Examples with KineticsParameter cbit.vcell.model.Kinetics.KineticsParameter used on opensource projects

Example 41 with KineticsParameter

use of cbit.vcell.model.Kinetics.KineticsParameter in project vcell by virtualcell.

the class SBPAXHMMRevLawBuilder method addKinetics.

public void addKinetics(KineticContext context) {
    try {
        ReactionStep reaction = context.getReaction();
        HMM_REVKinetics kinetics = new HMM_REVKinetics((SimpleReaction) reaction);
        NameScope modelScope = reaction.getModel().getNameScope();
        ModelParameter kMichaelisFwd = context.getParameter(SBOList.MICHAELIS_CONST_FORW);
        if (kMichaelisFwd != null) {
            KineticsParameter kmfParameter = kinetics.getKmFwdParameter();
            kmfParameter.setExpression(new Expression(kMichaelisFwd, modelScope));
            kmfParameter.setUnitDefinition(kMichaelisFwd.getUnitDefinition());
        }
        ModelParameter kcatf = context.getParameter(SBOList.CATALYTIC_RATE_CONST_FORW);
        if (kcatf != null && context.getCatalysts().size() == 1) {
            KineticsParameter vmaxfParameter = kinetics.getVmaxFwdParameter();
            Catalyst catalyst = context.getCatalysts().iterator().next();
            vmaxfParameter.setExpression(Expression.mult(new Expression(kcatf, modelScope), new Expression(catalyst.getSpeciesContext(), modelScope)));
        // vmaxParameter.setUnitDefinition(vMax.getUnitDefinition());
        } else {
            ModelParameter vMaxf = context.getParameter(SBOList.MAXIMAL_VELOCITY_FORW);
            if (vMaxf != null) {
                KineticsParameter vmaxfParameter = kinetics.getVmaxFwdParameter();
                vmaxfParameter.setExpression(new Expression(vMaxf, modelScope));
                vmaxfParameter.setUnitDefinition(vMaxf.getUnitDefinition());
            }
        }
        ModelParameter kMichaelisRev = context.getParameter(SBOList.MICHAELIS_CONST_REV);
        if (kMichaelisRev != null) {
            KineticsParameter kmrParameter = kinetics.getKmRevParameter();
            kmrParameter.setExpression(new Expression(kMichaelisRev, modelScope));
            kmrParameter.setUnitDefinition(kMichaelisRev.getUnitDefinition());
        }
        ModelParameter kcatr = context.getParameter(SBOList.CATALYTIC_RATE_CONST_FORW);
        if (kcatr != null && context.getCatalysts().size() == 1) {
            KineticsParameter vmaxrParameter = kinetics.getVmaxRevParameter();
            Catalyst catalyst = context.getCatalysts().iterator().next();
            vmaxrParameter.setExpression(Expression.mult(new Expression(kcatr, modelScope), new Expression(catalyst.getSpeciesContext(), modelScope)));
        // vmaxParameter.setUnitDefinition(vMax.getUnitDefinition());
        } else {
            ModelParameter vMaxr = context.getParameter(SBOList.MAXIMAL_VELOCITY_REV);
            if (vMaxr != null) {
                KineticsParameter vmaxrParameter = kinetics.getVmaxRevParameter();
                vmaxrParameter.setExpression(new Expression(vMaxr, modelScope));
                vmaxrParameter.setUnitDefinition(vMaxr.getUnitDefinition());
            }
        }
    } catch (ExpressionException e) {
        e.printStackTrace();
    }
}

Example 42 with KineticsParameter

use of cbit.vcell.model.Kinetics.KineticsParameter in project vcell by virtualcell.

the class SBPAXKineticsExtractor method setVMForwardParam.

private static void setVMForwardParam(ReactionStep reaction, SBOParam kVMForward, Kinetics kinetics) throws ExpressionException, PropertyVetoException {
    if (kVMForward != null) {
        KineticsParameter fwdParam = ((HMM_IRRKinetics) kinetics).getVmaxParameter();
        kinetics.setParameterValue(fwdParam, new Expression(kVMForward.getNumber()));
        String unitF = SBOParam.formatUnit(kVMForward.getUnit());
        VCUnitDefinition fwdUnit = reaction.getModel().getUnitSystem().getInstance(unitF);
        fwdParam.setUnitDefinition(fwdUnit);
    }
}

Example 43 with KineticsParameter

use of cbit.vcell.model.Kinetics.KineticsParameter in project vcell by virtualcell.

the class SBPAXKineticsExtractor method setVMForwardParamAsExpression.

private static void setVMForwardParamAsExpression(ReactionStep reaction, SBOParam kCat, Kinetics kinetics) throws ExpressionException, PropertyVetoException {
    if (kCat != null) {
        KineticsParameter Vmax = ((HMM_IRRKinetics) kinetics).getVmaxParameter();
        String unitF = SBOParam.formatUnit(kCat.getUnit());
        VCUnitDefinition kCatUnit = reaction.getModel().getUnitSystem().getInstance(unitF);
        Double numberKCat = 0.0;
        if (kCat.hasNumber()) {
            numberKCat = kCat.getNumber();
        }
        Expression KCatExpression = new Expression(numberKCat);
        KineticsParameter Kcat = kinetics.addUserDefinedKineticsParameter("Kcat", KCatExpression, kCatUnit);
        String enzymeName = "";
        ReactionParticipant[] participants = reaction.getReactionParticipants();
        for (int i = 0; i < participants.length; i++) {
            ReactionParticipant rp = participants[i];
            if (rp instanceof Catalyst) {
                enzymeName = rp.getName();
            }
        }
        SpeciesContext enzyme = reaction.getModel().getSpeciesContext(enzymeName);
        Vmax.setExpression(Expression.mult(new Expression(Kcat, reaction.getNameScope()), new Expression(enzyme, reaction.getNameScope())));
    }
}

Example 44 with KineticsParameter

use of cbit.vcell.model.Kinetics.KineticsParameter in project vcell by virtualcell.

the class SBPAXKineticsExtractor method setMichaelisForwardParam.

private static void setMichaelisForwardParam(ReactionStep reaction, SBOParam kMichaelis, Kinetics kinetics) throws ExpressionException, PropertyVetoException {
    if (kMichaelis != null) {
        KineticsParameter fwdParam = ((HMM_IRRKinetics) kinetics).getKmParameter();
        kinetics.setParameterValue(fwdParam, new Expression(kMichaelis.getNumber()));
        String unitF = SBOParam.formatUnit(kMichaelis.getUnit());
        VCUnitDefinition fwdUnit = reaction.getModel().getUnitSystem().getInstance(unitF);
        fwdParam.setUnitDefinition(fwdUnit);
    }
}

Example 45 with KineticsParameter

use of cbit.vcell.model.Kinetics.KineticsParameter in project vcell by virtualcell.

the class Generate2DSimBioModelOp method generateBioModel.

public BioModel generateBioModel(Extent extent, ROI cellROI_2D, double[] timeStamps, Integer indexFirstPostbleach, double primaryDiffusionRate, double primaryFraction, double bleachMonitorRate, Double secondaryDiffusionRate, double secondaryFraction, Double bindingSiteConcentration, double bindingOnRate, double bindingOffRate, String extracellularName, String cytosolName, User owner, KeyValue simKey) throws PropertyVetoException, ExpressionException, ModelException, GeometryException, ImageException, MappingException, MathException, MatrixException {
    if (owner == null) {
        throw new IllegalArgumentException("Owner is not defined");
    }
    double df = primaryDiffusionRate;
    double ff = primaryFraction;
    double bwmRate = bleachMonitorRate;
    double dc = 0.0;
    double fc = 0.0;
    if (secondaryDiffusionRate != null) {
        dc = secondaryDiffusionRate;
        fc = secondaryFraction;
    }
    double bs = 0.0;
    double onRate = 0.0;
    double offRate = 0.0;
    if (bindingSiteConcentration != null) {
        bs = bindingSiteConcentration;
        onRate = bindingOnRate;
        offRate = bindingOffRate;
    }
    // immobile fraction
    double fimm = 1 - ff - fc;
    if (fimm < epsilon && fimm > (0 - epsilon)) {
        fimm = 0;
    }
    if (fimm < (1 + epsilon) && fimm > (1 - epsilon)) {
        fimm = 1;
    }
    int startingIndexForRecovery = indexFirstPostbleach;
    TimeBounds timeBounds = new TimeBounds(0.0, timeStamps[timeStamps.length - 1] - timeStamps[startingIndexForRecovery]);
    double timeStepVal = timeStamps[startingIndexForRecovery + 1] - timeStamps[startingIndexForRecovery];
    ROI cellROI = cellROI_2D;
    int numX = cellROI.getISize().getX();
    int numY = cellROI.getISize().getY();
    int numZ = cellROI.getISize().getZ();
    short[] shortPixels = cellROI.getRoiImages()[0].getPixels();
    byte[] bytePixels = new byte[numX * numY * numZ];
    final byte EXTRACELLULAR_PIXVAL = 0;
    final byte CYTOSOL_PIXVAL = 1;
    for (int i = 0; i < bytePixels.length; i++) {
        if (shortPixels[i] != 0) {
            bytePixels[i] = CYTOSOL_PIXVAL;
        }
    }
    VCImage maskImage;
    try {
        maskImage = new VCImageUncompressed(null, bytePixels, extent, numX, numY, numZ);
    } catch (ImageException e) {
        e.printStackTrace();
        throw new RuntimeException("failed to create mask image for geometry");
    }
    Geometry geometry = new Geometry("geometry", maskImage);
    if (geometry.getGeometrySpec().getNumSubVolumes() != 2) {
        throw new IllegalArgumentException("Cell ROI has no ExtraCellular.");
    }
    String EXTRACELLULAR_NAME = extracellularName;
    String CYTOSOL_NAME = cytosolName;
    int subVolume0PixVal = ((ImageSubVolume) geometry.getGeometrySpec().getSubVolume(0)).getPixelValue();
    geometry.getGeometrySpec().getSubVolume(0).setName((subVolume0PixVal == EXTRACELLULAR_PIXVAL ? EXTRACELLULAR_NAME : CYTOSOL_NAME));
    int subVolume1PixVal = ((ImageSubVolume) geometry.getGeometrySpec().getSubVolume(1)).getPixelValue();
    geometry.getGeometrySpec().getSubVolume(1).setName((subVolume1PixVal == CYTOSOL_PIXVAL ? CYTOSOL_NAME : EXTRACELLULAR_NAME));
    geometry.getGeometrySurfaceDescription().updateAll();
    BioModel bioModel = new BioModel(null);
    bioModel.setName("unnamed");
    Model model = new Model("model");
    bioModel.setModel(model);
    model.addFeature(EXTRACELLULAR_NAME);
    Feature extracellular = (Feature) model.getStructure(EXTRACELLULAR_NAME);
    model.addFeature(CYTOSOL_NAME);
    Feature cytosol = (Feature) model.getStructure(CYTOSOL_NAME);
    // Membrane mem = model.addMembrane(EXTRACELLULAR_CYTOSOL_MEM_NAME);
    // model.getStructureTopology().setInsideFeature(mem, cytosol);
    // model.getStructureTopology().setOutsideFeature(mem, extracellular);
    String roiDataName = ROI_EXTDATA_NAME;
    final int SPECIES_COUNT = 4;
    final int FREE_SPECIES_INDEX = 0;
    final int BS_SPECIES_INDEX = 1;
    final int COMPLEX_SPECIES_INDEX = 2;
    final int IMMOBILE_SPECIES_INDEX = 3;
    Expression[] diffusionConstants = null;
    Species[] species = null;
    SpeciesContext[] speciesContexts = null;
    Expression[] initialConditions = null;
    diffusionConstants = new Expression[SPECIES_COUNT];
    species = new Species[SPECIES_COUNT];
    speciesContexts = new SpeciesContext[SPECIES_COUNT];
    initialConditions = new Expression[SPECIES_COUNT];
    // total initial condition
    FieldFunctionArguments postBleach_first = new FieldFunctionArguments(roiDataName, "postbleach_first", new Expression(0), VariableType.VOLUME);
    FieldFunctionArguments prebleach_avg = new FieldFunctionArguments(roiDataName, "prebleach_avg", new Expression(0), VariableType.VOLUME);
    Expression expPostBleach_first = new Expression(postBleach_first.infix());
    Expression expPreBleach_avg = new Expression(prebleach_avg.infix());
    Expression totalIniCondition = Expression.div(expPostBleach_first, expPreBleach_avg);
    // Free Species
    diffusionConstants[FREE_SPECIES_INDEX] = new Expression(df);
    species[FREE_SPECIES_INDEX] = new Species(SPECIES_NAME_PREFIX_MOBILE, "Mobile bleachable species");
    speciesContexts[FREE_SPECIES_INDEX] = new SpeciesContext(null, species[FREE_SPECIES_INDEX].getCommonName(), species[FREE_SPECIES_INDEX], cytosol);
    initialConditions[FREE_SPECIES_INDEX] = Expression.mult(new Expression(ff), totalIniCondition);
    // Immobile Species (No diffusion)
    // Set very small diffusion rate on immobile to force evaluation as state variable (instead of FieldData function)
    // If left as a function errors occur because functions involving FieldData require a database connection
    final String IMMOBILE_DIFFUSION_KLUDGE = "1e-14";
    diffusionConstants[IMMOBILE_SPECIES_INDEX] = new Expression(IMMOBILE_DIFFUSION_KLUDGE);
    species[IMMOBILE_SPECIES_INDEX] = new Species(SPECIES_NAME_PREFIX_IMMOBILE, "Immobile bleachable species");
    speciesContexts[IMMOBILE_SPECIES_INDEX] = new SpeciesContext(null, species[IMMOBILE_SPECIES_INDEX].getCommonName(), species[IMMOBILE_SPECIES_INDEX], cytosol);
    initialConditions[IMMOBILE_SPECIES_INDEX] = Expression.mult(new Expression(fimm), totalIniCondition);
    // BS Species
    diffusionConstants[BS_SPECIES_INDEX] = new Expression(IMMOBILE_DIFFUSION_KLUDGE);
    species[BS_SPECIES_INDEX] = new Species(SPECIES_NAME_PREFIX_BINDING_SITE, "Binding Site species");
    speciesContexts[BS_SPECIES_INDEX] = new SpeciesContext(null, species[BS_SPECIES_INDEX].getCommonName(), species[BS_SPECIES_INDEX], cytosol);
    initialConditions[BS_SPECIES_INDEX] = Expression.mult(new Expression(bs), totalIniCondition);
    // Complex species
    diffusionConstants[COMPLEX_SPECIES_INDEX] = new Expression(dc);
    species[COMPLEX_SPECIES_INDEX] = new Species(SPECIES_NAME_PREFIX_SLOW_MOBILE, "Slower mobile bleachable species");
    speciesContexts[COMPLEX_SPECIES_INDEX] = new SpeciesContext(null, species[COMPLEX_SPECIES_INDEX].getCommonName(), species[COMPLEX_SPECIES_INDEX], cytosol);
    initialConditions[COMPLEX_SPECIES_INDEX] = Expression.mult(new Expression(fc), totalIniCondition);
    // add reactions to species if there is bleachWhileMonitoring rate.
    for (int i = 0; i < initialConditions.length; i++) {
        model.addSpecies(species[i]);
        model.addSpeciesContext(speciesContexts[i]);
        // reaction with BMW rate, which should not be applied to binding site
        if (!(species[i].getCommonName().equals(SPECIES_NAME_PREFIX_BINDING_SITE))) {
            SimpleReaction simpleReaction = new SimpleReaction(model, cytosol, speciesContexts[i].getName() + "_bleach", true);
            model.addReactionStep(simpleReaction);
            simpleReaction.addReactant(speciesContexts[i], 1);
            MassActionKinetics massActionKinetics = new MassActionKinetics(simpleReaction);
            simpleReaction.setKinetics(massActionKinetics);
            KineticsParameter kforward = massActionKinetics.getForwardRateParameter();
            simpleReaction.getKinetics().setParameterValue(kforward, new Expression(new Double(bwmRate)));
        }
    }
    // add the binding reaction: F + BS <-> C
    SimpleReaction simpleReaction2 = new SimpleReaction(model, cytosol, "reac_binding", true);
    model.addReactionStep(simpleReaction2);
    simpleReaction2.addReactant(speciesContexts[FREE_SPECIES_INDEX], 1);
    simpleReaction2.addReactant(speciesContexts[BS_SPECIES_INDEX], 1);
    simpleReaction2.addProduct(speciesContexts[COMPLEX_SPECIES_INDEX], 1);
    MassActionKinetics massActionKinetics = new MassActionKinetics(simpleReaction2);
    simpleReaction2.setKinetics(massActionKinetics);
    KineticsParameter kforward = massActionKinetics.getForwardRateParameter();
    KineticsParameter kreverse = massActionKinetics.getReverseRateParameter();
    simpleReaction2.getKinetics().setParameterValue(kforward, new Expression(new Double(onRate)));
    simpleReaction2.getKinetics().setParameterValue(kreverse, new Expression(new Double(offRate)));
    // create simulation context
    SimulationContext simContext = new SimulationContext(bioModel.getModel(), geometry);
    bioModel.addSimulationContext(simContext);
    FeatureMapping cytosolFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(cytosol);
    FeatureMapping extracellularFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(extracellular);
    SubVolume cytSubVolume = geometry.getGeometrySpec().getSubVolume(CYTOSOL_NAME);
    SubVolume exSubVolume = geometry.getGeometrySpec().getSubVolume(EXTRACELLULAR_NAME);
    SurfaceClass pmSurfaceClass = geometry.getGeometrySurfaceDescription().getSurfaceClass(exSubVolume, cytSubVolume);
    cytosolFeatureMapping.setGeometryClass(cytSubVolume);
    extracellularFeatureMapping.setGeometryClass(exSubVolume);
    cytosolFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    extracellularFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    for (int i = 0; i < speciesContexts.length; i++) {
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(speciesContexts[i]);
        scs.getInitialConditionParameter().setExpression(initialConditions[i]);
        scs.getDiffusionParameter().setExpression(diffusionConstants[i]);
    }
    MathMapping mathMapping = simContext.createNewMathMapping();
    MathDescription mathDesc = mathMapping.getMathDescription();
    // Add total fluorescence as function of mobile(optional: and slower mobile) and immobile fractions
    mathDesc.addVariable(new Function(SPECIES_NAME_PREFIX_COMBINED, new Expression(species[FREE_SPECIES_INDEX].getCommonName() + "+" + species[COMPLEX_SPECIES_INDEX].getCommonName() + "+" + species[IMMOBILE_SPECIES_INDEX].getCommonName()), null));
    simContext.setMathDescription(mathDesc);
    SimulationVersion simVersion = new SimulationVersion(simKey, "sim1", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation newSimulation = new Simulation(simVersion, mathDesc);
    simContext.addSimulation(newSimulation);
    newSimulation.getSolverTaskDescription().setTimeBounds(timeBounds);
    newSimulation.getMeshSpecification().setSamplingSize(cellROI.getISize());
    // newSimulation.getSolverTaskDescription().setTimeStep(timeStep); // Sundials doesn't need time step
    newSimulation.getSolverTaskDescription().setSolverDescription(SolverDescription.SundialsPDE);
    // use exp time step as output time spec
    newSimulation.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec(timeStepVal));
    return bioModel;
}