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

Example 36 with Model

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

the class RulebasedMathMapping method refreshMathDescription.

/**
 * This method was created in VisualAge.
 */
@Override
protected void refreshMathDescription() throws MappingException, MatrixException, MathException, ExpressionException, ModelException {
    // use local variable instead of using getter all the time.
    SimulationContext simContext = getSimulationContext();
    GeometryClass geometryClass = simContext.getGeometry().getGeometrySpec().getSubVolumes()[0];
    Domain domain = new Domain(geometryClass);
    // local structure mapping list
    StructureMapping[] structureMappings = simContext.getGeometryContext().getStructureMappings();
    // We have to check if all the reactions are able to transform 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);
    }
    simContext.checkValidity();
    // 
    if (simContext.getGeometry().getDimension() > 0) {
        throw new MappingException("rule-based particle math mapping not implemented for spatial geometry - dimension >= 1");
    }
    // 
    for (int i = 0; i < structureMappings.length; i++) {
        if (structureMappings[i] instanceof MembraneMapping) {
            if (((MembraneMapping) structureMappings[i]).getCalculateVoltage()) {
                throw new MappingException("electric potential not yet supported for particle models");
            }
        }
    }
    // 
    // fail if any events
    // 
    BioEvent[] bioEvents = simContext.getBioEvents();
    if (bioEvents != null && bioEvents.length > 0) {
        throw new MappingException("events not yet supported for particle-based models");
    }
    // 
    // 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 && ((FeatureMapping) sm).getGeometryClass() == 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++) {
        Structure[] mappedStructures = simContext.getGeometryContext().getStructuresFromGeometryClass(subVolumes[i]);
        if (mappedStructures == null || mappedStructures.length == 0) {
            throw new MappingException("geometry subVolume '" + subVolumes[i].getName() + "' not mapped from a model structure");
        }
    }
    // 
    // gather only those reactionRules that are not "excluded"
    // 
    ArrayList<ReactionRule> rrList = new ArrayList<ReactionRule>();
    for (ReactionRuleSpec reactionRuleSpec : simContext.getReactionContext().getReactionRuleSpecs()) {
        if (!reactionRuleSpec.isExcluded()) {
            rrList.add(reactionRuleSpec.getReactionRule());
        }
    }
    // 
    for (ReactionRule reactionRule : rrList) {
        UnresolvedParameter[] unresolvedParameters = reactionRule.getKineticLaw().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("In Application '" + simContext.getName() + "', " + reactionRule.getDisplayType() + " '" + reactionRule.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();
    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.getPI_CONSTANT(), null), getIdentifierSubstitutions(model.getPI_CONSTANT().getExpression(), model.getPI_CONSTANT().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());
        }
    }
    // 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(), geometryClass);
        varHash.addVariable(newFunctionOrConstant(getMathSymbol(modelParameters[j], geometryClass), expr, geometryClass));
    }
    // 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.getGeometryClass()), getIdentifierSubstitutions(memMapping.getInitialVoltageParameter().getExpression(), memMapping.getInitialVoltageParameter().getUnitDefinition(), memMapping.getGeometryClass()), memMapping.getGeometryClass()));
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new MappingException("Membrane initial voltage: " + initialVoltageParm.getName() + " cannot be evaluated as constant.");
            }
        }
    }
    // 
    for (ReactionRule reactionRule : rrList) {
        // if (reactionRule.getKineticLaw() instanceof LumpedKinetics){
        // throw new RuntimeException("Lumped Kinetics not yet supported for RuleBased Modeling");
        // }
        LocalParameter[] parameters = reactionRule.getKineticLaw().getLocalParameters();
        for (LocalParameter parameter : parameters) {
            // 
            if ((parameter.getRole() == RbmKineticLawParameterType.RuleRate)) {
                continue;
            }
            // 
            if (!reactionRule.isReversible() && parameter.getRole() == RbmKineticLawParameterType.MassActionReverseRate) {
                continue;
            }
            Expression expr = getSubstitutedExpr(parameter.getExpression(), true, false);
            varHash.addVariable(newFunctionOrConstant(getMathSymbol(parameter, geometryClass), getIdentifierSubstitutions(expr, parameter.getUnitDefinition(), geometryClass), geometryClass));
        }
    }
    // 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.getGeometryClass()), 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.");
            }
        }
    }
    SpeciesContextSpec[] speciesContextSpecs = getSimulationContext().getReactionContext().getSpeciesContextSpecs();
    addInitialConditions(domain, speciesContextSpecs, varHash);
    // 
    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 in Application " + simContext.getName());
    }
    // 
    // create subDomains
    // 
    SubVolume subVolume = simContext.getGeometry().getGeometrySpec().getSubVolumes()[0];
    SubDomain subDomain = new CompartmentSubDomain(subVolume.getName(), 0);
    mathDesc.addSubDomain(subDomain);
    // 
    // define all molecules and unique species patterns (add molecules to mathDesc and speciesPatterns to varHash).
    // 
    HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> speciesPatternMap = addSpeciesPatterns(domain, rrList);
    HashSet<VolumeParticleSpeciesPattern> uniqueParticleSpeciesPatterns = new HashSet<>(speciesPatternMap.values());
    for (VolumeParticleSpeciesPattern volumeParticleSpeciesPattern : uniqueParticleSpeciesPatterns) {
        varHash.addVariable(volumeParticleSpeciesPattern);
    }
    // 
    // define observables (those explicitly declared and those corresponding to seed species.
    // 
    List<ParticleObservable> observables = addObservables(geometryClass, domain, speciesPatternMap);
    for (ParticleObservable particleObservable : observables) {
        varHash.addVariable(particleObservable);
    }
    try {
        addParticleJumpProcesses(varHash, geometryClass, subDomain, speciesPatternMap);
    } catch (PropertyVetoException e1) {
        e1.printStackTrace();
        throw new MappingException(e1.getMessage(), e1);
    }
    // 
    for (int i = 0; i < fieldMathMappingParameters.length; i++) {
        if (fieldMathMappingParameters[i] instanceof UnitFactorParameter || fieldMathMappingParameters[i] instanceof ObservableConcentrationParameter) {
            varHash.addVariable(newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], geometryClass), getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), geometryClass), fieldMathMappingParameters[i].getGeometryClass()));
        }
    }
    // 
    // set Variables to MathDescription all at once with the order resolved by "VariableHash"
    // 
    mathDesc.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
    // 
    for (SpeciesContext sc : model.getSpeciesContexts()) {
        if (!sc.hasSpeciesPattern()) {
            throw new MappingException("species " + sc.getName() + " has no molecular pattern");
        }
        VolumeParticleSpeciesPattern volumeParticleSpeciesPattern = speciesPatternMap.get(sc.getSpeciesPattern());
        ArrayList<ParticleInitialCondition> particleInitialConditions = new ArrayList<ParticleProperties.ParticleInitialCondition>();
        // initial conditions from scs
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
        Parameter initialCountParameter = scs.getInitialCountParameter();
        Expression e = getIdentifierSubstitutions(new Expression(initialCountParameter, getNameScope()), initialCountParameter.getUnitDefinition(), geometryClass);
        particleInitialConditions.add(new ParticleInitialConditionCount(e, new Expression(0.0), new Expression(0.0), new Expression(0.0)));
        ParticleProperties particleProperies = new ParticleProperties(volumeParticleSpeciesPattern, new Expression(0.0), new Expression(0.0), new Expression(0.0), new Expression(0.0), particleInitialConditions);
        subDomain.addParticleProperties(particleProperies);
    }
    // 
    for (int i = 0; i < fieldMathMappingParameters.length; i++) {
        if (fieldMathMappingParameters[i] instanceof UnitFactorParameter) {
            Variable variable = newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], geometryClass), getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), geometryClass), fieldMathMappingParameters[i].getGeometryClass());
            if (mathDesc.getVariable(variable.getName()) == null) {
                mathDesc.addVariable(variable);
            }
        }
        if (fieldMathMappingParameters[i] instanceof ObservableConcentrationParameter) {
            Variable variable = newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], geometryClass), getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), geometryClass), fieldMathMappingParameters[i].getGeometryClass());
            if (mathDesc.getVariable(variable.getName()) == null) {
                mathDesc.addVariable(variable);
            }
        }
    }
    if (!mathDesc.isValid()) {
        System.out.println(mathDesc.getVCML_database());
        throw new MappingException("generated an invalid mathDescription: " + mathDesc.getWarning());
    }
}

Example 37 with Model

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

the class RulebasedTransformer method convertToBngl.

public String convertToBngl(SimulationContext simulationContext, boolean ignoreFunctions, MathMappingCallback mathMappingCallback, NetworkGenerationRequirements networkGenerationRequirements) {
    StringWriter bnglStringWriter = new StringWriter();
    PrintWriter pw = new PrintWriter(bnglStringWriter);
    Model model = simulationContext.getModel();
    if (model.getNumStructures() > 1) {
        // 
        // we ignore compartment info and ask bionetgen to behave as if there's only one compartment
        // instead, we add an extra site with the compartments as states
        // ATTENTION: we MUST use the extra sites, otherwise the symmetry factor will be wrong, the next 2 reactions give different symmetry factors:
        // @c:A.A -> @c:A + @c:A	flattened into AA -> 2*A
        // @c:A.A -> @m:A + @c:A    flattened into AA -> A + A (different species)
        // 
        RbmNetworkGenerator.writeBngl_internal(simulationContext, pw, kineticsParameterMap, speciesEquivalenceMap, networkGenerationRequirements, CompartmentMode.asSite);
    } else {
        // for consistency, always make this call here the new way (CompartmentMode.asSite, never CompartmentMode.hide), so that we always have
        // a compartment site, even when there's only 1 compartment
        // as it happens, since the compartment site has only one state (and so can't change between reactant and product) here we can make the
        // call either CompartmentMode.asSite or CompartmentMode.hide
        // 
        RbmNetworkGenerator.writeBngl_internal(simulationContext, pw, kineticsParameterMap, speciesEquivalenceMap, networkGenerationRequirements, CompartmentMode.asSite);
    }
    String bngl = bnglStringWriter.toString();
    pw.close();
    return bngl;
}

Example 38 with Model

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

the class RulebasedTransformer method transform.

private void transform(SimulationContext originalSimContext, SimulationContext transformedSimulationContext, ArrayList<ModelEntityMapping> entityMappings, MathMappingCallback mathMappingCallback) throws PropertyVetoException {
    Model newModel = transformedSimulationContext.getModel();
    Model originalModel = originalSimContext.getModel();
    ModelEntityMapping em = null;
    // list of rules created from the reactions; we apply the symmetry factor computed by bionetgen only to these
    Set<ReactionRule> fromReactions = new HashSet<>();
    for (SpeciesContext newSpeciesContext : newModel.getSpeciesContexts()) {
        final SpeciesContext originalSpeciesContext = originalModel.getSpeciesContext(newSpeciesContext.getName());
        // map new and old species contexts
        em = new ModelEntityMapping(originalSpeciesContext, newSpeciesContext);
        entityMappings.add(em);
        if (newSpeciesContext.hasSpeciesPattern()) {
            // it's perfect already and can't be improved
            continue;
        }
        try {
            MolecularType newmt = newModel.getRbmModelContainer().createMolecularType();
            newModel.getRbmModelContainer().addMolecularType(newmt, false);
            MolecularTypePattern newmtp_sc = new MolecularTypePattern(newmt);
            SpeciesPattern newsp_sc = new SpeciesPattern();
            newsp_sc.addMolecularTypePattern(newmtp_sc);
            newSpeciesContext.setSpeciesPattern(newsp_sc);
            RbmObservable newo = new RbmObservable(newModel, "O0_" + newmt.getName() + "_tot", newSpeciesContext.getStructure(), RbmObservable.ObservableType.Molecules);
            MolecularTypePattern newmtp_ob = new MolecularTypePattern(newmt);
            SpeciesPattern newsp_ob = new SpeciesPattern();
            newsp_ob.addMolecularTypePattern(newmtp_ob);
            newo.addSpeciesPattern(newsp_ob);
            newModel.getRbmModelContainer().addObservable(newo);
            // map new observable to old species context
            em = new ModelEntityMapping(originalSpeciesContext, newo);
            entityMappings.add(em);
        } catch (ModelException e) {
            e.printStackTrace();
            throw new RuntimeException("unable to transform species context: " + e.getMessage());
        } catch (PropertyVetoException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    ReactionSpec[] reactionSpecs = transformedSimulationContext.getReactionContext().getReactionSpecs();
    for (ReactionSpec reactionSpec : reactionSpecs) {
        if (reactionSpec.isExcluded()) {
            // we create rules only from those reactions which are not excluded
            continue;
        }
        ReactionStep rs = reactionSpec.getReactionStep();
        String name = rs.getName();
        String mangled = TokenMangler.fixTokenStrict(name);
        mangled = newModel.getReactionName(mangled);
        Kinetics k = rs.getKinetics();
        if (!(k instanceof MassActionKinetics)) {
            throw new RuntimeException("Only Mass Action Kinetics supported at this time, reaction \"" + rs.getName() + "\" uses kinetic law type \"" + rs.getKinetics().getName() + "\"");
        }
        boolean bReversible = rs.isReversible();
        ReactionRule rr = new ReactionRule(newModel, mangled, rs.getStructure(), bReversible);
        fromReactions.add(rr);
        MassActionKinetics massActionKinetics = (MassActionKinetics) k;
        List<Reactant> rList = rs.getReactants();
        List<Product> pList = rs.getProducts();
        // counting the stoichiometry - 2A+B means 3 reactants
        int numReactants = 0;
        for (Reactant r : rList) {
            numReactants += r.getStoichiometry();
            if (numReactants > 2) {
                String message = "NFSim doesn't support more than 2 reactants within a reaction: " + name;
                throw new RuntimeException(message);
            }
        }
        int numProducts = 0;
        for (Product p : pList) {
            numProducts += p.getStoichiometry();
            if (bReversible && numProducts > 2) {
                String message = "NFSim doesn't support more than 2 products within a reversible reaction: " + name;
                throw new RuntimeException(message);
            }
        }
        RateLawType rateLawType = RateLawType.MassAction;
        RbmKineticLaw kineticLaw = new RbmKineticLaw(rr, rateLawType);
        try {
            String forwardRateName = massActionKinetics.getForwardRateParameter().getName();
            Expression forwardRateExp = massActionKinetics.getForwardRateParameter().getExpression();
            String reverseRateName = massActionKinetics.getReverseRateParameter().getName();
            Expression reverseRateExp = massActionKinetics.getReverseRateParameter().getExpression();
            LocalParameter fR = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate);
            fR.setName(forwardRateName);
            LocalParameter rR = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate);
            rR.setName(reverseRateName);
            if (rs.hasReactant()) {
                kineticLaw.setParameterValue(fR, forwardRateExp, true);
            }
            if (rs.hasProduct()) {
                kineticLaw.setParameterValue(rR, reverseRateExp, true);
            }
            // 
            for (KineticsParameter reaction_p : massActionKinetics.getKineticsParameters()) {
                if (reaction_p.getRole() == Kinetics.ROLE_UserDefined) {
                    LocalParameter rule_p = kineticLaw.getLocalParameter(reaction_p.getName());
                    if (rule_p == null) {
                        // 
                        // after lazy parameter creation we didn't find a user-defined rule parameter with this same name.
                        // 
                        // there must be a global symbol with the same name, that the local reaction parameter has overridden.
                        // 
                        ParameterContext.LocalProxyParameter rule_proxy_parameter = null;
                        for (ProxyParameter proxyParameter : kineticLaw.getProxyParameters()) {
                            if (proxyParameter.getName().equals(reaction_p.getName())) {
                                rule_proxy_parameter = (LocalProxyParameter) proxyParameter;
                            }
                        }
                        if (rule_proxy_parameter != null) {
                            // we want to convert to local
                            boolean bConvertToGlobal = false;
                            kineticLaw.convertParameterType(rule_proxy_parameter, bConvertToGlobal);
                        } else {
                            // could find neither local parameter nor proxy parameter
                            throw new RuntimeException("user defined parameter " + reaction_p.getName() + " from reaction " + rs.getName() + " didn't map to a reactionRule parameter");
                        }
                    } else if (rule_p.getRole() == RbmKineticLawParameterType.UserDefined) {
                        kineticLaw.setParameterValue(rule_p, reaction_p.getExpression(), true);
                        rule_p.setUnitDefinition(reaction_p.getUnitDefinition());
                    } else {
                        throw new RuntimeException("user defined parameter " + reaction_p.getName() + " from reaction " + rs.getName() + " mapped to a reactionRule parameter with unexpected role " + rule_p.getRole().getDescription());
                    }
                }
            }
        } catch (ExpressionException e) {
            e.printStackTrace();
            throw new RuntimeException("Problem attempting to set RbmKineticLaw expression: " + e.getMessage());
        }
        rr.setKineticLaw(kineticLaw);
        KineticsParameter[] kpList = k.getKineticsParameters();
        ModelParameter[] mpList = rs.getModel().getModelParameters();
        ModelParameter mp = rs.getModel().getModelParameter(kpList[0].getName());
        ReactionParticipant[] rpList = rs.getReactionParticipants();
        for (ReactionParticipant p : rpList) {
            if (p instanceof Reactant) {
                int stoichiometry = p.getStoichiometry();
                for (int i = 0; i < stoichiometry; i++) {
                    SpeciesPattern speciesPattern = new SpeciesPattern(rs.getModel(), p.getSpeciesContext().getSpeciesPattern());
                    ReactantPattern reactantPattern = new ReactantPattern(speciesPattern, p.getStructure());
                    rr.addReactant(reactantPattern);
                }
            } else if (p instanceof Product) {
                int stoichiometry = p.getStoichiometry();
                for (int i = 0; i < stoichiometry; i++) {
                    SpeciesPattern speciesPattern = new SpeciesPattern(rs.getModel(), p.getSpeciesContext().getSpeciesPattern());
                    ProductPattern productPattern = new ProductPattern(speciesPattern, p.getStructure());
                    rr.addProduct(productPattern);
                }
            }
        }
        // commented code below is probably obsolete, we verify (above) in the reaction the number of participants,
        // no need to do it again in the corresponding rule
        // if(rr.getReactantPatterns().size() > 2) {
        // String message = "NFSim doesn't support more than 2 reactants within a reaction: " + name;
        // throw new RuntimeException(message);
        // }
        // if(rr.getProductPatterns().size() > 2) {
        // String message = "NFSim doesn't support more than 2 products within a reaction: " + name;
        // throw new RuntimeException(message);
        // }
        newModel.removeReactionStep(rs);
        newModel.getRbmModelContainer().addReactionRule(rr);
    }
    for (ReactionRuleSpec rrs : transformedSimulationContext.getReactionContext().getReactionRuleSpecs()) {
        if (rrs == null) {
            continue;
        }
        ReactionRule rr = rrs.getReactionRule();
        if (rrs.isExcluded()) {
            // delete those rules which are disabled (excluded) in the Specifications / Reaction table
            newModel.getRbmModelContainer().removeReactionRule(rr);
            continue;
        }
    }
    // now that we generated the rules we can delete the reaction steps they're coming from
    for (ReactionStep rs : newModel.getReactionSteps()) {
        newModel.removeReactionStep(rs);
    }
    try {
        // we invoke bngl just for the purpose of generating the xml file, which we'll then use to extract the symmetry factor
        generateNetwork(transformedSimulationContext, fromReactions, mathMappingCallback);
    } catch (ClassNotFoundException | IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    System.out.println("Finished RuleBased Transformer.");
}

Example 39 with Model

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

the class RulebasedTransformer method parseObservablesBngOutput.

private void parseObservablesBngOutput(SimulationContext simContext, BNGOutput bngOutput) {
    Model model = simContext.getModel();
    Document bngNFSimXMLDocument = bngOutput.getNFSimXMLDocument();
    bngRootElement = bngNFSimXMLDocument.getRootElement();
    Element modelElement = bngRootElement.getChild("model", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
    Element listOfObservablesElement = modelElement.getChild("ListOfObservables", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
    XMLOutputter outp = new XMLOutputter();
    String sTheirs = outp.outputString(listOfObservablesElement);
    sTheirs = sTheirs.replace("xmlns=\"http://www.sbml.org/sbml/level3\"", "");
    // System.out.println("==================== Their Observables ===================================================================");
    // System.out.println(sTheirs);
    // System.out.println("=======================================================================================");
    saveAsText("c:\\TEMP\\ddd\\theirObservables.txt", sTheirs);
// sTheirs = sTheirs.replaceAll("\\s+","");
}

Example 40 with Model

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

the class RulebasedTransformer method parseBngOutput.

private void parseBngOutput(SimulationContext simContext, Set<ReactionRule> fromReactions, BNGOutput bngOutput) {
    Model model = simContext.getModel();
    Document bngNFSimXMLDocument = bngOutput.getNFSimXMLDocument();
    bngRootElement = bngNFSimXMLDocument.getRootElement();
    Element modelElement = bngRootElement.getChild("model", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
    Element listOfReactionRulesElement = modelElement.getChild("ListOfReactionRules", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
    List<Element> reactionRuleChildren = new ArrayList<Element>();
    reactionRuleChildren = listOfReactionRulesElement.getChildren("ReactionRule", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
    for (Element reactionRuleElement : reactionRuleChildren) {
        ReactionRuleAnalysisReport rar = new ReactionRuleAnalysisReport();
        boolean bForward = true;
        String rule_id_str = reactionRuleElement.getAttributeValue("id");
        ruleElementMap.put(rule_id_str, reactionRuleElement);
        String rule_name_str = reactionRuleElement.getAttributeValue("name");
        String symmetry_factor_str = reactionRuleElement.getAttributeValue("symmetry_factor");
        Double symmetry_factor_double = Double.parseDouble(symmetry_factor_str);
        ReactionRule rr = null;
        if (rule_name_str.startsWith("_reverse_")) {
            bForward = false;
            rule_name_str = rule_name_str.substring("_reverse_".length());
            rr = model.getRbmModelContainer().getReactionRule(rule_name_str);
            RbmKineticLaw rkl = rr.getKineticLaw();
            try {
                if (symmetry_factor_double != 1.0 && fromReactions.contains(rr)) {
                    Expression expression = rkl.getLocalParameterValue(RbmKineticLawParameterType.MassActionReverseRate);
                    expression = Expression.div(expression, new Expression(symmetry_factor_double));
                    rkl.setLocalParameterValue(RbmKineticLawParameterType.MassActionReverseRate, expression);
                }
            } catch (ExpressionException | PropertyVetoException exc) {
                exc.printStackTrace();
                throw new RuntimeException("Unexpected transform exception: " + exc.getMessage());
            }
            rulesReverseMap.put(rr, rar);
        } else {
            rr = model.getRbmModelContainer().getReactionRule(rule_name_str);
            RbmKineticLaw rkl = rr.getKineticLaw();
            try {
                if (symmetry_factor_double != 1.0 && fromReactions.contains(rr)) {
                    Expression expression = rkl.getLocalParameterValue(RbmKineticLawParameterType.MassActionForwardRate);
                    expression = Expression.div(expression, new Expression(symmetry_factor_double));
                    rkl.setLocalParameterValue(RbmKineticLawParameterType.MassActionForwardRate, expression);
                }
            } catch (ExpressionException | PropertyVetoException exc) {
                exc.printStackTrace();
                throw new RuntimeException("Unexpected transform exception: " + exc.getMessage());
            }
            rulesForwardMap.put(rr, rar);
        }
        rar.symmetryFactor = symmetry_factor_double;
        System.out.println("rule id=" + rule_id_str + ", name=" + rule_name_str + ", symmetry factor=" + symmetry_factor_str);
        keyMap.put(rule_id_str, rr);
        Element listOfReactantPatternsElement = reactionRuleElement.getChild("ListOfReactantPatterns", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        List<Element> reactantPatternChildren = new ArrayList<Element>();
        reactantPatternChildren = listOfReactantPatternsElement.getChildren("ReactantPattern", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (int i = 0; i < reactantPatternChildren.size(); i++) {
            Element reactantPatternElement = reactantPatternChildren.get(i);
            String pattern_id_str = reactantPatternElement.getAttributeValue("id");
            ReactionRuleParticipant p = bForward ? rr.getReactantPattern(i) : rr.getProductPattern(i);
            SpeciesPattern sp = p.getSpeciesPattern();
            System.out.println("  reactant id=" + pattern_id_str + ", name=" + sp.toString());
            keyMap.put(pattern_id_str, sp);
            // list of molecules
            extractMolecules(sp, model, reactantPatternElement);
            // list of bonds (not implemented)
            extractBonds(reactantPatternElement);
        }
        Element listOfProductPatternsElement = reactionRuleElement.getChild("ListOfProductPatterns", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        List<Element> productPatternChildren = new ArrayList<Element>();
        productPatternChildren = listOfProductPatternsElement.getChildren("ProductPattern", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (int i = 0; i < productPatternChildren.size(); i++) {
            Element productPatternElement = productPatternChildren.get(i);
            String pattern_id_str = productPatternElement.getAttributeValue("id");
            ReactionRuleParticipant p = bForward ? rr.getProductPattern(i) : rr.getReactantPattern(i);
            SpeciesPattern sp = p.getSpeciesPattern();
            System.out.println("  product  id=" + pattern_id_str + ", name=" + sp.toString());
            keyMap.put(pattern_id_str, sp);
            extractMolecules(sp, model, productPatternElement);
            extractBonds(productPatternElement);
        }
        // extract the Map for this rule
        Element listOfMapElement = reactionRuleElement.getChild("Map", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        List<Element> mapChildren = new ArrayList<Element>();
        mapChildren = listOfMapElement.getChildren("MapItem", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (Element mapElement : mapChildren) {
            String target_id_str = mapElement.getAttributeValue("targetID");
            String source_id_str = mapElement.getAttributeValue("sourceID");
            System.out.println("Map: target=" + target_id_str + " source=" + source_id_str);
            RbmObject target_object = keyMap.get(target_id_str);
            RbmObject source_object = keyMap.get(source_id_str);
            if (target_object == null)
                System.out.println("!!! Missing map target  " + target_id_str);
            if (source_object == null)
                System.out.println("!!! Missing map source " + source_id_str);
            if (source_object != null) {
                // target_object may be null
                System.out.println("      target=" + target_object + " source=" + source_object);
                Pair<RbmObject, RbmObject> mapEntry = new Pair<RbmObject, RbmObject>(target_object, source_object);
                rar.objmappingList.add(mapEntry);
            }
            Pair<String, String> idmapEntry = new Pair<String, String>(target_id_str, source_id_str);
            rar.idmappingList.add(idmapEntry);
        }
        // ListOfOperations
        Element listOfOperationsElement = reactionRuleElement.getChild("ListOfOperations", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        List<Element> operationsChildren = new ArrayList<Element>();
        operationsChildren = listOfOperationsElement.getChildren("StateChange", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        System.out.println("ListOfOperations");
        for (Element operationsElement : operationsChildren) {
            String finalState_str = operationsElement.getAttributeValue("finalState");
            String site_str = operationsElement.getAttributeValue("site");
            RbmObject site_object = keyMap.get(site_str);
            if (site_object == null)
                System.out.println("!!! Missing map object " + site_str);
            if (site_object != null) {
                System.out.println("   finalState=" + finalState_str + " site=" + site_object);
                StateChangeOperation sco = new StateChangeOperation(finalState_str, site_str, site_object);
                rar.operationsList.add(sco);
            }
        }
        operationsChildren = listOfOperationsElement.getChildren("AddBond", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (Element operationsElement : operationsChildren) {
            String site1_str = operationsElement.getAttributeValue("site1");
            String site2_str = operationsElement.getAttributeValue("site2");
            RbmObject site1_object = keyMap.get(site1_str);
            RbmObject site2_object = keyMap.get(site2_str);
            if (site1_object == null)
                System.out.println("!!! Missing map object " + site1_str);
            if (site2_object == null)
                System.out.println("!!! Missing map object " + site2_str);
            if (site1_object != null && site2_object != null) {
                System.out.println("   site1=" + site1_object + " site2=" + site2_object);
                AddBondOperation abo = new AddBondOperation(site1_str, site2_str, site1_object, site2_object);
                rar.operationsList.add(abo);
            }
        }
        operationsChildren = listOfOperationsElement.getChildren("DeleteBond", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (Element operationsElement : operationsChildren) {
            String site1_str = operationsElement.getAttributeValue("site1");
            String site2_str = operationsElement.getAttributeValue("site2");
            RbmObject site1_object = keyMap.get(site1_str);
            RbmObject site2_object = keyMap.get(site2_str);
            if (site1_object == null)
                System.out.println("!!! Missing map object " + site1_str);
            if (site2_object == null)
                System.out.println("!!! Missing map object " + site2_str);
            if (site1_object != null && site2_object != null) {
                System.out.println("   site1=" + site1_object + " site2=" + site2_object);
                DeleteBondOperation dbo = new DeleteBondOperation(site1_str, site2_str, site1_object, site2_object);
                rar.operationsList.add(dbo);
            }
        }
        operationsChildren = listOfOperationsElement.getChildren("Add", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (Element operationsElement : operationsChildren) {
            String id_str = operationsElement.getAttributeValue("id");
            RbmObject id_object = keyMap.get(id_str);
            if (id_object == null)
                System.out.println("!!! Missing map object " + id_str);
            if (id_object != null) {
                System.out.println("   id=" + id_str);
                AddOperation ao = new AddOperation(id_str, id_object);
                rar.operationsList.add(ao);
            }
        }
        operationsChildren = listOfOperationsElement.getChildren("Delete", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (Element operationsElement : operationsChildren) {
            String id_str = operationsElement.getAttributeValue("id");
            String delete_molecules_str = operationsElement.getAttributeValue("DeleteMolecules");
            RbmObject id_object = keyMap.get(id_str);
            if (id_object == null)
                System.out.println("!!! Missing map object " + id_str);
            int delete_molecules_int = 0;
            if (delete_molecules_str != null) {
                delete_molecules_int = Integer.parseInt(delete_molecules_str);
            }
            if (id_object != null) {
                System.out.println("   id=" + id_str + ", DeleteMolecules=" + delete_molecules_str);
                DeleteOperation dop = new DeleteOperation(id_str, id_object, delete_molecules_int);
                rar.operationsList.add(dop);
            }
        }
    }
    System.out.println("done parsing xml file");
}