Examples with ReactionSpec cbit.vcell.mapping.ReactionSpec used on opensource projects

Example 21 with ReactionSpec

use of cbit.vcell.mapping.ReactionSpec in project vcell by virtualcell.

the class StructureAnalyzer method refreshFastSpeciesContextMappings.

/**
 * This method was created in VisualAge.
 */
private void refreshFastSpeciesContextMappings() {
    // System.out.println("StructureAnalyzer.refreshFastSpeciesContextMappings()");
    // GeometryContext geoContext = mathMapping.getSimulationContext().getGeometryContext();
    Vector<SpeciesContextMapping> scFastList = new Vector<SpeciesContextMapping>();
    // 
    if (structures == null) {
        return;
    }
    for (int i = 0; i < structures.length; i++) {
        SpeciesContext[] speciesContexts = mathMapping_4_8.getSimulationContext().getReactionContext().getModel().getSpeciesContexts(structures[i]);
        for (int j = 0; j < speciesContexts.length; j++) {
            SpeciesContext sc = speciesContexts[j];
            SpeciesContextMapping scm = mathMapping_4_8.getSpeciesContextMapping(sc);
            SpeciesContextSpec scs = mathMapping_4_8.getSimulationContext().getReactionContext().getSpeciesContextSpec(sc);
            if (scm.getDependencyExpression() == null && scs.isConstant() == false) {
                // right now all independent vars
                scFastList.addElement(scm);
            }
        }
    }
    if (scFastList.size() > 0) {
        fastSpeciesContextMappings = new SpeciesContextMapping[scFastList.size()];
        scFastList.copyInto(fastSpeciesContextMappings);
    // for (int i=0;i<fastSpeciesContextMappings.length;i++){
    // System.out.println("fastSpeciesContextMappings["+i+"] = "+fastSpeciesContextMappings[i].getSpeciesContext().getName());
    // }
    } else {
        fastSpeciesContextMappings = null;
    }
    // System.out.println("StructureAnalyzer.refreshFastSpeciesContextMapping(), fastSpeciesContextMappings.length = "+scFastList.size());
    // 
    // for each reaction, get all reactionSteps associated with these structures
    // 
    Vector<ReactionStep> rsFastList = new Vector<ReactionStep>();
    ReactionSpec[] reactionSpecs = mathMapping_4_8.getSimulationContext().getReactionContext().getReactionSpecs();
    for (int i = 0; i < reactionSpecs.length; i++) {
        ReactionStep rs = reactionSpecs[i].getReactionStep();
        if (reactionSpecs[i].isExcluded()) {
            continue;
        }
        for (int j = 0; j < structures.length; j++) {
            if (rs.getStructure() == structures[j]) {
                if (reactionSpecs[i].isFast()) {
                    rsFastList.addElement(rs);
                }
            }
        }
    }
    if (rsFastList.size() > 0) {
        fastReactionSteps = new ReactionStep[rsFastList.size()];
        rsFastList.copyInto(fastReactionSteps);
    } else {
        fastReactionSteps = null;
        fastSpeciesContextMappings = null;
    }
// System.out.println("StructureAnalyzer.refreshFastSpeciesContextMapping(), reactionSteps.length = "+scFastList.size());
}

Example 22 with ReactionSpec

use of cbit.vcell.mapping.ReactionSpec in project vcell by virtualcell.

the class StructureAnalyzer method refreshTotalSpeciesContextMappings.

/**
 * This method was created in VisualAge.
 */
private void refreshTotalSpeciesContextMappings() throws java.beans.PropertyVetoException {
    if (structures == null) {
        return;
    }
    // System.out.println("StructureAnalyzer.refreshSpeciesContextMappings()");
    // GeometryContext geoContext = mathMapping.getSimulationContext().getGeometryContext();
    Model model = mathMapping_4_8.getSimulationContext().getReactionContext().getModel();
    // 
    // note, the order of species is specified such that the first species have priority
    // when the null space is solved for dependent variables.  So the order of priority
    // for elimination are as follows:
    // 
    // 1) Species involved with fast reactions.
    // 2) Species not involved with fast reactions.
    // 
    Vector<SpeciesContextMapping> scmList = new Vector<SpeciesContextMapping>();
    // 
    for (int i = 0; i < structures.length; i++) {
        SpeciesContext[] speciesContexts = model.getSpeciesContexts(structures[i]);
        for (int j = 0; j < speciesContexts.length; j++) {
            SpeciesContext sc = speciesContexts[j];
            SpeciesContextMapping scm = mathMapping_4_8.getSpeciesContextMapping(sc);
            SpeciesContextSpec scs = mathMapping_4_8.getSimulationContext().getReactionContext().getSpeciesContextSpec(sc);
            if (scm.isFastParticipant() && !scs.isConstant()) {
                scmList.addElement(scm);
            }
        }
    }
    // 
    for (int i = 0; i < structures.length; i++) {
        SpeciesContext[] speciesContexts = model.getSpeciesContexts(structures[i]);
        for (int j = 0; j < speciesContexts.length; j++) {
            SpeciesContext sc = speciesContexts[j];
            SpeciesContextMapping scm = mathMapping_4_8.getSpeciesContextMapping(sc);
            SpeciesContextSpec scs = mathMapping_4_8.getSimulationContext().getReactionContext().getSpeciesContextSpec(sc);
            if (!scm.isFastParticipant() && !scs.isConstant()) {
                scmList.addElement(scm);
            }
        }
    }
    if (scmList.size() > 0) {
        speciesContextMappings = new SpeciesContextMapping[scmList.size()];
        scmList.copyInto(speciesContextMappings);
        for (int i = 0; i < speciesContextMappings.length; i++) {
            speciesContextMappings[i].setRate(new Expression(0.0));
        // System.out.println("speciesContextMappings["+i+"] = "+speciesContextMappings[i].getSpeciesContext().getName());
        }
    } else {
        speciesContextMappings = null;
    }
    // System.out.println("StructureAnalyzer.refreshTotalSpeciesContextMapping(), speciesContextMappings.length = "+scmList.size());
    // 
    // get all reactionSteps associated with these structures
    // 
    Vector<ReactionStep> rsList = new Vector<ReactionStep>();
    ReactionSpec[] allReactionSpecs = mathMapping_4_8.getSimulationContext().getReactionContext().getReactionSpecs();
    for (int i = 0; i < allReactionSpecs.length; i++) {
        if (allReactionSpecs[i].isExcluded()) {
            continue;
        }
        ReactionStep rs = allReactionSpecs[i].getReactionStep();
        for (int j = 0; j < structures.length; j++) {
            if (rs.getStructure() == structures[j]) {
                rsList.addElement(rs);
            }
        }
    }
    // 
    for (int i = 0; i < scmList.size(); i++) {
        SpeciesContextMapping scm = (SpeciesContextMapping) scmList.elementAt(i);
        if (scm.isPDERequired()) {
            rsList.addElement(new DiffusionDummyReactionStep("DiffusionDummyReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
        }
        if (scm.hasEventAssignment()) {
            rsList.addElement(new EventDummyReactionStep("EventDummyReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
        }
        if (scm.hasHybridReaction()) {
            rsList.addElement(new HybridDummyReactionStep("HybridDummyReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
        }
        SimulationContext simContext = mathMapping_4_8.getSimulationContext();
        if (simContext.isStoch() && simContext.getGeometry().getDimension() > 0 && !simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext()).isForceContinuous()) {
            rsList.addElement(new ParticleDummyReactionStep("ParticleDummyReactionStep" + i, model, scm.getSpeciesContext().getStructure(), scm.getSpeciesContext()));
        }
    }
    if (rsList.size() > 0) {
        reactionSteps = new ReactionStep[rsList.size()];
        rsList.copyInto(reactionSteps);
    } else {
        reactionSteps = null;
    }
// System.out.println("StructureAnalyzer.refreshTotalSpeciesContextMapping(), reactionSteps.length = "+scmList.size());
}

Example 23 with ReactionSpec

use of cbit.vcell.mapping.ReactionSpec in project vcell by virtualcell.

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a ReactionContext object.
 * Creation date: (3/1/2001 9:03:52 PM)
 * @return Element
 * @param param cbit.vcell.mapping.ReactionContext
 */
private Element getXML(ReactionContext param) {
    Element reactioncontext = new Element(XMLTags.ReactionContextTag);
    // Add SpeciesContextSpecs
    SpeciesContextSpec[] array = param.getSpeciesContextSpecs();
    for (int i = 0; i < array.length; i++) {
        reactioncontext.addContent(getXML(array[i]));
    }
    // Add ReactionSpecs
    ReactionSpec[] reactionarray = param.getReactionSpecs();
    for (int i = 0; i < reactionarray.length; i++) {
        reactioncontext.addContent(getXML(reactionarray[i]));
    }
    // Add ReactionRuleSpecs
    ReactionRuleSpec[] reactionRuleArray = param.getReactionRuleSpecs();
    if (reactionRuleArray.length > 0) {
        reactioncontext.addContent(getXML(reactionRuleArray));
    }
    return reactioncontext;
}

Example 24 with ReactionSpec

use of cbit.vcell.mapping.ReactionSpec in project vcell by virtualcell.

the class ModelOptimizationSpec method getModelParameters.

/**
 * Insert the method's description here.
 * Creation date: (8/22/2005 10:38:04 AM)
 * @return cbit.vcell.model.Parameter[]
 */
private Parameter[] getModelParameters() {
    java.util.Vector<Parameter> modelParameterList = new java.util.Vector<Parameter>();
    Model model = getSimulationContext().getModel();
    // 
    // get Model (global) parameters
    // 
    ModelParameter[] globalParams = model.getModelParameters();
    for (int i = 0; i < globalParams.length; i++) {
        if (globalParams[i] != null && globalParams[i].getExpression() != null && globalParams[i].getExpression().isNumeric()) {
            modelParameterList.add(globalParams[i]);
        }
    }
    // 
    // get kinetic parameters that are numbers
    // 
    ReactionStep[] reactionSteps = model.getReactionSteps();
    for (int i = 0; i < reactionSteps.length; i++) {
        // 
        // make sure ReactionSteps are "enabled"
        // 
        ReactionSpec reactionSpec = getSimulationContext().getReactionContext().getReactionSpec(reactionSteps[i]);
        if (reactionSpec == null || reactionSpec.isExcluded()) {
            continue;
        }
        Kinetics.KineticsParameter[] kineticsParameters = reactionSteps[i].getKinetics().getKineticsParameters();
        for (int j = 0; j < kineticsParameters.length; j++) {
            if (kineticsParameters[j].getExpression() != null && kineticsParameters[j].getExpression().isNumeric()) {
                if (((kineticsParameters[j].getRole() == Kinetics.ROLE_CurrentDensity) || (kineticsParameters[j].getRole() == Kinetics.ROLE_LumpedCurrent)) && reactionSteps[i].getPhysicsOptions() == ReactionStep.PHYSICS_MOLECULAR_ONLY) {
                    continue;
                }
                if (((kineticsParameters[j].getRole() == Kinetics.ROLE_ReactionRate) || (kineticsParameters[j].getRole() == Kinetics.ROLE_LumpedReactionRate)) && reactionSteps[i].getPhysicsOptions() == ReactionStep.PHYSICS_ELECTRICAL_ONLY) {
                    continue;
                }
                modelParameterList.add(kineticsParameters[j]);
            }
        }
    }
    // 
    // get initial conditions that are numbers
    // 
    SpeciesContextSpec[] speciesContextSpecs = getSimulationContext().getReactionContext().getSpeciesContextSpecs();
    for (int i = 0; i < speciesContextSpecs.length; i++) {
        SpeciesContextSpec.SpeciesContextSpecParameter initParam = speciesContextSpecs[i].getInitialConditionParameter();
        if (initParam != null && initParam.getExpression() != null && initParam.getExpression().isNumeric()) {
            modelParameterList.add(initParam);
        }
    }
    // 
    // get structure parameters
    // 
    StructureMapping[] structureMappings = getSimulationContext().getGeometryContext().getStructureMappings();
    for (int i = 0; i < structureMappings.length; i++) {
        StructureMapping.StructureMappingParameter[] parameters = structureMappings[i].getParameters();
        for (int j = 0; j < parameters.length; j++) {
            if (parameters[j].getRole() == StructureMapping.ROLE_SpecificCapacitance && structureMappings[i] instanceof MembraneMapping && !((MembraneMapping) structureMappings[i]).getCalculateVoltage()) {
                continue;
            }
            if (parameters[j].getExpression() != null && parameters[j].getExpression().isNumeric()) {
                modelParameterList.add(parameters[j]);
            }
        }
    }
    Parameter[] modelParameters = (Parameter[]) BeanUtils.getArray(modelParameterList, Parameter.class);
    return modelParameters;
}