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

Example 31 with ReactionParticipant

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

the class DBReactionWizardPanel method parameterNameSelectionChanged.

/**
 * Comment
 */
private void parameterNameSelectionChanged() {
    try {
        javax.swing.DefaultListModel dlm = (javax.swing.DefaultListModel) getParameterValuesJList().getModel();
        dlm.removeAllElements();
        // 
        if (getParameterNamesJList().getSelectedValue() != null) {
            // final cbit.vcell.clientdb.DocumentManager docManager = getDocumentManager();
            // final javax.swing.JList jlist = getReactionsJList();
            final MapStringToObject parameNameMSO = (MapStringToObject) getParameterNamesJList().getSelectedValue();
            final KeyValue reactionStepKey = ((ReactionStepInfo) parameNameMSO.getToObject()).getReactionKey();
            // 
            final String RXSTEP_HASH_VALUE_KEY = "rxStep";
            AsynchClientTask searchReactions = new AsynchClientTask("Getting Full Reaction", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                public void run(Hashtable<String, Object> hash) throws Exception {
                    Model reactionModel = getDocumentManager().getReactionStepAsModel(reactionStepKey);
                    ReactionStep rStep = reactionModel.getReactionStep(((ReactionStepInfo) parameNameMSO.getToObject()).getReactionName());
                    if (rStep != null) {
                        rStep.rebindAllToModel(reactionModel);
                        hash.put(RXSTEP_HASH_VALUE_KEY, rStep);
                    }
                }
            };
            // 
            AsynchClientTask updateRXParams = new AsynchClientTask("updateRXParams", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                public void run(Hashtable<String, Object> hash) throws DataAccessException {
                    ReactionStep rStep = (ReactionStep) hash.get(RXSTEP_HASH_VALUE_KEY);
                    if (rStep != null) {
                        Kinetics.KineticsParameter[] kpArr = rStep.getKinetics().getKineticsParameters();
                        ReactionParticipant[] rpArr = rStep.getReactionParticipants();
                        // 
                        javax.swing.DefaultListModel pvdlm = (javax.swing.DefaultListModel) getParameterValuesJList().getModel();
                        pvdlm.removeAllElements();
                        for (int i = 0; i < kpArr.length; i += 1) {
                            pvdlm.addElement("Parameter - " + kpArr[i].getName().toString() + " = " + kpArr[i].getExpression().infix());
                        }
                        pvdlm.addElement("PhysicsOption=" + rStep.getPhysicsOptions());
                        for (int i = 0; i < rpArr.length; i += 1) {
                            String role = "Unknown";
                            if (rpArr[i] instanceof Reactant) {
                                role = "Reactant";
                            } else if (rpArr[i] instanceof Product) {
                                role = "Product";
                            } else if (rpArr[i] instanceof Catalyst) {
                                role = "Catalyst";
                            }
                            String fluxFlag = "";
                            // if(rStep instanceof FluxReaction){
                            // Membrane rStepStruct = (Membrane)rStep.getStructure();
                            // if(rpArr[i] instanceof Flux){
                            // if(rpArr[i].getStructure().equals(getModel().getStructureTopology().getOutsideFeature(rStepStruct))){
                            // fluxFlag = "Outside";
                            // }else{
                            // fluxFlag = "Inside";
                            // }
                            // }
                            // }
                            pvdlm.addElement("RXParticipant(" + role + ") " + fluxFlag + " " + (rpArr[i].getSpecies().getDBSpecies() != null ? "*" : "-") + " " + rpArr[i].getSpeciesContext().getName());
                        }
                    }
                    setReactionStep(rStep);
                    configureBFN();
                }
            };
            // 
            Hashtable<String, Object> hashTemp = new Hashtable<String, Object>();
            ClientTaskDispatcher.dispatch(this, hashTemp, new AsynchClientTask[] { searchReactions, updateRXParams }, true);
        } else {
            setReactionStep(null);
        }
    } catch (Exception e) {
        PopupGenerator.showErrorDialog(this, e.getMessage(), e);
    }
    // 
    configureBFN();
}

Example 32 with ReactionParticipant

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

the class SimulationContext method checkValidity.

public void checkValidity() throws MappingException {
    // spatial
    if (getGeometry().getDimension() > 0) {
    // 
    // fail if any enabled Reactions have LumpedKinetics.
    // 
    // StringBuffer buffer = new StringBuffer();
    // ReactionSpec[] reactionSpecs = getReactionContext().getReactionSpecs();
    // for (int i = 0; i < reactionSpecs.length; i++) {
    // if (!reactionSpecs[i].isExcluded() && reactionSpecs[i].getReactionStep().getKinetics() instanceof LumpedKinetics){
    // buffer.append("reaction \""+reactionSpecs[i].getReactionStep().getName()+"\" in compartment \""+reactionSpecs[i].getReactionStep().getStructure().getName()+"\"\n");
    // }
    // }
    // if (buffer.length()>0){
    // throw new MappingException("Spatial application \""+getName()+"\" cannot process reactions with spatially lumped kinetics, see kinetics for :\n"+buffer.toString());
    // 
    // }
    } else {
        // old-style ODE models should still work
        if (applicationType == Application.NETWORK_DETERMINISTIC && getGeometryContext().isAllVolFracAndSurfVolSpecified() && getGeometryContext().isAllSizeSpecifiedNull()) {
            // old style ODE models
            return;
        }
        // otherwise, all sizes should be present and positive.
        if (!getGeometryContext().isAllSizeSpecifiedPositive()) {
            throw new MappingException("Application " + getName() + ":\nAll structure sizes must be assigned positive values.\nPlease go to StructureMapping tab to check the sizes.");
        }
        // if rate rules are present, if any species has a rate rules, it should not be a reaction participant in any reaction.
        RateRule[] rateRules = getRateRules();
        if (rateRules != null && rateRules.length > 0) {
            if (getModel() != null) {
                ReactionStep[] reactionSteps = getModel().getReactionSteps();
                ReactionParticipant[] reactionParticipants = null;
                for (ReactionStep rs : reactionSteps) {
                    reactionParticipants = rs.getReactionParticipants();
                    for (ReactionParticipant rp : reactionParticipants) {
                        if (rp instanceof Reactant || rp instanceof Product) {
                            if (getRateRule(rp.getSpeciesContext()) != null) {
                                throw new RuntimeException("Species '" + rp.getSpeciesContext().getName() + "' is a reactant/product in reaction '" + rs.getName() + "' ; cannot also have a rate rule.");
                            }
                        }
                    }
                }
            }
        }
    }
}

Example 33 with ReactionParticipant

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

the class SpeciesContextSpec method gatherIssues.

/**
 * Insert the method's description here.
 * Creation date: (11/1/2005 10:03:46 AM)
 * @param issueVector java.util.Vector
 */
public void gatherIssues(IssueContext issueContext, List<Issue> issueVector) {
    issueContext = issueContext.newChildContext(ContextType.SpeciesContextSpec, this);
    // 
    for (int i = 0; i < fieldParameters.length; i++) {
        RealInterval simpleBounds = parameterBounds[fieldParameters[i].getRole()];
        if (simpleBounds != null) {
            String parmName = fieldParameters[i].getNameScope().getName() + "." + fieldParameters[i].getName();
            issueVector.add(new SimpleBoundsIssue(fieldParameters[i], issueContext, simpleBounds, "parameter " + parmName + ": must be within " + simpleBounds.toString()));
        }
    }
    if (bForceContinuous && !bConstant && getSimulationContext().isStoch() && (getSimulationContext().getGeometry().getDimension() > 0)) {
        // if it's particle or constant we're good
        SpeciesContext sc = getSpeciesContext();
        ReactionContext rc = getSimulationContext().getReactionContext();
        ReactionSpec[] rsArray = rc.getReactionSpecs();
        for (ReactionSpec rs : rsArray) {
            if (!rs.isExcluded()) {
                // we only care about reactions which are not excluded
                // true if "this" is part of current reaction
                boolean iAmParticipant = false;
                // true if current reaction has at least a particle participant
                boolean haveParticle = false;
                ReactionStep step = rs.getReactionStep();
                for (ReactionParticipant p : step.getReactionParticipants()) {
                    if (p instanceof Product || p instanceof Reactant) {
                        SpeciesContextSpec candidate = rc.getSpeciesContextSpec(p.getSpeciesContext());
                        if (candidate == this) {
                            iAmParticipant = true;
                        } else if (!candidate.isForceContinuous() && !candidate.isConstant()) {
                            haveParticle = true;
                        }
                    }
                }
                if (iAmParticipant && haveParticle) {
                    String msg = "Continuous Species won't conserve mass in particle reaction " + rs.getReactionStep().getName() + ".";
                    String tip = "Mass conservation for reactions of binding between discrete and continuous species is handled approximately. <br>" + "To avoid any algorithmic approximation, which may produce undesired results, the user is advised to indicate <br>" + "the continuous species in those reactions as modifiers (i.e. 'catalysts') in the physiology.";
                    issueVector.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, tip, Issue.SEVERITY_WARNING));
                    // we issue warning as soon as we found the first reaction which satisfies criteria
                    break;
                }
            }
        }
    }
    if (!bForceContinuous && bConstant) {
        if (getSimulationContext().isStoch() && (getSimulationContext().getGeometry().getDimension() > 0)) {
            String msg = "Clamped Species must be continuous rather than particles.";
            String tip = "If choose 'clamped', must also choose 'forceContinuous'";
            issueVector.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, tip, Issue.SEVERITY_ERROR));
        }
    }
    if (bForceContinuous && !bConstant) {
        if (getSimulationContext().isStoch() && (getSimulationContext().getGeometry().getDimension() == 0)) {
            String msg = "Non-constant species is forced continuous, not supported for nonspatial stochastic applications.";
            issueVector.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_ERROR));
        }
    }
}

Example 34 with ReactionParticipant

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

the class StochMathMapping method getProbabilityRate.

/**
 * Get probability expression for the specific elementary reaction.
 * Input: ReactionStep, the reaction. isForwardDirection, if the elementary reaction is forward from the reactionstep.
 * Output: Expression. the probability expression.
 * Creation date: (9/14/2006 3:22:58 PM)
 * @throws ExpressionException
 */
private Expression getProbabilityRate(ReactionStep reactionStep, Expression rateConstantExpr, boolean isForwardDirection) throws MappingException, ExpressionException, ModelException {
    // the structure where reaction happens
    StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(reactionStep.getStructure());
    Model model = getSimulationContext().getModel();
    Expression reactionStructureSize = new Expression(sm.getStructure().getStructureSize(), getNameScope());
    VCUnitDefinition reactionSubstanceUnit = model.getUnitSystem().getSubstanceUnit(reactionStep.getStructure());
    VCUnitDefinition stochasticSubstanceUnit = model.getUnitSystem().getStochasticSubstanceUnit();
    Expression reactionSubstanceUnitFactor = getUnitFactor(stochasticSubstanceUnit.divideBy(reactionSubstanceUnit));
    Expression factorExpr = Expression.mult(reactionStructureSize, reactionSubstanceUnitFactor);
    // Using the MassActionFunction to write out the math description
    MassActionSolver.MassActionFunction maFunc = null;
    Kinetics kinetics = reactionStep.getKinetics();
    if (kinetics.getKineticsDescription().equals(KineticsDescription.MassAction) || kinetics.getKineticsDescription().equals(KineticsDescription.General) || kinetics.getKineticsDescription().equals(KineticsDescription.GeneralPermeability)) {
        Expression rateExp = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate).getExpression();
        Parameter forwardRateParameter = null;
        Parameter reverseRateParameter = null;
        if (kinetics.getKineticsDescription().equals(KineticsDescription.MassAction)) {
            forwardRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KForward);
            reverseRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KReverse);
        } else if (kinetics.getKineticsDescription().equals(KineticsDescription.GeneralPermeability)) {
            forwardRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_Permeability);
            reverseRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_Permeability);
        }
        maFunc = MassActionSolver.solveMassAction(forwardRateParameter, reverseRateParameter, 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 {
        throw new MappingException("Cannot generate stochastic math mapping for the reaction:" + reactionStep.getName() + "\n. Unsupported kinetic type " + kinetics.getKineticsDescription().getName());
    }
    List<ReactionParticipant> reacPart;
    if (isForwardDirection) {
        reacPart = maFunc.getReactants();
        System.out.println("forward reaction rate (coefficient?) is " + maFunc.getForwardRate().infix());
    } else {
        reacPart = maFunc.getProducts();
        System.out.println("reverse reaction rate (coefficient?) is " + maFunc.getReverseRate().infix());
    }
    Expression rxnProbabilityExpr = null;
    for (int i = 0; i < reacPart.size(); i++) {
        VCUnitDefinition speciesSubstanceUnit = model.getUnitSystem().getSubstanceUnit(reacPart.get(i).getStructure());
        Expression speciesUnitFactor = getUnitFactor(speciesSubstanceUnit.divideBy(stochasticSubstanceUnit));
        int stoichiometry = 0;
        stoichiometry = reacPart.get(i).getStoichiometry();
        // ******the following part is to form the s*(s-1)(s-2)..(s-stoi+1).portion of the probability rate.
        Expression speciesStructureSize = new Expression(reacPart.get(i).getStructure().getStructureSize(), getNameScope());
        Expression speciesFactor = Expression.div(speciesUnitFactor, speciesStructureSize);
        // s*(s-1)(s-2)..(s-stoi+1)
        SpeciesCountParameter spCountParam = getSpeciesCountParameter(reacPart.get(i).getSpeciesContext());
        Expression spCount_exp = new Expression(spCountParam, getNameScope());
        // species from uM to No. of Particles, form s*(s-1)*(s-2)
        Expression speciesFactorial = new Expression(spCount_exp);
        for (int j = 1; j < stoichiometry; j++) {
            speciesFactorial = Expression.mult(speciesFactorial, Expression.add(spCount_exp, new Expression(-j)));
        }
        // update total factor with speceies factor
        if (stoichiometry == 1) {
            factorExpr = Expression.mult(factorExpr, speciesFactor);
        } else if (stoichiometry > 1) {
            // rxnProbExpr * (structSize^stoichiometry)
            factorExpr = Expression.mult(factorExpr, Expression.power(speciesFactor, new Expression(stoichiometry)));
        }
        if (rxnProbabilityExpr == null) {
            rxnProbabilityExpr = new Expression(speciesFactorial);
        } else {
            // for more than one reactant
            rxnProbabilityExpr = Expression.mult(rxnProbabilityExpr, speciesFactorial);
        }
    }
    // Now construct the probability expression.
    Expression probExp = null;
    if (rateConstantExpr == null) {
        throw new MappingException("Can not find reaction rate constant in reaction: " + reactionStep.getName());
    } else if (rxnProbabilityExpr == null) {
        probExp = new Expression(rateConstantExpr);
    } else if ((rateConstantExpr != null) && (rxnProbabilityExpr != null)) {
        probExp = Expression.mult(rateConstantExpr, rxnProbabilityExpr);
    }
    // simplify the factor
    RationalExp factorRatExp = RationalExpUtils.getRationalExp(factorExpr);
    factorExpr = new Expression(factorRatExp.infixString());
    factorExpr.bindExpression(this);
    // get probability rate with converting factor
    probExp = Expression.mult(probExp, factorExpr);
    probExp = probExp.flatten();
    return probExp;
}

Example 35 with ReactionParticipant

use of cbit.vcell.model.ReactionParticipant 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;
    }
}