (maFunc.getForwardRate() == null && maFunc.getReverseRate() == null) {
                    throw new MappingException("Cannot generate stochastic math mapping for the reaction:" + reactionStep.getName() + "\nLooking for the rate function according to the form of k1*Reactant1^Stoir1*Reactant2^Stoir2...-k2*Product1^Stoip1*Product2^Stoip2.");
                } else {
                    if (maFunc.getForwardRate() != null) {
                        forwardRate = maFunc.getForwardRate();
                    }
                    if (maFunc.getReverseRate() != null) {
                        reverseRate = maFunc.getReverseRate();
                    }
                }
            }
            /*else if (kinetics.getKineticsDescription().getName().compareTo(KineticsDescription.HMM_irreversible.getName())==0)
			    {
				    forwardRate = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_Km).getExpression();
				}
			    else if (kinetics.getKineticsDescription().getName().compareTo(KineticsDescription.HMM_reversible.getName())==0)
			    {
					forwardRate = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KmFwd).getExpression();
					reverseRate = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KmRev).getExpression();
				}*/
            boolean isForwardRatePresent = false;
            boolean isReverseRatePresent = false;
            if (forwardRate != null) {
                isForwardRatePresent = true;
            }
            if (reverseRate != null) {
                isReverseRatePresent = true;
            }
            // we process it as forward reaction
            if ((isForwardRatePresent)) /*|| ((forwardRate == null) && (reverseRate == null))*/
            {
                // get jump process name
                String jpName = TokenMangler.mangleToSName(reactionStep.getName());
                // get probability
                Expression exp = null;
                // reactions are mass actions
                exp = getProbabilityRate(reactionStep, true);
                // bind symbol table before substitute identifiers in the reaction step
                exp.bindExpression(this);
                MathMapping_4_8.ProbabilityParameter probParm = null;
                try {
                    probParm = addProbabilityParameter("P_" + jpName, exp, MathMapping_4_8.PARAMETER_ROLE_P, probabilityParamUnit, reactionSpecs[i]);
                } catch (PropertyVetoException pve) {
                    pve.printStackTrace();
                    throw new MappingException(pve.getMessage());
                }
                // add probability to function or constant
                varHash.addVariable(newFunctionOrConstant(getMathSymbol(probParm, sm), getIdentifierSubstitutions(exp, probabilityParamUnit, sm)));
                JumpProcess jp = new JumpProcess(jpName, new Expression(getMathSymbol(probParm, sm)));
                // actions
                ReactionParticipant[] reacPart = reactionStep.getReactionParticipants();
                for (int j = 0; j < reacPart.length; j++) {
                    Action action = null;
                    SpeciesCountParameter spCountParam = getSpeciesCountParameter(reacPart[j].getSpeciesContext());
                    if (reacPart[j] instanceof Reactant) {
                        // check if the reactant is a constant. If the species is a constant, there will be no action taken on this species
                        if (// not a constant
                        !simContext.getReactionContext().getSpeciesContextSpec(reacPart[j].getSpeciesContext()).isConstant()) {
                            int stoi = ((Reactant) reacPart[j]).getStoichiometry();
                            action = new Action(varHash.getVariable(getMathSymbol(spCountParam, sm)), "inc", new Expression("-" + String.valueOf(stoi)));
                            jp.addAction(action);
                        }
                    } else if (reacPart[j] instanceof Product) {
                        // check if the product is a constant. If the product is a constant, there will be no action taken on this species
                        if (// not a constant
                        !simContext.getReactionContext().getSpeciesContextSpec(reacPart[j].getSpeciesContext()).isConstant()) {
                            int stoi = ((Product) reacPart[j]).getStoichiometry();
                            action = new Action(varHash.getVariable(getMathSymbol(spCountParam, sm)), "inc", new Expression(stoi));
                            jp.addAction(action);
                        }
                    }
                }
                // add jump process to compartment subDomain
                subDomain.addJumpProcess(jp);
            }
            if (// one more jump process for a reversible reaction
            isReverseRatePresent) {
                // get jump process name
                String jpName = TokenMangler.mangleToSName(reactionStep.getName()) + "_reverse";
                Expression exp = null;
                // reactions are mass actions
                exp = getProbabilityRate(reactionStep, false);
                // bind symbol table before substitute identifiers in the reaction step
                exp.bindExpression(this);
                MathMapping_4_8.ProbabilityParameter probRevParm = null;
                try {
                    probRevParm = addProbabilityParameter("P_" + jpName, exp, MathMapping_4_8.PARAMETER_ROLE_P_reverse, probabilityParamUnit, reactionSpecs[i]);
                } catch (PropertyVetoException pve) {
                    pve.printStackTrace();
                    throw new MappingException(pve.getMessage());
                }
                // add probability to function or constant
                varHash.addVariable(newFunctionOrConstant(getMathSymbol(probRevParm, sm), getIdentifierSubstitutions(exp, probabilityParamUnit, sm)));
                JumpProcess jp = new JumpProcess(jpName, new Expression(getMathSymbol(probRevParm, sm)));
                // actions
                ReactionParticipant[] reacPart = reactionStep.getReactionParticipants();
                for (int j = 0; j < reacPart.length; j++) {
                    Action action = null;
                    SpeciesCountParameter spCountParam = getSpeciesCountParameter(reacPart[j].getSpeciesContext());
                    if (reacPart[j] instanceof Reactant) {
                        // check if the reactant is a constant. If the species is a constant, there will be no action taken on this species
                        if (// not a constant
                        !simContext.getReactionContext().getSpeciesContextSpec(reacPart[j].getSpeciesContext()).isConstant()) {
                            int stoi = ((Reactant) reacPart[j]).getStoichiometry();
                            action = new Action(varHash.getVariable(getMathSymbol(spCountParam, sm)), "inc", new Expression(stoi));
                            jp.addAction(action);
                        }
                    } else if (reacPart[j] instanceof Product) {
                        // check if the product is a constant. If the product is a constant, there will be no action taken on this species
                        if (// not a constant
                        !simContext.getReactionContext().getSpeciesContextSpec(reacPart[j].getSpeciesContext()).isConstant()) {
                            int stoi = ((Product) reacPart[j]).getStoichiometry();
                            action = new Action(varHash.getVariable(getMathSymbol(spCountParam, sm)), "inc", new Expression("-" + String.valueOf(stoi)));
                            jp.addAction(action);
                        }
                    }
                }
                // add jump process to compartment subDomain
                subDomain.addJumpProcess(jp);
            }
        // end of if(isForwardRateNonZero), if(isReverseRateNonRate)
        } else if (// flux reactions
        reactionStep instanceof FluxReaction) {
            // we could set jump processes for general flux rate in forms of p1*Sout + p2*Sin
            if (kinetics.getKineticsDescription().equals(KineticsDescription.General)) {
                Expression fluxRate = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate).getExpression();
                // we have to pass the math description para to flux solver, coz somehow math description in simulation context is not updated.
                MassActionSolver.MassActionFunction fluxFunc = MassActionSolver.solveMassAction(null, null, fluxRate, (FluxReaction) reactionStep);
                // create jump process for forward flux if it exists.
                if (fluxFunc.getForwardRate() != null && !fluxFunc.getForwardRate().isZero()) {
                    // jump process name
                    // +"_reverse";
                    String jpName = TokenMangler.mangleToSName(reactionStep.getName());
                    // we do it here instead of fluxsolver, coz we need to use getMathSymbol0(), structuremapping...etc.
                    Expression rate = fluxFunc.getForwardRate();
                    // get species expression (depend on structure, if mem: Species/mem_Size, if vol: species*KMOLE/vol_size)
                    SpeciesContext scOut = fluxFunc.getReactants().get(0).getSpeciesContext();
                    Expression speciesFactor = null;
                    if (scOut.getStructure() instanceof Feature) {
                        Expression exp1 = new Expression(1.0 / 602.0);
                        Expression exp2 = new Expression(scOut.getStructure().getStructureSize(), getNameScope());
                        speciesFactor = Expression.div(Expression.invert(exp1), exp2);
                    } else {
                        throw new MappingException("Species involved in a flux have to be volume species.");
                    }
                    Expression speciesExp = Expression.mult(speciesFactor, new Expression(scOut, getNameScope()));
                    // get probability expression by adding factor to rate (rate: rate*size_mem/KMOLE)
                    Expression expr1 = Expression.mult(rate, speciesExp);
                    Expression numeratorExpr = Expression.mult(expr1, new Expression(sm.getStructure().getStructureSize(), getNameScope()));
                    Expression exp = new Expression(1.0 / 602.0);
                    Expression probExp = Expression.mult(numeratorExpr, exp);
                    // bind symbol table before substitute identifiers in the reaction step
                    probExp.bindExpression(reactionStep);
                    MathMapping_4_8.ProbabilityParameter probParm = null;
                    try {
                        probParm = addProbabilityParameter("P_" + jpName, probExp, MathMapping_4_8.PARAMETER_ROLE_P, probabilityParamUnit, reactionSpecs[i]);
                    } catch (PropertyVetoException pve) {
                        pve.printStackTrace();
                        throw new MappingException(pve.getMessage());
                    }
                    // add probability to function or constant
                    varHash.addVariable(newFunctionOrConstant(getMathSymbol(probParm, sm), getIdentifierSubstitutions(probExp, probabilityParamUnit, sm)));
                    JumpProcess jp = new JumpProcess(jpName, new Expression(getMathSymbol(probParm, sm)));
                    // actions
                    Action action = null;
                    SpeciesContext sc = fluxFunc.getReactants().get(0).getSpeciesContext();
                    if (!simContext.getReactionContext().getSpeciesContextSpec(sc).isConstant()) {
                        SpeciesCountParameter spCountParam = getSpeciesCountParameter(sc);
                        action = new Action(varHash.getVariable(getMathSymbol(spCountParam, sm)), "inc", new Expression(-1));
                        jp.addAction(action);
                    }
                    sc = fluxFunc.getProducts().get(0).getSpeciesContext();
                    if (!simContext.getReactionContext().getSpeciesContextSpec(sc).isConstant()) {
                        SpeciesCountParameter spCountParam = getSpeciesCountParameter(sc);
                        action = new Action(varHash.getVariable(getMathSymbol(spCountParam, sm)), "inc", new Expression(1));
                        jp.addAction(action);
                    }
                    subDomain.addJumpProcess(jp);
                }
                if (fluxFunc.getReverseRate() != null && !fluxFunc.getReverseRate().isZero()) {
                    // jump process name
                    String jpName = TokenMangler.mangleToSName(reactionStep.getName()) + "_reverse";
                    Expression rate = fluxFunc.getReverseRate();
                    // get species expression (depend on structure, if mem: Species/mem_Size, if vol: species*KMOLE/vol_size)
                    SpeciesContext scIn = fluxFunc.getProducts().get(0).getSpeciesContext();
                    Expression speciesFactor = null;
                    if (scIn.getStructure() instanceof Feature) {
                        Expression exp1 = new Expression(1.0 / 602.0);
                        Expression exp2 = new Expression(scIn.getStructure().getStructureSize(), getNameScope());
                        speciesFactor = Expression.div(Expression.invert(exp1), exp2);
                    } else {
                        throw new MappingException("Species involved in a flux have to be volume species.");
                    }
                    Expression speciesExp = Expression.mult(speciesFactor, new Expression(scIn, getNameScope()));
                    // get probability expression by adding factor to rate (rate: rate*size_mem/KMOLE)
                    Expression expr1 = Expression.mult(rate, speciesExp);
                    Expression numeratorExpr = Expression.mult(expr1, new Expression(sm.getStructure().getStructureSize(), getNameScope()));
                    Expression exp = new Expression(1.0 / 602.0);
                    Expression probRevExp = Expression.mult(numeratorExpr, exp);
                    // bind symbol table before substitute identifiers in the reaction step
                    probRevExp.bindExpression(reactionStep);
                    MathMapping_4_8.ProbabilityParameter probRevParm = null;
                    try {
                        probRevParm = addProbabilityParameter("P_" + jpName, probRevExp, MathMapping_4_8.PARAMETER_ROLE_P_reverse, probabilityParamUnit, reactionSpecs[i]);
                    } catch (PropertyVetoException pve) {
                        pve.printStackTrace();
                        throw new MappingException(pve.getMessage());
                    }
                    // add probability to function or constant
                    varHash.addVariable(newFunctionOrConstant(getMathSymbol(probRevParm, sm), getIdentifierSubstitutions(probRevExp, probabilityParamUnit, sm)));
                    JumpProcess jp = new JumpProcess(jpName, new Expression(getMathSymbol(probRevParm, sm)));
                    // actions
                    Action action = null;
                    SpeciesContext sc = fluxFunc.getReactants().get(0).getSpeciesContext();
                    if (!simContext.getReactionContext().getSpeciesContextSpec(sc).isConstant()) {
                        SpeciesCountParameter spCountParam = getSpeciesCountParameter(sc);
                        action = new Action(varHash.getVariable(getMathSymbol(spCountParam, sm)), "inc", new Expression(1));
                        jp.addAction(action);
                    }
                    sc = fluxFunc.getProducts().get(0).getSpeciesContext();
                    if (!simContext.getReactionContext().getSpeciesContextSpec(sc).isConstant()) {
                        SpeciesCountParameter spCountParam = getSpeciesCountParameter(sc);
                        action = new Action(varHash.getVariable(getMathSymbol(spCountParam, sm)), "inc", new Expression(-1));
                        jp.addAction(action);
                    }
                    subDomain.addJumpProcess(jp);
                }
            }
        }
    // end of if (simplereaction)...else if(fluxreaction)
    }
    // end of reaction step loop
    // 
    // set Variables to MathDescription all at once with the order resolved by "VariableHash"
    // 
    mathDesc.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
    // set up variable initial conditions in subDomain
    SpeciesContextSpec[] scSpecs = simContext.getReactionContext().getSpeciesContextSpecs();
    for (int i = 0; i < speciesContextSpecs.length; i++) {
        // get stochastic variable by name
        SpeciesCountParameter spCountParam = getSpeciesCountParameter(speciesContextSpecs[i].getSpeciesContext());
        StructureMapping sm = simContext.getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
        String varName = getMathSymbol(spCountParam, sm);
        if (scSpecs[i].isConstant()) {
            continue;
        }
        StochVolVariable var = (StochVolVariable) mathDesc.getVariable(varName);
        // stochastic use initial number of particles
        SpeciesContextSpec.SpeciesContextSpecParameter initParm = scSpecs[i].getInitialCountParameter();
        // stochastic variables initial expression.
        if (initParm != null) {
            VarIniCondition varIni = new VarIniCount(var, new Expression(getMathSymbol(initParm, sm)));
            subDomain.addVarIniCondition(varIni);
        }
    }
    if (!mathDesc.isValid()) {
        throw new MappingException("generated an invalid mathDescription: " + mathDesc.getWarning());
    }
}

Example 99 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class StructureAnalyzer method refreshTotalMatrices.

/**
 * This method was created in VisualAge.
 */
private void refreshTotalMatrices() throws Exception {
    // System.out.println("StructureAnalyzer.refreshTotalMatrices()");
    // 
    // update scheme matrix for full system (slow and fast)
    // 
    ReactionSpec[] reactionSpecs = new ReactionSpec[reactionSteps.length];
    for (int j = 0; j < reactionSteps.length; j++) {
        reactionSpecs[j] = mathMapping_4_8.getSimulationContext().getReactionContext().getReactionSpec(reactionSteps[j]);
    }
    // 
    // initialize rate expressions for speciesContext's due to scheme matrix
    // 
    totalSchemeMatrix = new RationalNumberMatrix(speciesContextMappings.length, reactionSteps.length);
    for (int i = 0; i < speciesContextMappings.length; i++) {
        SpeciesContextMapping scm = speciesContextMappings[i];
        SpeciesContext sc = scm.getSpeciesContext();
        // 
        // collect slow rate expression (fast handled by FastSystem)
        // 
        Expression exp = new Expression(0.0);
        for (int j = 0; j < reactionSteps.length; j++) {
            int stoichiometry = reactionSteps[j].getStoichiometry(sc);
            totalSchemeMatrix.set_elem(i, j, stoichiometry);
            if (stoichiometry != 0) {
                if (!(reactionSteps[j] instanceof DummyReactionStep) && !reactionSpecs[j].isFast() && !reactionSpecs[j].isExcluded()) {
                    ReactionParticipant[] rps1 = reactionSteps[j].getReactionParticipants();
                    ReactionParticipant rp0 = null;
                    for (ReactionParticipant rp : rps1) {
                        if (rp.getSpeciesContext() == sc) {
                            rp0 = rp;
                            break;
                        }
                    }
                    Structure structure = reactionSteps[j].getStructure();
                    // 
                    if (rp0 != null) {
                        Expression reactRateExp = getReactionRateExpression(reactionSteps[j], rp0).renameBoundSymbols(mathMapping_4_8.getNameScope());
                        if ((structure instanceof Membrane) && (sc.getStructure() != structure)) {
                            Membrane membrane = (Membrane) structure;
                            MembraneMapping membraneMapping = (MembraneMapping) mathMapping_4_8.getSimulationContext().getGeometryContext().getStructureMapping(membrane);
                            Parameter fluxCorrectionParameter = mathMapping_4_8.getFluxCorrectionParameter(membraneMapping, (Feature) sc.getStructure());
                            Expression fluxCorrection = new Expression(fluxCorrectionParameter, mathMapping_4_8.getNameScope());
                            if (reactionSteps[j] instanceof FluxReaction) {
                                exp = Expression.add(exp, Expression.mult(fluxCorrection, reactRateExp));
                            // Expression.add(exp,new Expression(fluxCorrectionParameterSymbolName+"*"+expInfix));
                            } else if (reactionSteps[j] instanceof SimpleReaction) {
                                ModelUnitSystem unitSystem = mathMapping_4_8.getSimulationContext().getModel().getUnitSystem();
                                Expression unitFactor = mathMapping_4_8.getUnitFactor(unitSystem.getVolumeSubstanceUnit().divideBy(unitSystem.getMembraneSubstanceUnit()));
                                exp = Expression.add(exp, Expression.mult(fluxCorrection, unitFactor, reactRateExp));
                            // exp = Expression.add(exp,new Expression(fluxCorrectionParameterSymbolName+"*"+ReservedSymbol.KMOLE.getName()+"*"+expInfix));
                            } else {
                                throw new RuntimeException("Internal Error: expected ReactionStep " + reactionSteps[j] + " to be of type SimpleReaction or FluxReaction");
                            }
                        } else {
                            exp = Expression.add(exp, reactRateExp);
                        }
                    }
                }
            }
        }
        // exp.bindExpression(mathMapping);
        scm.setRate(exp.flatten());
    }
    // 
    if (totalSchemeMatrix.getNumRows() > 1) {
        totalNullSpaceMatrix = (RationalMatrix) totalSchemeMatrix.findNullSpace();
    } else {
        totalNullSpaceMatrix = null;
    }
// if (totalNullSpaceMatrix==null){
// System.out.println("total system has full rank");
// }else{
// System.out.println("StructureAnalyzer.refreshTotalMatrices(), nullSpace matrix:");
// totalNullSpaceMatrix.show();
// }
}

Example 100 with SpeciesContext

use of cbit.vcell.model.SpeciesContext in project vcell by virtualcell.

the class StructureAnalyzer method refreshFastSpeciesContextMappings.

/**
 * This method was created in VisualAge.
 */
private void refreshFastSpeciesContextMappings() {
    // System.out.println("StructureAnalyzer.refreshFastSpeciesContextMappings()");
    // GeometryContext geoContext = mathMapping.getSimulationContext().getGeometryContext();
    Vector<SpeciesContextMapping> scFastList = new Vector<SpeciesContextMapping>();
    // 
    if (structures == null) {
        return;
    }
    for (int i = 0; i < structures.length; i++) {
        SpeciesContext[] speciesContexts = mathMapping_4_8.getSimulationContext().getReactionContext().getModel().getSpeciesContexts(structures[i]);
        for (int j = 0; j < speciesContexts.length; j++) {
            SpeciesContext sc = speciesContexts[j];
            SpeciesContextMapping scm = mathMapping_4_8.getSpeciesContextMapping(sc);
            SpeciesContextSpec scs = mathMapping_4_8.getSimulationContext().getReactionContext().getSpeciesContextSpec(sc);
            if (scm.getDependencyExpression() == null && scs.isConstant() == false) {
                // right now all independent vars
                scFastList.addElement(scm);
            }
        }
    }
    if (scFastList.size() > 0) {
        fastSpeciesContextMappings = new SpeciesContextMapping[scFastList.size()];
        scFastList.copyInto(fastSpeciesContextMappings);
    // for (int i=0;i<fastSpeciesContextMappings.length;i++){
    // System.out.println("fastSpeciesContextMappings["+i+"] = "+fastSpeciesContextMappings[i].getSpeciesContext().getName());
    // }
    } else {
        fastSpeciesContextMappings = null;
    }
    // System.out.println("StructureAnalyzer.refreshFastSpeciesContextMapping(), fastSpeciesContextMappings.length = "+scFastList.size());
    // 
    // for each reaction, get all reactionSteps associated with these structures
    // 
    Vector<ReactionStep> rsFastList = new Vector<ReactionStep>();
    ReactionSpec[] reactionSpecs = mathMapping_4_8.getSimulationContext().getReactionContext().getReactionSpecs();
    for (int i = 0; i < reactionSpecs.length; i++) {
        ReactionStep rs = reactionSpecs[i].getReactionStep();
        if (reactionSpecs[i].isExcluded()) {
            continue;
        }
        for (int j = 0; j < structures.length; j++) {
            if (rs.getStructure() == structures[j]) {
                if (reactionSpecs[i].isFast()) {
                    rsFastList.addElement(rs);
                }
            }
        }
    }
    if (rsFastList.size() > 0) {
        fastReactionSteps = new ReactionStep[rsFastList.size()];
        rsFastList.copyInto(fastReactionSteps);
    } else {
        fastReactionSteps = null;
        fastSpeciesContextMappings = null;
    }
// System.out.println("StructureAnalyzer.refreshFastSpeciesContextMapping(), reactionSteps.length = "+scFastList.size());
}