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

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Example 1 with VolumeRegionVariable

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

the class XmlReader method getJumpCondition.

/**
 * This method returns a JumpCondition object from a XML Element.
 * Creation date: (5/18/2001 5:10:10 PM)
 * @return cbit.vcell.math.JumpCondition
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private JumpCondition getJumpCondition(Element param, MathDescription mathDesc) throws XmlParseException {
    // get VolVariable ref
    String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    Variable var = mathDesc.getVariable(varname);
    if (var == null) {
        throw new XmlParseException("The reference to the Variable " + varname + ", could not be resolved!");
    }
    JumpCondition jumpCondition = null;
    if (var instanceof VolVariable) {
        jumpCondition = new JumpCondition((VolVariable) var);
    } else if (var instanceof VolumeRegionVariable) {
        jumpCondition = new JumpCondition((VolumeRegionVariable) var);
    } else {
        throw new XmlParseException("unexpected variable type for jump condition");
    }
    // process InFlux
    String temp = param.getChildText(XMLTags.InFluxTag, vcNamespace);
    Expression exp = unMangleExpression(temp);
    jumpCondition.setInFlux(exp);
    // process OutFlux
    temp = param.getChildText(XMLTags.OutFluxTag, vcNamespace);
    exp = unMangleExpression(temp);
    jumpCondition.setOutFlux(exp);
    return jumpCondition;
}
Also used : JumpCondition(cbit.vcell.math.JumpCondition) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) FilamentVariable(cbit.vcell.math.FilamentVariable) OutsideVariable(cbit.vcell.math.OutsideVariable) StochVolVariable(cbit.vcell.math.StochVolVariable) RandomVariable(cbit.vcell.math.RandomVariable) VolumeRandomVariable(cbit.vcell.math.VolumeRandomVariable) VolumeParticleVariable(cbit.vcell.math.VolumeParticleVariable) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) InsideVariable(cbit.vcell.math.InsideVariable) VolVariable(cbit.vcell.math.VolVariable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) PointVariable(cbit.vcell.math.PointVariable) MembraneRandomVariable(cbit.vcell.math.MembraneRandomVariable) MembraneParticleVariable(cbit.vcell.math.MembraneParticleVariable) ParticleVariable(cbit.vcell.math.ParticleVariable) MemVariable(cbit.vcell.math.MemVariable) FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) Variable(cbit.vcell.math.Variable) StochVolVariable(cbit.vcell.math.StochVolVariable) VolVariable(cbit.vcell.math.VolVariable) Expression(cbit.vcell.parser.Expression)

Example 2 with VolumeRegionVariable

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

the class XmlReader method getVolumeRegionVariable.

/**
 * This method returns a VolumeRegionVariable object from a XML Element.
 * Creation date: (5/16/2001 2:56:34 PM)
 * @return cbit.vcell.math.VolumeRegionVariable
 * @param param org.jdom.Element
 */
private VolumeRegionVariable getVolumeRegionVariable(Element param) {
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    // -- create new VolumeRegionVariable object
    VolumeRegionVariable volRegVariable = new VolumeRegionVariable(name, domain);
    transcribeComments(param, volRegVariable);
    return volRegVariable;
}
Also used : VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) FilamentSubDomain(cbit.vcell.math.FilamentSubDomain) PointSubDomain(cbit.vcell.math.PointSubDomain) Domain(cbit.vcell.math.Variable.Domain)

Example 3 with VolumeRegionVariable

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

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a MathDescription object.
 * Creation date: (3/2/2001 10:57:25 AM)
 * @return Element
 * @param mathdes cbit.vcell.math.MathDescription
 */
Element getXML(MathDescription mathdes) throws XmlParseException {
    Element math = new Element(XMLTags.MathDescriptionTag);
    // Add attributes
    math.setAttribute(XMLTags.NameAttrTag, mangle(mathdes.getName()));
    // Add annotation
    if (mathdes.getDescription() != null && mathdes.getDescription().length() > 0) {
        Element annotationElem = new Element(XMLTags.AnnotationTag);
        annotationElem.setText(mangle(mathdes.getDescription()));
        math.addContent(annotationElem);
    }
    List<ParticleMolecularType> particleMolecularTypes = mathdes.getParticleMolecularTypes();
    for (ParticleMolecularType particleMolecularType : particleMolecularTypes) {
        math.addContent(getXML(particleMolecularType));
    }
    // Add Constant subelements
    Enumeration<Variable> enum1 = mathdes.getVariables();
    /*java.util.Iterator k;
    try {
    	VariableHash varHash = new VariableHash();
    	while (enum1.hasMoreElements()) 
    	 	varHash.addVariable((Variable)enum1.nextElement());
    	Variable vars [] = varHash.getReorderedVariables();
    	k = new ArrayList(java.util.Arrays.asList(vars)).iterator();
    } catch (cbit.vcell.mapping.MappingException e) {
		e.printStackTrace();
		return null;
    }*/
    while (enum1.hasMoreElements()) {
        Variable var = enum1.nextElement();
        Element element = null;
        if (var instanceof Constant) {
            element = getXML((Constant) var);
        } else if (var instanceof FilamentRegionVariable) {
            element = getXML((FilamentRegionVariable) var);
        } else if (var instanceof FilamentVariable) {
            element = getXML((FilamentVariable) var);
        } else if (var instanceof PointVariable) {
            element = getXML((PointVariable) var);
        } else if (var instanceof Function) {
            element = getXML((Function) var);
        } else if (var instanceof RandomVariable) {
            element = getXML((RandomVariable) var);
        } else if (var instanceof InsideVariable) {
            // *** for internal use! Ignore it ***
            continue;
        } else if (var instanceof MembraneRegionVariable) {
            element = getXML((MembraneRegionVariable) var);
        } else if (var instanceof MemVariable) {
            element = getXML((MemVariable) var);
        } else if (var instanceof OutsideVariable) {
            // *** for internal use! Ignore it ****
            continue;
        } else if (var instanceof VolumeRegionVariable) {
            element = getXML((VolumeRegionVariable) var);
        } else if (var instanceof VolVariable) {
            element = getXML((VolVariable) var);
        } else if (var instanceof StochVolVariable) {
            // added for stochastic volumn variables
            element = getXML((StochVolVariable) var);
        } else if (var instanceof ParticleVariable) {
            element = getXML((ParticleVariable) var);
        } else if (var instanceof ParticleObservable) {
            element = getXML((ParticleObservable) var);
        } else {
            throw new XmlParseException("An unknown variable type " + var.getClass().getName() + " was found when parsing the mathdescription " + mathdes.getName() + "!");
        }
        transcribeComments(var, element);
        math.addContent(element);
    }
    // this was moved to the simspec!
    /*	buffer.append("\n");
    	if (geometry != null){
    		buffer.append(geometry.getXML());
    	}	
    	buffer.append("\n");*/
    // Add subdomains
    Enumeration<SubDomain> enum2 = mathdes.getSubDomains();
    while (enum2.hasMoreElements()) {
        SubDomain subDomain = enum2.nextElement();
        math.addContent(getXML(subDomain));
    }
    // Add Metadata (Version) if there is!
    if (mathdes.getVersion() != null) {
        math.addContent(getXML(mathdes.getVersion(), mathdes));
    }
    Iterator<Event> iter = mathdes.getEvents();
    while (iter.hasNext()) {
        math.addContent(getXML(iter.next()));
    }
    PostProcessingBlock postProcessingBlock = mathdes.getPostProcessingBlock();
    if (postProcessingBlock.getNumDataGenerators() > 0) {
        math.addContent(getXML(postProcessingBlock));
    }
    return math;
}
Also used : FilamentVariable(cbit.vcell.math.FilamentVariable) OutsideVariable(cbit.vcell.math.OutsideVariable) StochVolVariable(cbit.vcell.math.StochVolVariable) RandomVariable(cbit.vcell.math.RandomVariable) VolumeRandomVariable(cbit.vcell.math.VolumeRandomVariable) VolumeParticleVariable(cbit.vcell.math.VolumeParticleVariable) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) InsideVariable(cbit.vcell.math.InsideVariable) VolVariable(cbit.vcell.math.VolVariable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) PointVariable(cbit.vcell.math.PointVariable) MembraneParticleVariable(cbit.vcell.math.MembraneParticleVariable) ParticleVariable(cbit.vcell.math.ParticleVariable) MemVariable(cbit.vcell.math.MemVariable) FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) Variable(cbit.vcell.math.Variable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) MacroscopicRateConstant(cbit.vcell.math.MacroscopicRateConstant) Constant(cbit.vcell.math.Constant) VolumeParticleVariable(cbit.vcell.math.VolumeParticleVariable) MembraneParticleVariable(cbit.vcell.math.MembraneParticleVariable) ParticleVariable(cbit.vcell.math.ParticleVariable) Element(org.jdom.Element) RandomVariable(cbit.vcell.math.RandomVariable) VolumeRandomVariable(cbit.vcell.math.VolumeRandomVariable) InsideVariable(cbit.vcell.math.InsideVariable) PostProcessingBlock(cbit.vcell.math.PostProcessingBlock) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) SubDomain(cbit.vcell.math.SubDomain) MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) FilamentSubDomain(cbit.vcell.math.FilamentSubDomain) PointSubDomain(cbit.vcell.math.PointSubDomain) AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction) Function(cbit.vcell.math.Function) MemVariable(cbit.vcell.math.MemVariable) ParticleMolecularType(cbit.vcell.math.ParticleMolecularType) StochVolVariable(cbit.vcell.math.StochVolVariable) StochVolVariable(cbit.vcell.math.StochVolVariable) VolVariable(cbit.vcell.math.VolVariable) FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) FilamentVariable(cbit.vcell.math.FilamentVariable) Event(cbit.vcell.math.Event) BioEvent(cbit.vcell.mapping.BioEvent) PointVariable(cbit.vcell.math.PointVariable) OutsideVariable(cbit.vcell.math.OutsideVariable) VolumeParticleObservable(cbit.vcell.math.VolumeParticleObservable) ParticleObservable(cbit.vcell.math.ParticleObservable)

Example 4 with VolumeRegionVariable

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

the class DiffEquMathMapping method refreshVariables.

/**
 * This method was created in VisualAge.
 */
private void refreshVariables() throws MappingException {
    // System.out.println("MathMapping.refreshVariables()");
    // 
    // non-constant dependent variables require a function
    // 
    Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        if (scm.getDependencyExpression() != null && !scs.isConstant()) {
            // scm.setVariable(new Function(scm.getSpeciesContext().getName(),scm.getDependencyExpression()));
            scm.setVariable(null);
        }
        if (getSimulationContext().hasEventAssignment(scs.getSpeciesContext())) {
            scm.setDependencyExpression(null);
        }
    }
    // 
    // non-constant independent variables require either a membrane or volume variable
    // 
    enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        if (scm.getDependencyExpression() == null && (!scs.isConstant() || getSimulationContext().hasEventAssignment(scs.getSpeciesContext()))) {
            StructureMapping sm = simContext.getGeometryContext().getStructureMapping(scm.getSpeciesContext().getStructure());
            Structure struct = scm.getSpeciesContext().getStructure();
            Domain domain = null;
            if (sm.getGeometryClass() != null) {
                domain = new Domain(sm.getGeometryClass());
            }
            if (struct instanceof Feature || struct instanceof Membrane) {
                if (sm.getGeometryClass() instanceof SurfaceClass) {
                    if (scs.isWellMixed()) {
                        scm.setVariable(new MembraneRegionVariable(scm.getSpeciesContext().getName(), domain));
                    } else if (getSimulationContext().isStoch() && getSimulationContext().getGeometry().getDimension() > 0 && !scs.isForceContinuous()) {
                        scm.setVariable(new MemVariable(scm.getSpeciesContext().getName() + "_conc", domain));
                    } else {
                        scm.setVariable(new MemVariable(scm.getSpeciesContext().getName(), domain));
                    }
                } else {
                    if (scs.isWellMixed()) {
                        scm.setVariable(new VolumeRegionVariable(scm.getSpeciesContext().getName(), domain));
                    } else if (getSimulationContext().isStoch() && getSimulationContext().getGeometry().getDimension() > 0 && !scs.isForceContinuous()) {
                        scm.setVariable(new VolVariable(scm.getSpeciesContext().getName() + "_conc", domain));
                    } else {
                        scm.setVariable(new VolVariable(scm.getSpeciesContext().getName(), domain));
                    }
                }
            } else {
                throw new MappingException("class " + scm.getSpeciesContext().getStructure().getClass() + " not supported");
            }
            mathSymbolMapping.put(scm.getSpeciesContext(), scm.getVariable().getName());
        }
    }
}
Also used : MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) SurfaceClass(cbit.vcell.geometry.SurfaceClass) VolVariable(cbit.vcell.math.VolVariable) Feature(cbit.vcell.model.Feature) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) MemVariable(cbit.vcell.math.MemVariable) Membrane(cbit.vcell.model.Membrane) Structure(cbit.vcell.model.Structure) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) SubDomain(cbit.vcell.math.SubDomain) PointSubDomain(cbit.vcell.math.PointSubDomain) Domain(cbit.vcell.math.Variable.Domain) MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)

Example 5 with VolumeRegionVariable

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

the class TestingFrameworkWindowManager method getVariableNamesToCompare.

// /**
// * Insert the method's description here.
// * Creation date: (11/23/2004 1:53:11 PM)
// * @return java.lang.String[]
// * @param sim1 cbit.vcell.solver.Simulation
// * @param sim2 cbit.vcell.solver.Simulation
// */
// private VariablePair[] getVariableNamesToCompare(BioModel testBioModel,SimulationSymbolTable testSymboltable, SimulationSymbolTable refSymbolTable){
// Vector<VariablePair> variablePairs = new Vector<VariablePair>();
// 
// //
// // get Variables from Simulation 1
// //
// Variable refVars[] = refSymbolTable.getVariables();
// for (int i = 0;refVars!=null && i < refVars.length; i++){
// if (refVars[i] instanceof VolVariable ||
// refVars[i] instanceof StochVolVariable ||
// refVars[i] instanceof MemVariable ||
// refVars[i] instanceof VolumeRegionVariable ||
// refVars[i] instanceof MembraneRegionVariable ||
// refVars[i] instanceof FilamentVariable ||
// refVars[i] instanceof FilamentRegionVariable){
// 
// VariablePair varPair = new VariablePair();
// varPair.refVariable = refVars[i];
// varPair.domain = refVars[i].getDomain();
// varPair.testVariable = null;
// variablePairs.add(varPair);
// }
// //		Constant sensitivityParameter = simSymbolTable1.getSimulation().getSolverTaskDescription().getSensitivityParameter();
// //		if (sensitivityParameter != null) {
// //			if (simVars[i] instanceof VolVariable) {
// //				hashSet.add(SensVariable.getSensName((VolVariable)simVars[i], sensitivityParameter));
// //			}
// //		}
// }
// 
// //
// // add Variables from Simulation 2
// //
// Variable[] testVars = testSymboltable.getVariables();
// for (int i = 0;testVars!=null && i < testVars.length; i++){
// if (testVars[i] instanceof VolVariable ||
// testVars[i] instanceof MemVariable ||
// testVars[i] instanceof VolumeRegionVariable ||
// testVars[i] instanceof MembraneRegionVariable ||
// testVars[i] instanceof FilamentVariable ||
// testVars[i] instanceof FilamentRegionVariable){
// 
// if(testVars[i].getDomain() == null){
// boolean BFoundMatchingName = false;
// for (int j = 0; j < variablePairs.size(); j++) {
// VariablePair varPair = variablePairs.elementAt(j);
// if(varPair.refVariable.getName().equals(testVars[i].getName())){
// varPair.testVariable = testVars[i];
// BFoundMatchingName = true;
// break;
// }
// }
// if(!BFoundMatchingName){
// //Try to find other matching variable types (e.g. functions)
// Variable dataSet1Match = refSymbolTable.getVariable(testVars[i].getName());
// if(dataSet1Match != null){
// VariablePair varPair = new VariablePair();
// varPair.refVariable = dataSet1Match;
// varPair.testVariable = testVars[i];
// varPair.domain = varPair.refVariable.getDomain();
// variablePairs.add(varPair);
// }else{
// SpeciesContext testSpeciescontext0 = testBioModel.getModel().getSpeciesContext(testVars[i].getName());
// if(testSpeciescontext0 != null){
// Species refspecies = testSpeciescontext0.getSpecies();
// Variable refVariable = refSymbolTable.getVariable(refspecies.getCommonName());
// if(refVariable != null){
// VariablePair varPair = new VariablePair();
// varPair.refVariable = refVariable;
// varPair.testVariable = testVars[i];
// varPair.domain = varPair.refVariable.getDomain();
// variablePairs.add(varPair);
// }
// }else{
// Species testSpecies = testBioModel.getModel().getSpecies(testVars[i].getName());
// if(testSpecies != null){
// for (int j = 0; j < testBioModel.getModel().getSpeciesContexts().length; j++) {
// if(testBioModel.getModel().getSpeciesContexts()[j].getSpecies() == testSpecies){
// Variable refVar = refSymbolTable.getVariable(testBioModel.getModel().getSpeciesContexts()[j].getName());
// if(refVar != null){
// VariablePair varPair = new VariablePair();
// varPair.refVariable = refVar;
// varPair.testVariable = testVars[i];
// varPair.domain = varPair.refVariable.getDomain();
// variablePairs.add(varPair);
// }
// }
// }
// }
// }
// }
// }
// }else{
// 
// }
// hashSet.add(simVars[i].getName());
// }
// Constant sensitivityParameter = refSymbolTable.getSimulation().getSolverTaskDescription().getSensitivityParameter();
// if (sensitivityParameter != null) {
// if (simVars[i] instanceof VolVariable) {
// hashSet.add(SensVariable.getSensName((VolVariable)simVars[i], sensitivityParameter));
// }
// }
// }
// 
// return (String[])hashSet.toArray(new String[hashSet.size()]);
// }
/**
 * Insert the method's description here.
 * Creation date: (11/23/2004 1:53:11 PM)
 * @return java.lang.String[]
 * @param sim1 cbit.vcell.solver.Simulation
 * @param sim2 cbit.vcell.solver.Simulation
 */
private String[] getVariableNamesToCompare(SimulationSymbolTable simSymbolTable1, SimulationSymbolTable simSymbolTable2) {
    java.util.HashSet<String> hashSet = new java.util.HashSet<String>();
    // 
    // get Variables from Simulation 1
    // 
    Variable[] simVars = simSymbolTable1.getVariables();
    for (int i = 0; simVars != null && i < simVars.length; i++) {
        if (simVars[i] instanceof VolVariable || simVars[i] instanceof StochVolVariable || simVars[i] instanceof MemVariable || simVars[i] instanceof VolumeRegionVariable || simVars[i] instanceof MembraneRegionVariable || simVars[i] instanceof FilamentVariable || simVars[i] instanceof FilamentRegionVariable) {
            hashSet.add(simVars[i].getName());
        }
        Constant sensitivityParameter = simSymbolTable1.getSimulation().getSolverTaskDescription().getSensitivityParameter();
        if (sensitivityParameter != null) {
            if (simVars[i] instanceof VolVariable) {
                hashSet.add(SensVariable.getSensName((VolVariable) simVars[i], sensitivityParameter));
            }
        }
    }
    // 
    // add Variables from Simulation 2
    // 
    simVars = simSymbolTable2.getVariables();
    for (int i = 0; simVars != null && i < simVars.length; i++) {
        if (simVars[i] instanceof VolVariable || simVars[i] instanceof MemVariable || simVars[i] instanceof VolumeRegionVariable || simVars[i] instanceof MembraneRegionVariable || simVars[i] instanceof FilamentVariable || simVars[i] instanceof FilamentRegionVariable) {
            hashSet.add(simVars[i].getName());
        }
        Constant sensitivityParameter = simSymbolTable2.getSimulation().getSolverTaskDescription().getSensitivityParameter();
        if (sensitivityParameter != null) {
            if (simVars[i] instanceof VolVariable) {
                hashSet.add(SensVariable.getSensName((VolVariable) simVars[i], sensitivityParameter));
            }
        }
    }
    return (String[]) hashSet.toArray(new String[hashSet.size()]);
}
Also used : SensVariable(cbit.vcell.solver.ode.SensVariable) FilamentVariable(cbit.vcell.math.FilamentVariable) VolVariable(cbit.vcell.math.VolVariable) StochVolVariable(cbit.vcell.math.StochVolVariable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) MemVariable(cbit.vcell.math.MemVariable) FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) Variable(cbit.vcell.math.Variable) MembraneRegionVariable(cbit.vcell.math.MembraneRegionVariable) VolVariable(cbit.vcell.math.VolVariable) StochVolVariable(cbit.vcell.math.StochVolVariable) FilamentRegionVariable(cbit.vcell.math.FilamentRegionVariable) Constant(cbit.vcell.math.Constant) VolumeRegionVariable(cbit.vcell.math.VolumeRegionVariable) MemVariable(cbit.vcell.math.MemVariable) FilamentVariable(cbit.vcell.math.FilamentVariable) StochVolVariable(cbit.vcell.math.StochVolVariable) HashSet(java.util.HashSet)

Aggregations

VolumeRegionVariable (cbit.vcell.math.VolumeRegionVariable)17 MemVariable (cbit.vcell.math.MemVariable)14 MembraneRegionVariable (cbit.vcell.math.MembraneRegionVariable)14 VolVariable (cbit.vcell.math.VolVariable)14 Variable (cbit.vcell.math.Variable)11 FilamentVariable (cbit.vcell.math.FilamentVariable)10 Expression (cbit.vcell.parser.Expression)10 FilamentRegionVariable (cbit.vcell.math.FilamentRegionVariable)8 MembraneSubDomain (cbit.vcell.math.MembraneSubDomain)7 ReservedVariable (cbit.vcell.math.ReservedVariable)7 CompartmentSubDomain (cbit.vcell.math.CompartmentSubDomain)6 InsideVariable (cbit.vcell.math.InsideVariable)6 OutsideVariable (cbit.vcell.math.OutsideVariable)6 SubDomain (cbit.vcell.math.SubDomain)6 Constant (cbit.vcell.math.Constant)5 MathDescription (cbit.vcell.math.MathDescription)5 Function (cbit.vcell.math.Function)4 MembraneParticleVariable (cbit.vcell.math.MembraneParticleVariable)4 PointSubDomain (cbit.vcell.math.PointSubDomain)4 PointVariable (cbit.vcell.math.PointVariable)4
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