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

Example 1 with GeneralKinetics

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

the class SBMLImporter method addReactions.

/**
 * addReactions:
 */
protected void addReactions(VCMetaData metaData) {
    if (sbmlModel == null) {
        throw new SBMLImportException("SBML model is NULL");
    }
    ListOf<Reaction> reactions = sbmlModel.getListOfReactions();
    final int numReactions = reactions.size();
    if (numReactions == 0) {
        lg.info("No Reactions");
        return;
    }
    // all reactions
    ArrayList<ReactionStep> vcReactionList = new ArrayList<>();
    // just the fast ones
    ArrayList<ReactionStep> fastReactionList = new ArrayList<>();
    Model vcModel = vcBioModel.getSimulationContext(0).getModel();
    ModelUnitSystem vcModelUnitSystem = vcModel.getUnitSystem();
    SpeciesContext[] vcSpeciesContexts = vcModel.getSpeciesContexts();
    try {
        for (Reaction sbmlRxn : reactions) {
            ReactionStep vcReaction = null;
            String rxnName = sbmlRxn.getId();
            boolean bReversible = true;
            if (sbmlRxn.isSetReversible()) {
                bReversible = sbmlRxn.getReversible();
            }
            // Check of reaction annotation is present; if so, does it have
            // an embedded element (flux or simpleRxn).
            // Create a fluxReaction or simpleReaction accordingly.
            Element sbmlImportRelatedElement = sbmlAnnotationUtil.readVCellSpecificAnnotation(sbmlRxn);
            Structure reactionStructure = getReactionStructure(sbmlRxn, vcSpeciesContexts, sbmlImportRelatedElement);
            if (sbmlImportRelatedElement != null) {
                Element embeddedRxnElement = getEmbeddedElementInAnnotation(sbmlImportRelatedElement, REACTION);
                if (embeddedRxnElement != null) {
                    if (embeddedRxnElement.getName().equals(XMLTags.FluxStepTag)) {
                        // If embedded element is a flux reaction, set flux
                        // reaction's strucure, flux carrier, physicsOption
                        // from the element attributes.
                        String structName = embeddedRxnElement.getAttributeValue(XMLTags.StructureAttrTag);
                        CastInfo<Membrane> ci = SBMLHelper.getTypedStructure(Membrane.class, vcModel, structName);
                        if (!ci.isGood()) {
                            throw new SBMLImportException("Appears that the flux reaction is occuring on " + ci.actualName() + ", not a membrane.");
                        }
                        vcReaction = new FluxReaction(vcModel, ci.get(), null, rxnName, bReversible);
                        vcReaction.setModel(vcModel);
                        // Set the fluxOption on the flux reaction based on
                        // whether it is molecular, molecular & electrical,
                        // electrical.
                        String fluxOptionStr = embeddedRxnElement.getAttributeValue(XMLTags.FluxOptionAttrTag);
                        if (fluxOptionStr.equals(XMLTags.FluxOptionMolecularOnly)) {
                            ((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_MOLECULAR_ONLY);
                        } else if (fluxOptionStr.equals(XMLTags.FluxOptionMolecularAndElectrical)) {
                            ((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_MOLECULAR_AND_ELECTRICAL);
                        } else if (fluxOptionStr.equals(XMLTags.FluxOptionElectricalOnly)) {
                            ((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_ELECTRICAL_ONLY);
                        } else {
                            localIssueList.add(new Issue(vcReaction, issueContext, IssueCategory.SBMLImport_Reaction, "Unknown FluxOption : " + fluxOptionStr + " for SBML reaction : " + rxnName, Issue.SEVERITY_WARNING));
                        // logger.sendMessage(VCLogger.Priority.MediumPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Unknown FluxOption : " + fluxOptionStr +
                        // " for SBML reaction : " + rxnName);
                        }
                    } else if (embeddedRxnElement.getName().equals(XMLTags.SimpleReactionTag)) {
                        // if embedded element is a simple reaction, set
                        // simple reaction's structure from element
                        // attributes
                        vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnName, bReversible);
                    }
                } else {
                    vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnName, bReversible);
                }
            } else {
                vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnName, bReversible);
            }
            // set annotations and notes on vcReactions[i]
            sbmlAnnotationUtil.readAnnotation(vcReaction, sbmlRxn);
            sbmlAnnotationUtil.readNotes(vcReaction, sbmlRxn);
            // the limit on the reactionName length.
            if (rxnName.length() > 64) {
                String freeTextAnnotation = metaData.getFreeTextAnnotation(vcReaction);
                if (freeTextAnnotation == null) {
                    freeTextAnnotation = "";
                }
                StringBuffer oldRxnAnnotation = new StringBuffer(freeTextAnnotation);
                oldRxnAnnotation.append("\n\n" + rxnName);
                metaData.setFreeTextAnnotation(vcReaction, oldRxnAnnotation.toString());
            }
            // Now add the reactants, products, modifiers as specified by
            // the sbmlRxn
            addReactionParticipants(sbmlRxn, vcReaction);
            KineticLaw kLaw = sbmlRxn.getKineticLaw();
            Kinetics kinetics = null;
            if (kLaw != null) {
                // Convert the formula from kineticLaw into MathML and then
                // to an expression (infix) to be used in VCell kinetics
                ASTNode sbmlRateMath = kLaw.getMath();
                Expression kLawRateExpr = getExpressionFromFormula(sbmlRateMath);
                Expression vcRateExpression = new Expression(kLawRateExpr);
                // modifier (catalyst) to the reaction.
                for (int k = 0; k < vcSpeciesContexts.length; k++) {
                    if (vcRateExpression.hasSymbol(vcSpeciesContexts[k].getName())) {
                        if ((vcReaction.getReactant(vcSpeciesContexts[k].getName()) == null) && (vcReaction.getProduct(vcSpeciesContexts[k].getName()) == null) && (vcReaction.getCatalyst(vcSpeciesContexts[k].getName()) == null)) {
                            // This means that the speciesContext is not a
                            // reactant, product or modifier : it has to be
                            // added to the VC Rxn as a catalyst
                            vcReaction.addCatalyst(vcSpeciesContexts[k]);
                        }
                    }
                }
                // set kinetics on VCell reaction
                if (bSpatial) {
                    // if spatial SBML ('isSpatial' attribute set), create
                    // DistributedKinetics)
                    SpatialReactionPlugin ssrplugin = (SpatialReactionPlugin) sbmlRxn.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
                    // 'spatial'
                    if (ssrplugin != null && ssrplugin.getIsLocal()) {
                        kinetics = new GeneralKinetics(vcReaction);
                    } else {
                        kinetics = new GeneralLumpedKinetics(vcReaction);
                    }
                } else {
                    kinetics = new GeneralLumpedKinetics(vcReaction);
                }
                // set kinetics on vcReaction
                vcReaction.setKinetics(kinetics);
                // If the name of the rate parameter has been changed by
                // user, or matches with global/local param,
                // it has to be changed.
                resolveRxnParameterNameConflicts(sbmlRxn, kinetics, sbmlImportRelatedElement);
                /**
                 * Now, based on the kinetic law expression, see if the rate
                 * is expressed in concentration/time or substance/time : If
                 * the compartment_id of the compartment corresponding to
                 * the structure in which the reaction takes place occurs in
                 * the rate law expression, it is in concentration/time;
                 * divide it by the compartment size and bring in the rate
                 * law as 'Distributed' kinetics. If not, the rate law is in
                 * substance/time; bring it in (as is) as 'Lumped' kinetics.
                 */
                ListOf<LocalParameter> localParameters = kLaw.getListOfLocalParameters();
                for (LocalParameter p : localParameters) {
                    String paramName = p.getId();
                    KineticsParameter kineticsParameter = kinetics.getKineticsParameter(paramName);
                    if (kineticsParameter == null) {
                        // add unresolved for now to prevent errors in kinetics.setParameterValue(kp,vcRateExpression) below
                        kinetics.addUnresolvedParameter(paramName);
                    }
                }
                KineticsParameter kp = kinetics.getAuthoritativeParameter();
                if (lg.isDebugEnabled()) {
                    lg.debug("Setting " + kp.getName() + ":  " + vcRateExpression.infix());
                }
                kinetics.setParameterValue(kp, vcRateExpression);
                // If there are any global parameters used in the kinetics,
                // and if they have species,
                // check if the species are already reactionParticipants in
                // the reaction. If not, add them as catalysts.
                KineticsProxyParameter[] kpps = kinetics.getProxyParameters();
                for (int j = 0; j < kpps.length; j++) {
                    if (kpps[j].getTarget() instanceof ModelParameter) {
                        ModelParameter mp = (ModelParameter) kpps[j].getTarget();
                        HashSet<String> refSpeciesNameHash = new HashSet<String>();
                        getReferencedSpeciesInExpr(mp.getExpression(), refSpeciesNameHash);
                        java.util.Iterator<String> refSpIterator = refSpeciesNameHash.iterator();
                        while (refSpIterator.hasNext()) {
                            String spName = refSpIterator.next();
                            org.sbml.jsbml.Species sp = sbmlModel.getSpecies(spName);
                            ArrayList<ReactionParticipant> rpArray = getVCReactionParticipantsFromSymbol(vcReaction, sp.getId());
                            if (rpArray == null || rpArray.size() == 0) {
                                // This means that the speciesContext is not
                                // a reactant, product or modifier : it has
                                // to be added as a catalyst
                                vcReaction.addCatalyst(vcModel.getSpeciesContext(sp.getId()));
                            }
                        }
                    }
                }
                // model - local params cannot be defined by rules.
                for (LocalParameter param : localParameters) {
                    String paramName = param.getId();
                    Expression exp = new Expression(param.getValue());
                    String unitString = param.getUnits();
                    VCUnitDefinition paramUnit = sbmlUnitIdentifierHash.get(unitString);
                    if (paramUnit == null) {
                        paramUnit = vcModelUnitSystem.getInstance_TBD();
                    }
                    // check if sbml local param is in kinetic params list;
                    // if so, add its value.
                    boolean lpSet = false;
                    KineticsParameter kineticsParameter = kinetics.getKineticsParameter(paramName);
                    if (kineticsParameter != null) {
                        if (lg.isDebugEnabled()) {
                            lg.debug("Setting local " + kineticsParameter.getName() + ":  " + exp.infix());
                        }
                        kineticsParameter.setExpression(exp);
                        kineticsParameter.setUnitDefinition(paramUnit);
                        lpSet = true;
                    } else {
                        UnresolvedParameter ur = kinetics.getUnresolvedParameter(paramName);
                        if (ur != null) {
                            kinetics.addUserDefinedKineticsParameter(paramName, exp, paramUnit);
                            lpSet = true;
                        }
                    }
                    if (!lpSet) {
                        // check if it is a proxy parameter (specifically,
                        // speciesContext or model parameter (structureSize
                        // too)).
                        KineticsProxyParameter kpp = kinetics.getProxyParameter(paramName);
                        // and units to local param values
                        if (kpp != null && kpp.getTarget() instanceof ModelParameter) {
                            kinetics.convertParameterType(kpp, false);
                            kineticsParameter = kinetics.getKineticsParameter(paramName);
                            kinetics.setParameterValue(kineticsParameter, exp);
                            kineticsParameter.setUnitDefinition(paramUnit);
                        }
                    }
                }
            } else {
                // sbmlKLaw was null, so creating a GeneralKinetics with 0.0
                // as rate.
                kinetics = new GeneralKinetics(vcReaction);
            }
            // end - if-else KLaw != null
            // set the reaction kinetics, and add reaction to the vcell
            // model.
            kinetics.resolveUndefinedUnits();
            // System.out.println("ADDED SBML REACTION : \"" + rxnName +
            // "\" to VCModel");
            vcReactionList.add(vcReaction);
            if (sbmlRxn.isSetFast() && sbmlRxn.getFast()) {
                fastReactionList.add(vcReaction);
            }
        }
        // end - for vcReactions
        ReactionStep[] array = vcReactionList.toArray(new ReactionStep[vcReactionList.size()]);
        vcModel.setReactionSteps(array);
        final ReactionContext rc = vcBioModel.getSimulationContext(0).getReactionContext();
        for (ReactionStep frs : fastReactionList) {
            final ReactionSpec rs = rc.getReactionSpec(frs);
            rs.setReactionMapping(ReactionSpec.FAST);
        }
    } catch (ModelPropertyVetoException mpve) {
        throw new SBMLImportException(mpve.getMessage(), mpve);
    } catch (Exception e1) {
        e1.printStackTrace(System.out);
        throw new SBMLImportException(e1.getMessage(), e1);
    }
}

Example 2 with GeneralKinetics

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

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a Kinetics object type.
 * Creation date: (2/26/2001 7:31:43 PM)
 * @return Element
 * @param param cbit.vcell.model.Kinetics
 */
private Element getXML(Kinetics param) throws XmlParseException {
    String kineticsType = null;
    if (param instanceof GeneralKinetics) {
        // process a GeneralKinetics object
        kineticsType = XMLTags.KineticsTypeGeneralKinetics;
    } else if (param instanceof MassActionKinetics) {
        // Process a MassActionKinetics
        kineticsType = XMLTags.KineticsTypeMassAction;
    } else if (param instanceof NernstKinetics) {
        // Process a NernstKinetics
        kineticsType = XMLTags.KineticsTypeNernst;
    } else if (param instanceof GHKKinetics) {
        // Process a GHKKinetics
        kineticsType = XMLTags.KineticsTypeGHK;
    } else if (param instanceof GeneralCurrentKinetics) {
        // Process a GeneralCurrentKinetics
        kineticsType = XMLTags.KineticsTypeGeneralCurrentKinetics;
    } else if (param instanceof HMM_IRRKinetics) {
        // Process a HenriMichaelasMentenKinetics (irreversible)
        kineticsType = XMLTags.KineticsTypeHMM_Irr;
    } else if (param instanceof HMM_REVKinetics) {
        // Process a HenriMichaelasMentenKinetics (reversible)
        kineticsType = XMLTags.KineticsTypeHMM_Rev;
    } else if (param instanceof GeneralLumpedKinetics) {
        // Process a GeneralLumpedKinetics
        kineticsType = XMLTags.KineticsTypeGeneralLumped;
    } else if (param instanceof GeneralCurrentLumpedKinetics) {
        // Process a GeneralCurrentLumpedKinetics
        kineticsType = XMLTags.KineticsTypeGeneralCurrentLumped;
    } else if (param instanceof GeneralPermeabilityKinetics) {
        // Process a GeneralPermeabilityKinetics
        kineticsType = XMLTags.KineticsTypeGeneralPermeability;
    } else if (param instanceof Macroscopic_IRRKinetics) {
        // Process a Macroscopic_IRRKinetics
        kineticsType = XMLTags.KineticsTypeMacroscopic_Irr;
    } else if (param instanceof Microscopic_IRRKinetics) {
        // Process a Microscopic_IRRKinetics
        kineticsType = XMLTags.KineticsTypeMicroscopic_Irr;
    }
    Element kinetics = new Element(XMLTags.KineticsTag);
    // Add atributes
    kinetics.setAttribute(XMLTags.KineticsTypeAttrTag, kineticsType);
    // Add Kinetics Parameters
    Kinetics.KineticsParameter[] parameters = param.getKineticsParameters();
    for (int i = 0; i < parameters.length; i++) {
        Kinetics.KineticsParameter parm = parameters[i];
        Element tempparameter = new Element(XMLTags.ParameterTag);
        // Get parameter attributes
        tempparameter.setAttribute(XMLTags.NameAttrTag, mangle(parm.getName()));
        tempparameter.setAttribute(XMLTags.ParamRoleAttrTag, param.getDefaultParameterDesc(parm.getRole()));
        VCUnitDefinition unit = parm.getUnitDefinition();
        if (unit != null) {
            tempparameter.setAttribute(XMLTags.VCUnitDefinitionAttrTag, unit.getSymbol());
        }
        tempparameter.addContent(mangleExpression(parm.getExpression()));
        // Add the parameter to the general kinetics object
        kinetics.addContent(tempparameter);
    }
    return kinetics;
}

Example 3 with GeneralKinetics

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

the class Generate2DExpModelOpAbstract method generateModel.

public final GeneratedModelResults generateModel(double deltaX, double bleachRadius, double cellRadius, double bleachDuration, double bleachRate, double postbleachDelay, double postbleachDuration, double psfSigma, double outputTimeStep, double primaryDiffusionRate, double primaryFraction, double bleachMonitorRate, double secondaryDiffusionRate, double secondaryFraction, String extracellularName, String cytosolName, Context context) throws PropertyVetoException, ExpressionException, GeometryException, ImageException, ModelException, MappingException, MathException, MatrixException {
    double domainSize = 2.2 * cellRadius;
    Extent extent = new Extent(domainSize, domainSize, 1.0);
    Origin origin = new Origin(-extent.getX() / 2.0, -extent.getY() / 2.0, -extent.getZ() / 2.0);
    String EXTRACELLULAR_NAME = extracellularName;
    String CYTOSOL_NAME = cytosolName;
    AnalyticSubVolume cytosolSubVolume = new AnalyticSubVolume(CYTOSOL_NAME, new Expression("pow(x,2)+pow(y,2)<pow(" + cellRadius + ",2)"));
    AnalyticSubVolume extracellularSubVolume = new AnalyticSubVolume(EXTRACELLULAR_NAME, new Expression(1.0));
    Geometry geometry = new Geometry("geometry", 2);
    geometry.getGeometrySpec().setExtent(extent);
    geometry.getGeometrySpec().setOrigin(origin);
    geometry.getGeometrySpec().addSubVolume(extracellularSubVolume);
    geometry.getGeometrySpec().addSubVolume(cytosolSubVolume, true);
    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);
    SpeciesContext immobileSC = model.createSpeciesContext(cytosol);
    SpeciesContext primarySC = model.createSpeciesContext(cytosol);
    SpeciesContext secondarySC = model.createSpeciesContext(cytosol);
    // 
    // common bleaching rate for all species
    // 
    double bleachStart = 10 * outputTimeStep - bleachDuration - postbleachDelay;
    double bleachEnd = bleachStart + bleachDuration;
    Expression bleachRateExp = createBleachExpression(bleachRadius, bleachRate, bleachMonitorRate, bleachStart, bleachEnd);
    {
        SimpleReaction immobileBWM = model.createSimpleReaction(cytosol);
        GeneralKinetics immobileBWMKinetics = new GeneralKinetics(immobileBWM);
        immobileBWM.setKinetics(immobileBWMKinetics);
        immobileBWM.addReactant(immobileSC, 1);
        immobileBWMKinetics.getReactionRateParameter().setExpression(Expression.mult(bleachRateExp, new Expression(immobileSC.getName())));
    }
    {
        SimpleReaction primaryBWM = model.createSimpleReaction(cytosol);
        GeneralKinetics primaryBWMKinetics = new GeneralKinetics(primaryBWM);
        primaryBWM.setKinetics(primaryBWMKinetics);
        primaryBWM.addReactant(primarySC, 1);
        primaryBWMKinetics.getReactionRateParameter().setExpression(Expression.mult(bleachRateExp, new Expression(primarySC.getName())));
    }
    {
        SimpleReaction secondaryBWM = model.createSimpleReaction(cytosol);
        GeneralKinetics secondaryBWMKinetics = new GeneralKinetics(secondaryBWM);
        secondaryBWM.setKinetics(secondaryBWMKinetics);
        secondaryBWM.addReactant(secondarySC, 1);
        secondaryBWMKinetics.getReactionRateParameter().setExpression(Expression.mult(bleachRateExp, new Expression(secondarySC.getName())));
    }
    // create simulation context
    SimulationContext simContext = bioModel.addNewSimulationContext("simContext", SimulationContext.Application.NETWORK_DETERMINISTIC);
    simContext.setGeometry(geometry);
    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);
    // unused? 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));
    double fixedFraction = 1.0 - primaryFraction - secondaryFraction;
    SpeciesContextSpec immobileSCS = simContext.getReactionContext().getSpeciesContextSpec(immobileSC);
    immobileSCS.getInitialConditionParameter().setExpression(new Expression(fixedFraction));
    immobileSCS.getDiffusionParameter().setExpression(new Expression(0.0));
    SpeciesContextSpec primarySCS = simContext.getReactionContext().getSpeciesContextSpec(primarySC);
    primarySCS.getInitialConditionParameter().setExpression(new Expression(primaryFraction));
    primarySCS.getDiffusionParameter().setExpression(new Expression(primaryDiffusionRate));
    SpeciesContextSpec secondarySCS = simContext.getReactionContext().getSpeciesContextSpec(secondarySC);
    secondarySCS.getInitialConditionParameter().setExpression(new Expression(secondaryFraction));
    secondarySCS.getDiffusionParameter().setExpression(new Expression(secondaryDiffusionRate));
    simContext.getMicroscopeMeasurement().addFluorescentSpecies(immobileSC);
    simContext.getMicroscopeMeasurement().addFluorescentSpecies(primarySC);
    simContext.getMicroscopeMeasurement().addFluorescentSpecies(secondarySC);
    simContext.getMicroscopeMeasurement().setConvolutionKernel(new GaussianConvolutionKernel(new Expression(psfSigma), new Expression(psfSigma)));
    MathMapping mathMapping = simContext.createNewMathMapping();
    MathDescription mathDesc = mathMapping.getMathDescription();
    simContext.setMathDescription(mathDesc);
    User owner = context.getDefaultOwner();
    int meshSize = (int) (domainSize / deltaX);
    if (meshSize % 2 == 0) {
        // want an odd-sized mesh in x and y ... so centered at the origin.
        meshSize = meshSize + 1;
    }
    TimeBounds timeBounds = new TimeBounds(0.0, postbleachDuration);
    // 
    // simulation to use for data generation (output time steps as recorded by the microscope)
    // 
    double bleachBlackoutBegin = bleachStart - postbleachDelay;
    double bleachBlackoutEnd = bleachEnd + postbleachDelay;
    // ArrayList<Double> times = new ArrayList<Double>();
    // double time = 0;
    // while (time<=timeBounds.getEndingTime()){
    // if (time<=bleachBlackoutBegin || time>bleachBlackoutEnd){
    // // postbleachDelay is the time it takes to switch the filters.
    // times.add(time);
    // }
    // time += outputTimeStep.getData();
    // }
    // double[] timeArray = new double[times.size()];
    // for (int i=0;i<timeArray.length;i++){
    // timeArray[i] = times.get(i);
    // }
    // OutputTimeSpec fakeDataSimOutputTimeSpec = new ExplicitOutputTimeSpec(timeArray);
    OutputTimeSpec fakeDataSimOutputTimeSpec = new UniformOutputTimeSpec(outputTimeStep);
    KeyValue fakeDataSimKey = context.createNewKeyValue();
    SimulationVersion fakeDataSimVersion = new SimulationVersion(fakeDataSimKey, "fakeDataSim", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation fakeDataSim = new Simulation(fakeDataSimVersion, mathDesc);
    simContext.addSimulation(fakeDataSim);
    fakeDataSim.getSolverTaskDescription().setTimeBounds(timeBounds);
    fakeDataSim.getMeshSpecification().setSamplingSize(new ISize(meshSize, meshSize, 1));
    fakeDataSim.getSolverTaskDescription().setSolverDescription(SolverDescription.SundialsPDE);
    fakeDataSim.getSolverTaskDescription().setOutputTimeSpec(fakeDataSimOutputTimeSpec);
    // 
    // simulation to use for viewing the protocol (output time steps to understand the physics)
    // 
    KeyValue fullExperimentSimKey = context.createNewKeyValue();
    SimulationVersion fullExperimentSimVersion = new SimulationVersion(fullExperimentSimKey, "fullExperiment", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation fullExperimentSim = new Simulation(fullExperimentSimVersion, mathDesc);
    simContext.addSimulation(fullExperimentSim);
    OutputTimeSpec fullExperimentOutputTimeSpec = new UniformOutputTimeSpec(outputTimeStep / 10.0);
    fullExperimentSim.getSolverTaskDescription().setTimeBounds(timeBounds);
    fullExperimentSim.getMeshSpecification().setSamplingSize(new ISize(meshSize, meshSize, 1));
    fullExperimentSim.getSolverTaskDescription().setSolverDescription(SolverDescription.SundialsPDE);
    fullExperimentSim.getSolverTaskDescription().setOutputTimeSpec(fullExperimentOutputTimeSpec);
    GeneratedModelResults results = new GeneratedModelResults();
    results.bioModel_2D = bioModel;
    results.simulation_2D = fakeDataSim;
    results.bleachBlackoutBeginTime = bleachBlackoutBegin;
    results.bleachBlackoutEndTime = bleachBlackoutEnd;
    return results;
}

Example 4 with GeneralKinetics

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

the class XmlReader method getKinetics.

/**
 * This method returns a Kinetics object from a XML Element based on the value of the kinetics type attribute.
 * Creation date: (3/19/2001 4:42:04 PM)
 * @return cbit.vcell.model.Kinetics
 * @param param org.jdom.Element
 */
private Kinetics getKinetics(Element param, ReactionStep reaction, Model model) throws XmlParseException {
    VariableHash varHash = new VariableHash();
    addResevedSymbols(varHash, model);
    String type = param.getAttributeValue(XMLTags.KineticsTypeAttrTag);
    Kinetics newKinetics = null;
    try {
        if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralKinetics)) {
            // create a general kinetics
            newKinetics = new GeneralKinetics(reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralCurrentKinetics)) {
            // Create GeneralCurrentKinetics
            newKinetics = new GeneralCurrentKinetics(reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeMassAction) && reaction instanceof SimpleReaction) {
            // create a Mass Action kinetics
            newKinetics = new MassActionKinetics((SimpleReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeNernst) && reaction instanceof FluxReaction) {
            // create NernstKinetics
            newKinetics = new NernstKinetics((FluxReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGHK) && reaction instanceof FluxReaction) {
            // create GHKKinetics
            newKinetics = new GHKKinetics((FluxReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeHMM_Irr) && reaction instanceof SimpleReaction) {
            // create HMM_IrrKinetics
            newKinetics = new HMM_IRRKinetics((SimpleReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeHMM_Rev) && reaction instanceof SimpleReaction) {
            // create HMM_RevKinetics
            newKinetics = new HMM_REVKinetics((SimpleReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralTotal_oldname)) {
            // create GeneralTotalKinetics
            newKinetics = new GeneralLumpedKinetics(reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralLumped)) {
            // create GeneralLumpedKinetics
            newKinetics = new GeneralLumpedKinetics(reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralCurrentLumped)) {
            // create GeneralCurrentLumpedKinetics
            newKinetics = new GeneralCurrentLumpedKinetics(reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeGeneralPermeability) && reaction instanceof FluxReaction) {
            // create GeneralPermeabilityKinetics
            newKinetics = new GeneralPermeabilityKinetics((FluxReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeMacroscopic_Irr) && reaction instanceof SimpleReaction) {
            // create Macroscopic_IRRKinetics
            newKinetics = new Macroscopic_IRRKinetics((SimpleReaction) reaction);
        } else if (type.equalsIgnoreCase(XMLTags.KineticsTypeMicroscopic_Irr) && reaction instanceof SimpleReaction) {
            // create Microscopic_IRRKinetics
            newKinetics = new Microscopic_IRRKinetics((SimpleReaction) reaction);
        } else {
            throw new XmlParseException("Unknown kinetics type: " + type);
        }
    } catch (ExpressionException e) {
        e.printStackTrace();
        throw new XmlParseException("Error creating the kinetics for reaction: " + reaction.getName(), e);
    }
    try {
        // transaction begin flag ... yeah, this is a hack
        newKinetics.reading(true);
        // Read all of the parameters
        List<Element> list = param.getChildren(XMLTags.ParameterTag, vcNamespace);
        // add constants that may be used in kinetics.
        // VariableHash varHash = getVariablesHash();
        ArrayList<String> reserved = new ArrayList<String>();
        ReservedSymbol[] reservedSymbols = reaction.getModel().getReservedSymbols();
        for (ReservedSymbol rs : reservedSymbols) {
            reserved.add(rs.getName());
        }
        try {
            if (reaction.getStructure() instanceof Membrane) {
                Membrane membrane = (Membrane) reaction.getStructure();
                varHash.addVariable(new Constant(membrane.getMembraneVoltage().getName(), new Expression(0.0)));
                reserved.add(membrane.getMembraneVoltage().getName());
            }
            // 
            // add Reactants, Products, and Catalysts (ReactionParticipants)
            // 
            ReactionParticipant[] rp = reaction.getReactionParticipants();
            for (int i = 0; i < rp.length; i++) {
                varHash.addVariable(new Constant(rp[i].getName(), new Expression(0.0)));
            }
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException("error reordering parameters according to dependencies: ", e);
        }
        // 
        for (Element xmlParam : list) {
            String paramName = unMangle(xmlParam.getAttributeValue(XMLTags.NameAttrTag));
            String role = xmlParam.getAttributeValue(XMLTags.ParamRoleAttrTag);
            String paramExpStr = xmlParam.getText();
            Expression paramExp = unMangleExpression(paramExpStr);
            try {
                if (varHash.getVariable(paramName) == null) {
                    varHash.addVariable(new Function(paramName, paramExp, null));
                } else {
                    if (reserved.contains(paramName)) {
                        varHash.removeVariable(paramName);
                        varHash.addVariable(new Function(paramName, paramExp, null));
                    }
                }
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException("error reordering parameters according to dependencies: ", e);
            }
            Kinetics.KineticsParameter tempParam = null;
            if (!role.equals(XMLTags.ParamRoleUserDefinedTag)) {
                tempParam = newKinetics.getKineticsParameterFromRole(Kinetics.getParamRoleFromDefaultDesc(role));
            } else {
                continue;
            }
            // hack for bringing in General Total kinetics without breaking.
            if (tempParam == null && newKinetics instanceof GeneralLumpedKinetics) {
                if (role.equals(Kinetics.GTK_AssumedCompartmentSize_oldname) || role.equals(Kinetics.GTK_ReactionRate_oldname) || role.equals(Kinetics.GTK_CurrentDensity_oldname)) {
                    continue;
                } else if (role.equals(VCMODL.TotalRate_oldname)) {
                    tempParam = newKinetics.getKineticsParameterFromRole(Kinetics.ROLE_LumpedReactionRate);
                }
            }
            // hack from bringing in chargeValence parameters without breaking
            if (tempParam == null && Kinetics.getParamRoleFromDefaultDesc(role) == Kinetics.ROLE_ChargeValence) {
                tempParam = newKinetics.getChargeValenceParameter();
            }
            if (tempParam == null) {
                throw new XmlParseException("parameter with role '" + role + "' not found in kinetics type '" + type + "'");
            }
            // 
            if (!tempParam.getName().equals(paramName)) {
                Kinetics.KineticsParameter multNameParam = newKinetics.getKineticsParameter(paramName);
                int n = 0;
                while (multNameParam != null) {
                    String tempName = paramName + "_" + n++;
                    newKinetics.renameParameter(paramName, tempName);
                    multNameParam = newKinetics.getKineticsParameter(tempName);
                }
                newKinetics.renameParameter(tempParam.getName(), paramName);
            }
        }
        // 
        // create unresolved parameters for all unresolved symbols
        // 
        String unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        while (unresolvedSymbol != null) {
            try {
                // will turn into an UnresolvedParameter.
                varHash.addVariable(new Function(unresolvedSymbol, new Expression(0.0), null));
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new XmlParseException(e);
            }
            newKinetics.addUnresolvedParameter(unresolvedSymbol);
            unresolvedSymbol = varHash.getFirstUnresolvedSymbol();
        }
        Variable[] sortedVariables = varHash.getTopologicallyReorderedVariables();
        ModelUnitSystem modelUnitSystem = reaction.getModel().getUnitSystem();
        for (int i = sortedVariables.length - 1; i >= 0; i--) {
            if (sortedVariables[i] instanceof Function) {
                Function paramFunction = (Function) sortedVariables[i];
                Element xmlParam = null;
                for (int j = 0; j < list.size(); j++) {
                    Element tempParam = (Element) list.get(j);
                    if (paramFunction.getName().equals(unMangle(tempParam.getAttributeValue(XMLTags.NameAttrTag)))) {
                        xmlParam = tempParam;
                        break;
                    }
                }
                if (xmlParam == null) {
                    // must have been an unresolved parameter
                    continue;
                }
                String symbol = xmlParam.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
                VCUnitDefinition unit = null;
                if (symbol != null) {
                    unit = modelUnitSystem.getInstance(symbol);
                }
                Kinetics.KineticsParameter tempParam = newKinetics.getKineticsParameter(paramFunction.getName());
                if (tempParam == null) {
                    newKinetics.addUserDefinedKineticsParameter(paramFunction.getName(), paramFunction.getExpression(), unit);
                } else {
                    newKinetics.setParameterValue(tempParam, paramFunction.getExpression());
                    tempParam.setUnitDefinition(unit);
                }
            }
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception while setting parameters for Reaction : " + reaction.getName(), e);
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new XmlParseException("Exception while settings parameters for Reaction : " + reaction.getName(), e);
    } finally {
        newKinetics.reading(false);
    }
    return newKinetics;
}