Examples with JumpProcessRateDefinition cbit.vcell.math.JumpProcessRateDefinition used on opensource projects

Example 6 with JumpProcessRateDefinition

use of cbit.vcell.math.JumpProcessRateDefinition in project vcell by virtualcell.

the class RulebasedMathMapping method addStrictMassActionParticleJumpProcess.

private void addStrictMassActionParticleJumpProcess(VariableHash varHash, GeometryClass geometryClass, SubDomain subDomain, ReactionRule reactionRule, String jpName, ArrayList<ParticleVariable> reactantParticles, ArrayList<ParticleVariable> productParticles, ArrayList<Action> forwardActions, ArrayList<Action> reverseActions) throws ExpressionException, ExpressionBindingException, PropertyVetoException, MathException, MappingException {
    String reactionRuleName = reactionRule.getName();
    RbmKineticLaw kinetics = reactionRule.getKineticLaw();
    RulebasedTransformation ruleBasedTransformation = ((RulebasedTransformation) getTransformation());
    if (kinetics.getRateLawType() != RbmKineticLaw.RateLawType.MassAction) {
        throw new RuntimeException("expecting mass action kinetics for reaction rule " + reactionRuleName);
    }
    // 
    // construct stochastic forward or reverse rate expression (separately).  Transform from
    // original expression of "concentrationRate" in terms of rateParameter and reactants/products in concentrations
    // to
    // new stochastic expression of "molecularRate" in terms of forwardRateParameter, reactants/products in molecules, structure sizes, and unit conversions.
    // 
    // (1)  concentrationRate = K * [s0] * [s1]    [uM.s-1]  or   [molecules.um-3.s-1]   or   [molecules.um-2.s-1]  (or other)
    // (2)  molecularRate = P * <s0> * <s1>        [molecules.s-1]
    // 
    // in this math description, we are using <s_i> [molecules], but original kinetics were in [s_i] [uM or molecules.um-2].
    // so through a change in variable to get things in terms of <s_i>.  <<<< Here P is the desired stochastic rate coefficient. >>>
    // 
    // (3)  let [s_i] = <s_i>/structsize(s_i)*unitConversionFactor(substanceunit([s_i])/substanceunit(<s_i>))
    // 
    // in addition to the change in variables, we need to transform the entire expression from concentration/time to molecules/time
    // 
    // (4)  let molecularRate = concentrationRate * structSize(reaction) * unitConversionFactor(substanceunit(molecularRate)/substanceunit(concentrationRate))
    // 
    // (5)  in general, concentationRate = K * PRODUCT([s_i])
    // 
    // change of variables into stochastic variables used in MathDescription, substituting (3) into (5)
    // 
    // (6)  concentrationRate = K * PRODUCT(<s_i>/structsize(s_i)*unitConversionFactor(substanceunit([s_i])/substanceunit(<s_i>)))
    // 
    // reordering to separate the sizes, the unit conversions and the <s_i>
    // 
    // (7)  concentrationRate = K * PRODUCT(<s_i>) * PRODUCT(1/structsize(s_i)) * unitConversionFactor(PRODUCT(substanceunit([s_i])/substanceunit(<s_i>)))
    // 
    // combining (4) and (7)
    // 
    // (8) molecularRate = K * PRODUCT(<s_i>) * PRODUCT(1/structsize(s_i)) * unitConversionFactor(PRODUCT(substanceunit([s_i])/substanceunit(<s_i>))) * structSize(reaction) * unitConversionFactor(substanceunit(molecularRate)/substanceunit(concentrationRate))
    // 
    // collecting terms of sizes and unit conversions
    // 
    // (9)  molecularRate = K * PRODUCT(<s_i>) * structSize(reaction) / PRODUCT(structsize(s_i)) * unitConversionFactor(substanceunit(molecularRate)/substanceunit(concentrationRate) * PRODUCT(substanceunit([s_i])/substanceunit(<s_i>)))
    // 
    // (10) molecularRate = K * PRODUCT(<s_i>) * sizeFactor * unitConversionFactor(substanceConversionUnit)
    // 
    // where
    // 
    // (11) sizeFactor = structSize(reaction) / PRODUCT(structsize(s_i))
    // (12) substanceConversionUnit = substanceunit(molecularRate)/substanceunit(concentrationRate) * PRODUCT(substanceunit([s_i])/substanceunit(<s_i>))
    // 
    // The ParticleJumpCondition wants a single new rate stochastic, P from equation (2).  Note that PRODUCT(<s_i>) will be captured separately the the reactantPatterns.
    // comparing (2) and (10) we have found P.
    // 
    // (13) P = K * sizeFactor * unitConversionFactor(substanceConversionUnit)
    // 
    // the framework also needs the proper unit for P
    // 
    // (14) Unit(P) = Unit(K) * Unit(sizeFactor) * substanceConversionUnit
    // 
    // 
    ModelUnitSystem modelUnitSystem = getSimulationContext().getModel().getUnitSystem();
    VCUnitDefinition stochasticSubstanceUnit = modelUnitSystem.getStochasticSubstanceUnit();
    VCUnitDefinition reactionRuleSubstanceUnit = modelUnitSystem.getSubstanceUnit(reactionRule.getStructure());
    int forwardRuleIndex = 0;
    // 
    // get forward rate parameter and make sure it is constant valued.
    // 
    Parameter forward_rateParameter = kinetics.getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate);
    Expression substitutedForwardRate = MathUtilities.substituteModelParameters(forward_rateParameter.getExpression(), reactionRule.getNameScope().getScopedSymbolTable());
    if (!substitutedForwardRate.flatten().isNumeric()) {
        throw new MappingException("forward rate constant for reaction rule " + reactionRule.getName() + " is not constant");
    }
    // 
    // create forward sizeExp and forward unitFactor
    // 
    VCUnitDefinition forward_substanceConversionUnit = stochasticSubstanceUnit.divideBy(reactionRuleSubstanceUnit);
    VCUnitDefinition forward_sizeFactorUnit = reactionRule.getStructure().getStructureSize().getUnitDefinition();
    Expression forward_sizeFactor = new Expression(reactionRule.getStructure().getStructureSize(), getNameScope());
    for (ReactantPattern reactantPattern : reactionRule.getReactantPatterns()) {
        Expression reactantSizeExp = new Expression(reactantPattern.getStructure().getStructureSize(), getNameScope());
        VCUnitDefinition reactantSizeUnit = reactantPattern.getStructure().getStructureSize().getUnitDefinition();
        VCUnitDefinition reactantSubstanceUnit = modelUnitSystem.getSubstanceUnit(reactantPattern.getStructure());
        forward_sizeFactor = Expression.div(forward_sizeFactor, reactantSizeExp);
        forward_sizeFactorUnit = forward_sizeFactorUnit.divideBy(reactantSizeUnit);
        forward_substanceConversionUnit = forward_substanceConversionUnit.multiplyBy(reactantSubstanceUnit).divideBy(stochasticSubstanceUnit);
    }
    // simplify sizeFactor (often has size/size/size)
    try {
        forward_sizeFactor = RationalExpUtils.getRationalExp(forward_sizeFactor).simplifyAsExpression();
        forward_sizeFactor.bindExpression(getSimulationContext().getModel());
    } catch (ParseException e) {
        e.printStackTrace();
    }
    Expression forward_rateExp = Expression.mult(new Expression(forward_rateParameter, getNameScope()), forward_sizeFactor, getUnitFactor(forward_substanceConversionUnit)).flatten();
    VCUnitDefinition forward_rateUnit = forward_rateParameter.getUnitDefinition().multiplyBy(forward_sizeFactorUnit).multiplyBy(forward_substanceConversionUnit);
    ProbabilityParameter forward_probParm = addProbabilityParameter(PARAMETER_PROBABILITYRATE_PREFIX + jpName, forward_rateExp, PARAMETER_ROLE_P, forward_rateUnit, reactionRule);
    // add probability to function or constant
    varHash.addVariable(newFunctionOrConstant(getMathSymbol(forward_probParm, geometryClass), getIdentifierSubstitutions(forward_rateExp, forward_rateUnit, geometryClass), geometryClass));
    // add forward ParticleJumpProcess
    String forward_name = reactionRuleName;
    Expression forward_rate = getIdentifierSubstitutions(new Expression(forward_probParm, getNameScope()), forward_probParm.getUnitDefinition(), geometryClass);
    JumpProcessRateDefinition forward_rateDefinition = new MacroscopicRateConstant(forward_rate);
    ReactionRuleAnalysisReport rrarBiomodelForward = ruleBasedTransformation.getRulesForwardMap().get(reactionRule);
    ProcessSymmetryFactor forwardSymmetryFactor = new ProcessSymmetryFactor(rrarBiomodelForward.getSymmetryFactor());
    ParticleJumpProcess forward_particleJumpProcess = new ParticleJumpProcess(forward_name, reactantParticles, forward_rateDefinition, forwardActions, forwardSymmetryFactor);
    subDomain.addParticleJumpProcess(forward_particleJumpProcess);
    // 
    for (ReactionRule rr : getSimulationContext().getModel().getRbmModelContainer().getReactionRuleList()) {
        if (rr == reactionRule) {
            break;
        }
        forwardRuleIndex++;
        if (rr.isReversible()) {
            forwardRuleIndex++;
        }
    }
    // 
    if (reactionRule.isReversible()) {
        Parameter reverse_rateParameter = kinetics.getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate);
        if (reverse_rateParameter == null || reverse_rateParameter.getExpression() == null) {
            throw new MappingException("reverse rate constant for reaction rule " + reactionRule.getName() + " is missing");
        }
        {
            Expression substitutedReverseRate = MathUtilities.substituteModelParameters(reverse_rateParameter.getExpression(), reactionRule.getNameScope().getScopedSymbolTable());
            if (!substitutedReverseRate.flatten().isNumeric()) {
                throw new MappingException("reverse rate constant for reaction rule " + reactionRule.getName() + " is not constant");
            }
        }
        // 
        // create reverse sizeExp and reverse unitFactor
        // 
        VCUnitDefinition reverse_substanceConversionUnit = stochasticSubstanceUnit.divideBy(reactionRuleSubstanceUnit);
        VCUnitDefinition reverse_sizeFactorUnit = reactionRule.getStructure().getStructureSize().getUnitDefinition();
        Expression reverse_sizeFactor = new Expression(reactionRule.getStructure().getStructureSize(), getNameScope());
        for (ProductPattern productPattern : reactionRule.getProductPatterns()) {
            Expression reactantSizeExp = new Expression(productPattern.getStructure().getStructureSize(), getNameScope());
            VCUnitDefinition reactantSizeUnit = productPattern.getStructure().getStructureSize().getUnitDefinition();
            VCUnitDefinition reactantSubstanceUnit = modelUnitSystem.getSubstanceUnit(productPattern.getStructure());
            reverse_sizeFactor = Expression.div(reverse_sizeFactor, reactantSizeExp);
            reverse_sizeFactorUnit = reverse_sizeFactorUnit.divideBy(reactantSizeUnit);
            reverse_substanceConversionUnit = reverse_substanceConversionUnit.multiplyBy(reactantSubstanceUnit).divideBy(stochasticSubstanceUnit);
        }
        // simplify sizeFactor (often has size/size/size)
        try {
            reverse_sizeFactor = RationalExpUtils.getRationalExp(reverse_sizeFactor).simplifyAsExpression();
            reverse_sizeFactor.bindExpression(getSimulationContext().getModel());
        } catch (ParseException e) {
            e.printStackTrace();
        }
        Expression reverse_rateExp = Expression.mult(new Expression(reverse_rateParameter, getNameScope()), reverse_sizeFactor, getUnitFactor(reverse_substanceConversionUnit)).flatten();
        VCUnitDefinition reverse_rateUnit = reverse_rateParameter.getUnitDefinition().multiplyBy(reverse_sizeFactorUnit).multiplyBy(reverse_substanceConversionUnit);
        // if the reaction has forward rate (Mass action,HMMs), or don't have either forward or reverse rate (some other rate laws--like general)
        // we process it as forward reaction
        // get jump process name
        ProbabilityParameter reverse_probParm = addProbabilityParameter(PARAMETER_PROBABILITYRATE_PREFIX + jpName + "_reverse", reverse_rateExp, PARAMETER_ROLE_P_reverse, reverse_rateUnit, reactionRule);
        // add probability to function or constant
        varHash.addVariable(newFunctionOrConstant(getMathSymbol(reverse_probParm, geometryClass), getIdentifierSubstitutions(reverse_rateExp, reverse_rateUnit, geometryClass), geometryClass));
        // add reverse ParticleJumpProcess
        Expression reverse_rate = getIdentifierSubstitutions(new Expression(reverse_probParm, getNameScope()), reverse_probParm.getUnitDefinition(), geometryClass);
        String reverse_name = reactionRuleName + "_reverse";
        JumpProcessRateDefinition reverse_rateDefinition = new MacroscopicRateConstant(reverse_rate);
        ReactionRuleAnalysisReport rrarBiomodelReverse = ruleBasedTransformation.getRulesReverseMap().get(reactionRule);
        ProcessSymmetryFactor reverseSymmetryFactor = new ProcessSymmetryFactor(rrarBiomodelReverse.getSymmetryFactor());
        ParticleJumpProcess reverse_particleJumpProcess = new ParticleJumpProcess(reverse_name, productParticles, reverse_rateDefinition, reverseActions, reverseSymmetryFactor);
        subDomain.addParticleJumpProcess(reverse_particleJumpProcess);
        // 
        // check reverse direction mapping and operations with RuleAnalysis.
        // 
        int reverseRuleIndex = forwardRuleIndex + 1;
        ReactionRuleAnalysisReport rrar = ruleBasedTransformation.getRulesReverseMap().get(reactionRule);
        jumpProcessMap.put(reverse_particleJumpProcess, rrar);
    }
}

Example 7 with JumpProcessRateDefinition

use of cbit.vcell.math.JumpProcessRateDefinition in project vcell by virtualcell.

the class Xmlproducer method getXML.

private org.jdom.Element getXML(ParticleJumpProcess param) {
    org.jdom.Element particleJumpProcessElement = new org.jdom.Element(XMLTags.ParticleJumpProcessTag);
    // name
    particleJumpProcessElement.setAttribute(XMLTags.NameAttrTag, mangle(param.getName()));
    if (param.getProcessSymmetryFactor() != null) {
        particleJumpProcessElement.setAttribute(XMLTags.ProcessSymmetryFactorAttrTag, Double.toString(param.getProcessSymmetryFactor().getFactor()));
    }
    // Selected Particle
    for (ParticleVariable vpv : param.getParticleVariables()) {
        Element e = new Element(XMLTags.SelectedParticleTag);
        e.setAttribute(XMLTags.NameAttrTag, mangle(vpv.getName()));
        particleJumpProcessElement.addContent(e);
    }
    // probability rate
    Element prob = null;
    JumpProcessRateDefinition particleProbabilityRate = param.getParticleRateDefinition();
    if (particleProbabilityRate instanceof MacroscopicRateConstant) {
        prob = new Element(XMLTags.MacroscopicRateConstantTag);
        prob.addContent(mangleExpression(((MacroscopicRateConstant) particleProbabilityRate).getExpression()));
    } else if (particleProbabilityRate instanceof InteractionRadius) {
        prob = new Element(XMLTags.InteractionRadiusTag);
        prob.addContent(mangleExpression(((InteractionRadius) particleProbabilityRate).getExpression()));
    } else {
        throw new RuntimeException("ParticleRateDefinition in XmlProducer not implemented");
    }
    particleJumpProcessElement.addContent(prob);
    // Actions
    for (Action action : param.getActions()) {
        particleJumpProcessElement.addContent(getXML(action));
    }
    return particleJumpProcessElement;
}