Example 6 with Kinetics
use of cbit.vcell.model.Kinetics in project vcell by virtualcell.
the class StochMathMapping method addJumpProcesses.
private void addJumpProcesses(VariableHash varHash, GeometryClass geometryClass, SubDomain subDomain) throws ExpressionException, ModelException, MappingException, MathException {
// set up jump processes
// get all the reactions from simulation context
// ReactionSpec[] reactionSpecs = simContext.getReactionContext().getReactionSpecs();---need to take a look here!
ModelUnitSystem modelUnitSystem = getSimulationContext().getModel().getUnitSystem();
ReactionSpec[] reactionSpecs = getSimulationContext().getReactionContext().getReactionSpecs();
for (ReactionSpec reactionSpec : reactionSpecs) {
if (reactionSpec.isExcluded()) {
continue;
}
// get the reaction
ReactionStep reactionStep = reactionSpec.getReactionStep();
Kinetics kinetics = reactionStep.getKinetics();
// probability parameter from modelUnitSystem
VCUnitDefinition probabilityParamUnit = modelUnitSystem.getStochasticSubstanceUnit().divideBy(modelUnitSystem.getTimeUnit());
// Different ways to deal with simple reactions and flux reactions
if (// simple reactions
reactionStep instanceof SimpleReaction) {
// check the reaction rate law to see if we need to decompose a reaction(reversible) into two jump processes.
// rate constants are important in calculating the probability rate.
// for Mass Action, we use KForward and KReverse,
// for General Kinetics we parse reaction rate J to see if it is in Mass Action form.
Expression forwardRate = null;
Expression reverseRate = null;
if (kinetics.getKineticsDescription().equals(KineticsDescription.MassAction) || kinetics.getKineticsDescription().equals(KineticsDescription.General)) {
Expression rateExp = new Expression(kinetics.getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate), reactionStep.getNameScope());
Parameter forwardRateParameter = null;
Parameter reverseRateParameter = null;
if (kinetics.getKineticsDescription().equals(KineticsDescription.MassAction)) {
forwardRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KForward);
reverseRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KReverse);
}
MassActionSolver.MassActionFunction maFunc = MassActionSolver.solveMassAction(forwardRateParameter, reverseRateParameter, rateExp, reactionStep);
if (maFunc.getForwardRate() == null && maFunc.getReverseRate() == null) {
throw new MappingException("Cannot generate stochastic math mapping for the reaction:" + reactionStep.getName() + "\nLooking for the rate function according to the form of k1*Reactant1^Stoir1*Reactant2^Stoir2...-k2*Product1^Stoip1*Product2^Stoip2.");
} else {
if (maFunc.getForwardRate() != null) {
forwardRate = maFunc.getForwardRate();
}
if (maFunc.getReverseRate() != null) {
reverseRate = maFunc.getReverseRate();
}
}
} else // if it's macro/microscopic kinetics, we'll have them set up as reactions with only forward rate.
if (kinetics.getKineticsDescription().equals(KineticsDescription.Macroscopic_irreversible) || kinetics.getKineticsDescription().equals(KineticsDescription.Microscopic_irreversible)) {
Expression Kon = getIdentifierSubstitutions(new Expression(reactionStep.getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_KOn), getNameScope()), reactionStep.getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_Binding_Radius).getUnitDefinition(), geometryClass);
if (Kon != null) {
Expression KonCopy = new Expression(Kon);
try {
MassActionSolver.substituteParameters(KonCopy, true).evaluateConstant();
forwardRate = new Expression(Kon);
} catch (ExpressionException e) {
throw new MathException(VCellErrorMessages.getMassActionSolverMessage(reactionStep.getName(), "Problem with Kon parameter in " + reactionStep.getName() + ": '" + KonCopy.infix() + "', " + e.getMessage()));
}
} else {
throw new MathException(VCellErrorMessages.getMassActionSolverMessage(reactionStep.getName(), "Kon parameter of " + reactionStep.getName() + " is null."));
}
}
boolean isForwardRatePresent = false;
boolean isReverseRatePresent = false;
if (forwardRate != null) {
isForwardRatePresent = true;
}
if (reverseRate != null) {
isReverseRatePresent = true;
}
// we process it as forward reaction
if ((isForwardRatePresent)) /*|| ((forwardRate == null) && (reverseRate == null))*/
{
// get jump process name
String jpName = TokenMangler.mangleToSName(reactionStep.getName());
// get probability
Expression exp = null;
// reactions are of mass action form
exp = getProbabilityRate(reactionStep, forwardRate, true);
ProbabilityParameter probParm = null;
try {
probParm = addProbabilityParameter(PARAMETER_PROBABILITYRATE_PREFIX + jpName, exp, PARAMETER_ROLE_P, probabilityParamUnit, reactionStep);
} catch (PropertyVetoException pve) {
pve.printStackTrace();
throw new MappingException(pve.getMessage());
}
// add probability to function or constant
varHash.addVariable(newFunctionOrConstant(getMathSymbol(probParm, geometryClass), getIdentifierSubstitutions(exp, probabilityParamUnit, geometryClass), geometryClass));
JumpProcess jp = new JumpProcess(jpName, new Expression(getMathSymbol(probParm, geometryClass)));
// actions
ReactionParticipant[] reacPart = reactionStep.getReactionParticipants();
for (int j = 0; j < reacPart.length; j++) {
Action action = null;
SpeciesCountParameter spCountParam = getSpeciesCountParameter(reacPart[j].getSpeciesContext());
if (reacPart[j] instanceof Reactant) {
// check if the reactant is a constant. If the species is a constant, there will be no action taken on this species
if (// not a constant
!simContext.getReactionContext().getSpeciesContextSpec(reacPart[j].getSpeciesContext()).isConstant()) {
int stoi = ((Reactant) reacPart[j]).getStoichiometry();
action = Action.createIncrementAction(varHash.getVariable(getMathSymbol(spCountParam, geometryClass)), new Expression(-stoi));
jp.addAction(action);
}
} else if (reacPart[j] instanceof Product) {
// check if the product is a constant. If the product is a constant, there will be no action taken on this species
if (// not a constant
!simContext.getReactionContext().getSpeciesContextSpec(reacPart[j].getSpeciesContext()).isConstant()) {
int stoi = ((Product) reacPart[j]).getStoichiometry();
action = Action.createIncrementAction(varHash.getVariable(getMathSymbol(spCountParam, geometryClass)), new Expression(stoi));
jp.addAction(action);
}
}
}
// add jump process to compartment subDomain
subDomain.addJumpProcess(jp);
}
if (// one more jump process for a reversible reaction
isReverseRatePresent) {
// get jump process name
String jpName = TokenMangler.mangleToSName(reactionStep.getName()) + PARAMETER_PROBABILITY_RATE_REVERSE_SUFFIX;
Expression exp = null;
// reactions are mass actions
exp = getProbabilityRate(reactionStep, reverseRate, false);
ProbabilityParameter probRevParm = null;
try {
probRevParm = addProbabilityParameter(PARAMETER_PROBABILITYRATE_PREFIX + jpName, exp, PARAMETER_ROLE_P_reverse, probabilityParamUnit, reactionStep);
} catch (PropertyVetoException pve) {
pve.printStackTrace();
throw new MappingException(pve.getMessage());
}
// add probability to function or constant
varHash.addVariable(newFunctionOrConstant(getMathSymbol(probRevParm, geometryClass), getIdentifierSubstitutions(exp, probabilityParamUnit, geometryClass), geometryClass));
JumpProcess jp = new JumpProcess(jpName, new Expression(getMathSymbol(probRevParm, geometryClass)));
// actions
ReactionParticipant[] reacPart = reactionStep.getReactionParticipants();
for (int j = 0; j < reacPart.length; j++) {
Action action = null;
SpeciesCountParameter spCountParam = getSpeciesCountParameter(reacPart[j].getSpeciesContext());
if (reacPart[j] instanceof Reactant) {
// check if the reactant is a constant. If the species is a constant, there will be no action taken on this species
if (// not a constant
!simContext.getReactionContext().getSpeciesContextSpec(reacPart[j].getSpeciesContext()).isConstant()) {
int stoi = ((Reactant) reacPart[j]).getStoichiometry();
action = Action.createIncrementAction(varHash.getVariable(getMathSymbol(spCountParam, geometryClass)), new Expression(stoi));
jp.addAction(action);
}
} else if (reacPart[j] instanceof Product) {
// check if the product is a constant. If the product is a constant, there will be no action taken on this species
if (// not a constant
!simContext.getReactionContext().getSpeciesContextSpec(reacPart[j].getSpeciesContext()).isConstant()) {
int stoi = ((Product) reacPart[j]).getStoichiometry();
action = Action.createIncrementAction(varHash.getVariable(getMathSymbol(spCountParam, geometryClass)), new Expression(-stoi));
jp.addAction(action);
}
}
}
// add jump process to compartment subDomain
subDomain.addJumpProcess(jp);
}
// end of if(isForwardRateNonZero), if(isReverseRateNonRate)
} else if (// flux reactions
reactionStep instanceof FluxReaction) {
// we could set jump processes for general flux rate in forms of p1*Sout + p2*Sin
if (kinetics.getKineticsDescription().equals(KineticsDescription.General) || kinetics.getKineticsDescription().equals(KineticsDescription.GeneralPermeability)) {
Expression fluxRate = new Expression(kinetics.getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate), reactionStep.getNameScope());
// we have to pass the math description para to flux solver, coz somehow math description in simulation context is not updated.
// forward and reverse rate parameters may be null
Parameter forwardRateParameter = null;
Parameter reverseRateParameter = null;
if (kinetics.getKineticsDescription().equals(KineticsDescription.GeneralPermeability)) {
forwardRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_Permeability);
reverseRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_Permeability);
}
MassActionSolver.MassActionFunction fluxFunc = MassActionSolver.solveMassAction(forwardRateParameter, reverseRateParameter, fluxRate, (FluxReaction) reactionStep);
// create jump process for forward flux if it exists.
Expression rsStructureSize = new Expression(reactionStep.getStructure().getStructureSize(), getNameScope());
VCUnitDefinition probRateUnit = modelUnitSystem.getStochasticSubstanceUnit().divideBy(modelUnitSystem.getAreaUnit()).divideBy(modelUnitSystem.getTimeUnit());
Expression rsRateUnitFactor = getUnitFactor(probRateUnit.divideBy(modelUnitSystem.getFluxReactionUnit()));
if (fluxFunc.getForwardRate() != null && !fluxFunc.getForwardRate().isZero()) {
Expression rate = fluxFunc.getForwardRate();
// get species expression (depend on structure, if mem: Species/mem_Size, if vol: species*KMOLE/vol_size)
if (fluxFunc.getReactants().size() != 1) {
throw new MappingException("Flux " + reactionStep.getName() + " should have only one reactant.");
}
SpeciesContext scReactant = fluxFunc.getReactants().get(0).getSpeciesContext();
Expression scConcExpr = new Expression(getSpeciesConcentrationParameter(scReactant), getNameScope());
Expression probExp = Expression.mult(rate, rsRateUnitFactor, rsStructureSize, scConcExpr);
// jump process name
// +"_reverse";
String jpName = TokenMangler.mangleToSName(reactionStep.getName());
ProbabilityParameter probParm = null;
try {
probParm = addProbabilityParameter(PARAMETER_PROBABILITYRATE_PREFIX + jpName, probExp, PARAMETER_ROLE_P, probabilityParamUnit, reactionStep);
} catch (PropertyVetoException pve) {
pve.printStackTrace();
throw new MappingException(pve.getMessage());
}
// add probability to function or constant
String ms = getMathSymbol(probParm, geometryClass);
Expression is = getIdentifierSubstitutions(probExp, probabilityParamUnit, geometryClass);
Variable nfoc = newFunctionOrConstant(ms, is, geometryClass);
varHash.addVariable(nfoc);
JumpProcess jp = new JumpProcess(jpName, new Expression(getMathSymbol(probParm, geometryClass)));
// actions
Action action = null;
SpeciesContext sc = fluxFunc.getReactants().get(0).getSpeciesContext();
if (!simContext.getReactionContext().getSpeciesContextSpec(sc).isConstant()) {
SpeciesCountParameter spCountParam = getSpeciesCountParameter(sc);
action = Action.createIncrementAction(varHash.getVariable(getMathSymbol(spCountParam, geometryClass)), new Expression(-1));
jp.addAction(action);
}
sc = fluxFunc.getProducts().get(0).getSpeciesContext();
if (!simContext.getReactionContext().getSpeciesContextSpec(sc).isConstant()) {
SpeciesCountParameter spCountParam = getSpeciesCountParameter(sc);
action = Action.createIncrementAction(varHash.getVariable(getMathSymbol(spCountParam, geometryClass)), new Expression(1));
jp.addAction(action);
}
subDomain.addJumpProcess(jp);
}
// create jump process for reverse flux if it exists.
if (fluxFunc.getReverseRate() != null && !fluxFunc.getReverseRate().isZero()) {
// jump process name
String jpName = TokenMangler.mangleToSName(reactionStep.getName()) + PARAMETER_PROBABILITY_RATE_REVERSE_SUFFIX;
Expression rate = fluxFunc.getReverseRate();
// get species expression (depend on structure, if mem: Species/mem_Size, if vol: species*KMOLE/vol_size)
if (fluxFunc.getProducts().size() != 1) {
throw new MappingException("Flux " + reactionStep.getName() + " should have only one product.");
}
SpeciesContext scProduct = fluxFunc.getProducts().get(0).getSpeciesContext();
Expression scConcExpr = new Expression(getSpeciesConcentrationParameter(scProduct), getNameScope());
Expression probExp = Expression.mult(rate, rsRateUnitFactor, rsStructureSize, scConcExpr);
ProbabilityParameter probRevParm = null;
try {
probRevParm = addProbabilityParameter(PARAMETER_PROBABILITYRATE_PREFIX + jpName, probExp, PARAMETER_ROLE_P_reverse, probabilityParamUnit, reactionStep);
} catch (PropertyVetoException pve) {
pve.printStackTrace();
throw new MappingException(pve.getMessage());
}
// add probability to function or constant
varHash.addVariable(newFunctionOrConstant(getMathSymbol(probRevParm, geometryClass), getIdentifierSubstitutions(probExp, probabilityParamUnit, geometryClass), geometryClass));
JumpProcess jp = new JumpProcess(jpName, new Expression(getMathSymbol(probRevParm, geometryClass)));
// actions
Action action = null;
SpeciesContext sc = fluxFunc.getReactants().get(0).getSpeciesContext();
if (!simContext.getReactionContext().getSpeciesContextSpec(sc).isConstant()) {
SpeciesCountParameter spCountParam = getSpeciesCountParameter(sc);
action = Action.createIncrementAction(varHash.getVariable(getMathSymbol(spCountParam, geometryClass)), new Expression(1));
jp.addAction(action);
}
sc = fluxFunc.getProducts().get(0).getSpeciesContext();
if (!simContext.getReactionContext().getSpeciesContextSpec(sc).isConstant()) {
SpeciesCountParameter spCountParam = getSpeciesCountParameter(sc);
action = Action.createIncrementAction(varHash.getVariable(getMathSymbol(spCountParam, geometryClass)), new Expression(-1));
jp.addAction(action);
}
subDomain.addJumpProcess(jp);
}
}
}
// end of if (simplereaction)...else if(fluxreaction)
}
// end of reaction step loop
}
Also used :
Action(cbit.vcell.math.Action)
StochVolVariable(cbit.vcell.math.StochVolVariable)
Variable(cbit.vcell.math.Variable)
Product(cbit.vcell.model.Product)
FluxReaction(cbit.vcell.model.FluxReaction)
SpeciesContext(cbit.vcell.model.SpeciesContext)
Reactant(cbit.vcell.model.Reactant)
ExpressionException(cbit.vcell.parser.ExpressionException)
JumpProcess(cbit.vcell.math.JumpProcess)
ModelUnitSystem(cbit.vcell.model.ModelUnitSystem)
SimpleReaction(cbit.vcell.model.SimpleReaction)
PropertyVetoException(java.beans.PropertyVetoException)
VCUnitDefinition(cbit.vcell.units.VCUnitDefinition)
Expression(cbit.vcell.parser.Expression)
MathException(cbit.vcell.math.MathException)
ReactionStep(cbit.vcell.model.ReactionStep)
Parameter(cbit.vcell.model.Parameter)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
Kinetics(cbit.vcell.model.Kinetics)
LumpedKinetics(cbit.vcell.model.LumpedKinetics)
MassActionSolver(cbit.vcell.model.MassActionSolver)
ReactionParticipant(cbit.vcell.model.ReactionParticipant)
Example 7 with Kinetics
use of cbit.vcell.model.Kinetics in project vcell by virtualcell.
the class ParameterTableModel method propertyChange.
/**
* This method gets called when a bound property is changed.
* @param evt A PropertyChangeEvent object describing the event source
* and the property that has changed.
*/
public void propertyChange(java.beans.PropertyChangeEvent evt) {
if (evt.getSource() == this && evt.getPropertyName().equals("reactionStep")) {
ReactionStep oldValue = (ReactionStep) evt.getOldValue();
if (oldValue != null) {
oldValue.removePropertyChangeListener(this);
oldValue.getKinetics().removePropertyChangeListener(this);
for (int i = 0; i < oldValue.getKinetics().getKineticsParameters().length; i++) {
oldValue.getKinetics().getKineticsParameters()[i].removePropertyChangeListener(this);
}
for (int i = 0; i < oldValue.getKinetics().getProxyParameters().length; i++) {
oldValue.getKinetics().getProxyParameters()[i].removePropertyChangeListener(this);
}
}
ReactionStep newValue = (ReactionStep) evt.getNewValue();
if (newValue != null) {
newValue.addPropertyChangeListener(this);
newValue.getKinetics().addPropertyChangeListener(this);
for (int i = 0; i < newValue.getKinetics().getKineticsParameters().length; i++) {
newValue.getKinetics().getKineticsParameters()[i].removePropertyChangeListener(this);
newValue.getKinetics().getKineticsParameters()[i].addPropertyChangeListener(this);
}
for (int i = 0; i < newValue.getKinetics().getProxyParameters().length; i++) {
newValue.getKinetics().getProxyParameters()[i].removePropertyChangeListener(this);
newValue.getKinetics().getProxyParameters()[i].addPropertyChangeListener(this);
}
autoCompleteSymbolFilter = reactionStep.getAutoCompleteSymbolFilter();
}
refreshData();
}
if (evt.getSource() == reactionStep && evt.getPropertyName().equals(ReactionStep.PROPERTY_NAME_KINETICS)) {
Kinetics oldValue = (Kinetics) evt.getOldValue();
if (oldValue != null) {
oldValue.removePropertyChangeListener(this);
for (int i = 0; i < oldValue.getKineticsParameters().length; i++) {
oldValue.getKineticsParameters()[i].removePropertyChangeListener(this);
}
for (int i = 0; i < oldValue.getProxyParameters().length; i++) {
oldValue.getProxyParameters()[i].removePropertyChangeListener(this);
}
}
Kinetics newValue = (Kinetics) evt.getNewValue();
if (newValue != null) {
newValue.addPropertyChangeListener(this);
for (int i = 0; i < newValue.getKineticsParameters().length; i++) {
newValue.getKineticsParameters()[i].removePropertyChangeListener(this);
newValue.getKineticsParameters()[i].addPropertyChangeListener(this);
}
for (int i = 0; i < newValue.getProxyParameters().length; i++) {
newValue.getProxyParameters()[i].removePropertyChangeListener(this);
newValue.getProxyParameters()[i].addPropertyChangeListener(this);
}
}
refreshData();
}
if (evt.getSource() instanceof Kinetics && (evt.getPropertyName().equals("kineticsParameters") || evt.getPropertyName().equals("proxyParameters"))) {
Parameter[] oldParams = (Parameter[]) evt.getOldValue();
Parameter[] newParams = (Parameter[]) evt.getNewValue();
for (int i = 0; oldParams != null && i < oldParams.length; i++) {
oldParams[i].removePropertyChangeListener(this);
}
for (int i = 0; newParams != null && i < newParams.length; i++) {
newParams[i].removePropertyChangeListener(this);
newParams[i].addPropertyChangeListener(this);
}
refreshData();
}
if (evt.getSource() instanceof Parameter) {
fireTableRowsUpdated(0, getRowCount() - 1);
}
}
Also used :
ReactionStep(cbit.vcell.model.ReactionStep)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
KineticsProxyParameter(cbit.vcell.model.Kinetics.KineticsProxyParameter)
Parameter(cbit.vcell.model.Parameter)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
UnresolvedParameter(cbit.vcell.model.Kinetics.UnresolvedParameter)
Kinetics(cbit.vcell.model.Kinetics)
Example 8 with Kinetics
use of cbit.vcell.model.Kinetics in project vcell by virtualcell.
the class TransformMassActionTableModel method saveTransformedReactions.
public void saveTransformedReactions() throws Exception {
// isTransformable and TransformedREactions are stored according to the indexes in model reaction steps.
boolean[] isTransformable = getTransformMassActions().getIsTransformable();
TransformMassActions.TransformedReaction[] trs = getTransformMassActions().getTransformedReactionSteps();
ReactionStep[] origReactions = getModel().getReactionSteps();
// names of those who can be transformed and will be transformed
String okTransReacNames = "";
// names of those who can be transformed and will not be transformed
String noTransReacNames = "";
// names of those who can not be transformed
String errReacNames = "";
for (int i = 0; i < isTransformable.length; i++) {
if (trs[i].getTransformType() == TransformMassActions.TransformedReaction.TRANSFORMABLE && getIsSelected(i)) {
okTransReacNames = okTransReacNames + origReactions[i].getName() + ",";
} else if (trs[i].getTransformType() == TransformMassActions.TransformedReaction.TRANSFORMABLE && !getIsSelected(i)) {
noTransReacNames = noTransReacNames + origReactions[i].getName() + ",";
} else if (!isTransformable[i]) {
errReacNames = errReacNames + origReactions[i].getName() + ",";
}
}
// set transformed Mass Action kinetics to model reactions
for (int i = 0; i < origReactions.length; i++) {
if (getIsSelected(i)) {
// for simple reaction, we replace the original kinetics with MassActionKinetics if it wasn't MassActionKinetics
if (origReactions[i] instanceof SimpleReaction) {
if (!(origReactions[i].getKinetics() instanceof MassActionKinetics)) {
// ***Below we will physically change the simple reaction***
// put all kinetic parameters together into array newKps
Vector<Kinetics.KineticsParameter> newKps = new Vector<Kinetics.KineticsParameter>();
// get original kinetic parameters which are not current density and reaction rate.
// those parameters are basically the symbols in rate expression.
Vector<Kinetics.KineticsParameter> origKps = new Vector<Kinetics.KineticsParameter>();
Kinetics.KineticsParameter[] Kps = origReactions[i].getKinetics().getKineticsParameters();
for (int j = 0; j < Kps.length; j++) {
if (!(Kps[j].getRole() == Kinetics.ROLE_CurrentDensity || Kps[j].getRole() == Kinetics.ROLE_ReactionRate)) {
origKps.add(Kps[j]);
}
}
// create mass action kinetics for the original reaction step
MassActionKinetics maKinetics = new MassActionKinetics(origReactions[i]);
maKinetics.getKineticsParameterFromRole(Kinetics.ROLE_KForward).setExpression(trs[i].getMassActionFunction().getForwardRate());
maKinetics.getKineticsParameterFromRole(Kinetics.ROLE_KReverse).setExpression(trs[i].getMassActionFunction().getReverseRate());
// Kinetics)
for (int j = 0; j < maKinetics.getKineticsParameters().length; j++) {
newKps.add(maKinetics.getKineticsParameters(j));
}
// copy other kinetic parameters from original kinetics
for (int j = 0; j < origKps.size(); j++) {
newKps.add(origKps.elementAt(j));
}
// add parameters to mass action kinetics
KineticsParameter[] newParameters = new KineticsParameter[newKps.size()];
newParameters = (KineticsParameter[]) newKps.toArray(newParameters);
maKinetics.addKineticsParameters(newParameters);
// after adding all the parameters, we bind the forward/reverse rate expression with symbol table (the reaction step itself)
origReactions[i].getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_KForward).getExpression().bindExpression(origReactions[i]);
origReactions[i].getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_KReverse).getExpression().bindExpression(origReactions[i]);
}
}
// for flux, we set the flux reaction back, coz we will parse it to mass action form in stochastic math mapping.
// However, we don't physically change it.
}
}
String msg = "";
if (!okTransReacNames.equals("")) {
msg = msg + okTransReacNames + " have been transformed.\n";
}
// message to be displayed in popupdialog of DocumentWindow
if (!msg.equals("")) {
throw new Exception(msg);
}
}
Also used :
SimpleReaction(cbit.vcell.model.SimpleReaction)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
ReactionStep(cbit.vcell.model.ReactionStep)
MassActionKinetics(cbit.vcell.model.MassActionKinetics)
MassActionKinetics(cbit.vcell.model.MassActionKinetics)
Kinetics(cbit.vcell.model.Kinetics)
Vector(java.util.Vector)
Example 9 with Kinetics
use of cbit.vcell.model.Kinetics in project vcell by virtualcell.
the class ParticleMathMapping method refreshMathDescription.
/**
* This method was created in VisualAge.
*/
private void refreshMathDescription() throws MappingException, MatrixException, MathException, ExpressionException, ModelException {
getSimulationContext().checkValidity();
if (getSimulationContext().getGeometry().getDimension() == 0) {
throw new MappingException("particle math mapping requires spatial geometry - dimension >= 1");
}
StructureMapping[] structureMappings = getSimulationContext().getGeometryContext().getStructureMappings();
for (int i = 0; i < structureMappings.length; i++) {
if (structureMappings[i] instanceof MembraneMapping) {
if (((MembraneMapping) structureMappings[i]).getCalculateVoltage()) {
throw new MappingException("electric potential not yet supported for particle models");
}
}
}
//
// fail if any events
//
BioEvent[] bioEvents = getSimulationContext().getBioEvents();
if (bioEvents != null && bioEvents.length > 0) {
throw new MappingException("events not yet supported for particle-based models");
}
//
// gather only those reactionSteps that are not "excluded"
//
ReactionSpec[] reactionSpecs = getSimulationContext().getReactionContext().getReactionSpecs();
Vector<ReactionStep> rsList = new Vector<ReactionStep>();
for (int i = 0; i < reactionSpecs.length; i++) {
if (reactionSpecs[i].isExcluded() == false) {
if (reactionSpecs[i].isFast()) {
throw new MappingException("fast reactions not supported for particle models");
}
rsList.add(reactionSpecs[i].getReactionStep());
}
}
ReactionStep[] reactionSteps = new ReactionStep[rsList.size()];
rsList.copyInto(reactionSteps);
//
for (int i = 0; i < reactionSteps.length; i++) {
Kinetics.UnresolvedParameter[] unresolvedParameters = reactionSteps[i].getKinetics().getUnresolvedParameters();
if (unresolvedParameters != null && unresolvedParameters.length > 0) {
StringBuffer buffer = new StringBuffer();
for (int j = 0; j < unresolvedParameters.length; j++) {
if (j > 0) {
buffer.append(", ");
}
buffer.append(unresolvedParameters[j].getName());
}
throw new MappingException(reactionSteps[i].getDisplayType() + " '" + reactionSteps[i].getName() + "' contains unresolved identifier(s): " + buffer);
}
}
//
// temporarily place all variables in a hashtable (before binding) and discarding duplicates (check for equality)
//
VariableHash varHash = new VariableHash();
// //
// // verify that all structures are mapped to geometry classes and all geometry classes are mapped to a structure
// //
// Structure structures[] = getSimulationContext().getGeometryContext().getModel().getStructures();
// for (int i = 0; i < structures.length; i++){
// StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(structures[i]);
// if (sm==null || (sm.getGeometryClass() == null)){
// throw new MappingException("model structure '"+structures[i].getName()+"' not mapped to a geometry subdomain");
// }
// if (sm.getUnitSizeParameter()!=null){
// Expression unitSizeExp = sm.getUnitSizeParameter().getExpression();
// if(unitSizeExp != null)
// {
// try {
// double unitSize = unitSizeExp.evaluateConstant();
// if (unitSize != 1.0){
// throw new MappingException("model structure '"+sm.getStructure().getName()+"' unit size = "+unitSize+" != 1.0 ... partial volume or surface mapping not yet supported for particles");
// }
// }catch (ExpressionException e){
// e.printStackTrace(System.out);
// throw new MappingException("couldn't evaluate unit size for model structure '"+sm.getStructure().getName()+"' : "+e.getMessage());
// }
// }
// }
// }
// {
// GeometryClass[] geometryClass = getSimulationContext().getGeometryContext().getGeometry().getGeometryClasses();
// for (int i = 0; i < geometryClass.length; i++){
// Structure[] mappedStructures = getSimulationContext().getGeometryContext().getStructuresFromGeometryClass(geometryClass[i]);
// if (mappedStructures==null || mappedStructures.length==0){
// throw new MappingException("geometryClass '"+geometryClass[i].getName()+"' not mapped from a model structure");
// }
// }
// }
// deals with model parameters
Model model = getSimulationContext().getModel();
ModelUnitSystem modelUnitSystem = model.getUnitSystem();
ModelParameter[] modelParameters = model.getModelParameters();
// populate in globalParameterVariants hashtable
for (int j = 0; j < modelParameters.length; j++) {
Expression modelParamExpr = modelParameters[j].getExpression();
GeometryClass geometryClass = getDefaultGeometryClass(modelParamExpr);
modelParamExpr = getIdentifierSubstitutions(modelParamExpr, modelParameters[j].getUnitDefinition(), geometryClass);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(modelParameters[j], geometryClass), modelParamExpr, geometryClass));
}
//
// create new MathDescription (based on simContext's previous MathDescription if possible)
//
MathDescription oldMathDesc = getSimulationContext().getMathDescription();
mathDesc = null;
if (oldMathDesc != null) {
if (oldMathDesc.getVersion() != null) {
mathDesc = new MathDescription(oldMathDesc.getVersion());
} else {
mathDesc = new MathDescription(oldMathDesc.getName());
}
} else {
mathDesc = new MathDescription(getSimulationContext().getName() + "_generated");
}
//
// volume particle variables
//
Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = enum1.nextElement();
if (scm.getVariable() instanceof ParticleVariable) {
if (!(mathDesc.getVariable(scm.getVariable().getName()) instanceof ParticleVariable)) {
varHash.addVariable(scm.getVariable());
}
}
}
varHash.addVariable(new Constant(getMathSymbol(model.getPI_CONSTANT(), null), getIdentifierSubstitutions(model.getPI_CONSTANT().getExpression(), model.getPI_CONSTANT().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getFARADAY_CONSTANT(), null), getIdentifierSubstitutions(model.getFARADAY_CONSTANT().getExpression(), model.getFARADAY_CONSTANT().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getFARADAY_CONSTANT_NMOLE(), null), getIdentifierSubstitutions(model.getFARADAY_CONSTANT_NMOLE().getExpression(), model.getFARADAY_CONSTANT_NMOLE().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getGAS_CONSTANT(), null), getIdentifierSubstitutions(model.getGAS_CONSTANT().getExpression(), model.getGAS_CONSTANT().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getTEMPERATURE(), null), getIdentifierSubstitutions(new Expression(getSimulationContext().getTemperatureKelvin()), model.getTEMPERATURE().getUnitDefinition(), null)));
//
for (int j = 0; j < structureMappings.length; j++) {
if (structureMappings[j] instanceof MembraneMapping) {
MembraneMapping membraneMapping = (MembraneMapping) structureMappings[j];
GeometryClass geometryClass = membraneMapping.getGeometryClass();
//
// don't calculate voltage, still may need it though
//
Parameter initialVoltageParm = membraneMapping.getInitialVoltageParameter();
Variable voltageFunction = newFunctionOrConstant(getMathSymbol(membraneMapping.getMembrane().getMembraneVoltage(), geometryClass), getIdentifierSubstitutions(initialVoltageParm.getExpression(), initialVoltageParm.getUnitDefinition(), geometryClass), geometryClass);
varHash.addVariable(voltageFunction);
varHash.addVariable(newFunctionOrConstant(getMathSymbol(membraneMapping.getMembrane().getMembraneVoltage(), membraneMapping.getGeometryClass()), getIdentifierSubstitutions(membraneMapping.getInitialVoltageParameter().getExpression(), membraneMapping.getInitialVoltageParameter().getUnitDefinition(), membraneMapping.getGeometryClass()), membraneMapping.getGeometryClass()));
}
}
//
for (int j = 0; j < reactionSteps.length; j++) {
ReactionStep rs = reactionSteps[j];
if (getSimulationContext().getReactionContext().getReactionSpec(rs).isExcluded()) {
continue;
}
Kinetics.KineticsParameter[] parameters = rs.getKinetics().getKineticsParameters();
GeometryClass geometryClass = null;
if (rs.getStructure() != null) {
geometryClass = getSimulationContext().getGeometryContext().getStructureMapping(rs.getStructure()).getGeometryClass();
}
if (parameters != null) {
for (int i = 0; i < parameters.length; i++) {
// Reaction rate, currentDensity, LumpedCurrent and null parameters are not going to displayed in the particle math description.
if (((parameters[i].getRole() == Kinetics.ROLE_CurrentDensity) || (parameters[i].getRole() == Kinetics.ROLE_LumpedCurrent) || (parameters[i].getRole() == Kinetics.ROLE_ReactionRate)) || (parameters[i].getExpression() == null)) {
continue;
}
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parameters[i], geometryClass), getIdentifierSubstitutions(parameters[i].getExpression(), parameters[i].getUnitDefinition(), geometryClass), geometryClass));
}
}
}
//
// initial constants (either function or constant)
//
SpeciesContextSpec[] speciesContextSpecs = getSimulationContext().getReactionContext().getSpeciesContextSpecs();
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpecParameter initParm = null;
Expression initExpr = null;
if (getSimulationContext().isUsingConcentration()) {
initParm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
initExpr = new Expression(initParm.getExpression());
// if (speciesContextSpecs[i].getSpeciesContext().getStructure() instanceof Feature) {
// initExpr = Expression.div(initExpr, new Expression(model.getKMOLE, getNameScope())).flatten();
// }
} else {
initParm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_InitialCount);
initExpr = new Expression(initParm.getExpression());
}
if (initExpr != null) {
StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
String[] symbols = initExpr.getSymbols();
// Check if 'initExpr' has other speciesContexts in its expression, need to replace it with 'spContext_init'
for (int j = 0; symbols != null && j < symbols.length; j++) {
// if symbol is a speciesContext, replacing it with a reference to initial condition for that speciesContext.
SpeciesContext spC = null;
SymbolTableEntry ste = initExpr.getSymbolBinding(symbols[j]);
if (ste instanceof SpeciesContextSpecProxyParameter) {
SpeciesContextSpecProxyParameter spspp = (SpeciesContextSpecProxyParameter) ste;
if (spspp.getTarget() instanceof SpeciesContext) {
spC = (SpeciesContext) spspp.getTarget();
SpeciesContextSpec spcspec = getSimulationContext().getReactionContext().getSpeciesContextSpec(spC);
SpeciesContextSpecParameter spCInitParm = spcspec.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
// if initConc param expression is null, try initCount
if (spCInitParm.getExpression() == null) {
spCInitParm = spcspec.getParameterFromRole(SpeciesContextSpec.ROLE_InitialCount);
}
// need to get init condn expression, but can't get it from getMathSymbol() (mapping between bio and math), hence get it as below.
Expression scsInitExpr = new Expression(spCInitParm, getNameScope());
// scsInitExpr.bindExpression(this);
initExpr.substituteInPlace(new Expression(spC.getName()), scsInitExpr);
}
}
}
// now create the appropriate function for the current speciesContextSpec.
varHash.addVariable(newFunctionOrConstant(getMathSymbol(initParm, sm.getGeometryClass()), getIdentifierSubstitutions(initExpr, initParm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
//
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpec.SpeciesContextSpecParameter diffParm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_DiffusionRate);
if (diffParm != null) {
StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
varHash.addVariable(newFunctionOrConstant(getMathSymbol(diffParm, sm.getGeometryClass()), getIdentifierSubstitutions(diffParm.getExpression(), diffParm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
//
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpec.SpeciesContextSpecParameter bc_xm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueXm);
StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
if (bc_xm != null && (bc_xm.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_xm, sm.getGeometryClass()), getIdentifierSubstitutions(bc_xm.getExpression(), bc_xm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_xp = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueXp);
if (bc_xp != null && (bc_xp.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_xp, sm.getGeometryClass()), getIdentifierSubstitutions(bc_xp.getExpression(), bc_xp.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_ym = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueYm);
if (bc_ym != null && (bc_ym.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_ym, sm.getGeometryClass()), getIdentifierSubstitutions(bc_ym.getExpression(), bc_ym.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_yp = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueYp);
if (bc_yp != null && (bc_yp.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_yp, sm.getGeometryClass()), getIdentifierSubstitutions(bc_yp.getExpression(), bc_yp.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_zm = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueZm);
if (bc_zm != null && (bc_zm.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_zm, sm.getGeometryClass()), getIdentifierSubstitutions(bc_zm.getExpression(), bc_zm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
SpeciesContextSpec.SpeciesContextSpecParameter bc_zp = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_BoundaryValueZp);
if (bc_zp != null && (bc_zp.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(bc_zp, sm.getGeometryClass()), getIdentifierSubstitutions(bc_zp.getExpression(), bc_zp.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
//
for (int i = 0; i < speciesContextSpecs.length; i++) {
SpeciesContextSpec.SpeciesContextSpecParameter advection_velX = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityX);
StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(speciesContextSpecs[i].getSpeciesContext().getStructure());
GeometryClass geometryClass = sm.getGeometryClass();
if (advection_velX != null && (advection_velX.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velX, geometryClass), getIdentifierSubstitutions(advection_velX.getExpression(), advection_velX.getUnitDefinition(), geometryClass), geometryClass));
}
SpeciesContextSpec.SpeciesContextSpecParameter advection_velY = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityY);
if (advection_velY != null && (advection_velY.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velY, geometryClass), getIdentifierSubstitutions(advection_velY.getExpression(), advection_velY.getUnitDefinition(), geometryClass), geometryClass));
}
SpeciesContextSpec.SpeciesContextSpecParameter advection_velZ = speciesContextSpecs[i].getParameterFromRole(SpeciesContextSpec.ROLE_VelocityZ);
if (advection_velZ != null && (advection_velZ.getExpression() != null)) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(advection_velZ, geometryClass), getIdentifierSubstitutions(advection_velZ.getExpression(), advection_velZ.getUnitDefinition(), geometryClass), geometryClass));
}
}
//
// constant species (either function or constant)
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() instanceof Constant) {
varHash.addVariable(scm.getVariable());
}
}
//
// conversion factors
//
varHash.addVariable(new Constant(getMathSymbol(model.getKMOLE(), null), getIdentifierSubstitutions(model.getKMOLE().getExpression(), model.getKMOLE().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getN_PMOLE(), null), getIdentifierSubstitutions(model.getN_PMOLE().getExpression(), model.getN_PMOLE().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getKMILLIVOLTS(), null), getIdentifierSubstitutions(model.getKMILLIVOLTS().getExpression(), model.getKMILLIVOLTS().getUnitDefinition(), null)));
varHash.addVariable(new Constant(getMathSymbol(model.getK_GHK(), null), getIdentifierSubstitutions(model.getK_GHK().getExpression(), model.getK_GHK().getUnitDefinition(), null)));
//
for (int i = 0; i < structureMappings.length; i++) {
StructureMapping sm = structureMappings[i];
if (getSimulationContext().getGeometry().getDimension() == 0) {
StructureMappingParameter sizeParm = sm.getSizeParameter();
if (sizeParm != null && sizeParm.getExpression() != null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(sizeParm, sm.getGeometryClass()), getIdentifierSubstitutions(sizeParm.getExpression(), sizeParm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
} else {
if (sm instanceof MembraneMapping) {
MembraneMapping mm = (MembraneMapping) sm;
StructureMappingParameter volFrac = mm.getVolumeFractionParameter();
if (volFrac != null && volFrac.getExpression() != null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(volFrac, sm.getGeometryClass()), getIdentifierSubstitutions(volFrac.getExpression(), volFrac.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
StructureMappingParameter surfToVol = mm.getSurfaceToVolumeParameter();
if (surfToVol != null && surfToVol.getExpression() != null) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(surfToVol, sm.getGeometryClass()), getIdentifierSubstitutions(surfToVol.getExpression(), surfToVol.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
}
} else {
Parameter parm = sm.getParameterFromRole(StructureMapping.ROLE_AreaPerUnitArea);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SurfaceClass) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm.getGeometryClass()), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_AreaPerUnitVolume);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SubVolume) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm.getGeometryClass()), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_VolumePerUnitArea);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SurfaceClass) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm.getGeometryClass()), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
parm = sm.getParameterFromRole(StructureMapping.ROLE_VolumePerUnitVolume);
if (parm != null && parm.getExpression() != null && sm.getGeometryClass() instanceof SubVolume) {
varHash.addVariable(newFunctionOrConstant(getMathSymbol(parm, sm.getGeometryClass()), getIdentifierSubstitutions(parm.getExpression(), parm.getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass()));
}
}
}
//
// functions
//
enum1 = getSpeciesContextMappings();
while (enum1.hasMoreElements()) {
SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
if (scm.getVariable() == null && scm.getDependencyExpression() != null) {
StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(scm.getSpeciesContext().getStructure());
Variable dependentVariable = newFunctionOrConstant(getMathSymbol(scm.getSpeciesContext(), sm.getGeometryClass()), getIdentifierSubstitutions(scm.getDependencyExpression(), scm.getSpeciesContext().getUnitDefinition(), sm.getGeometryClass()), sm.getGeometryClass());
dependentVariable.setDomain(new Domain(sm.getGeometryClass()));
varHash.addVariable(dependentVariable);
}
}
//
for (int i = 0; i < fieldMathMappingParameters.length; i++) {
if (fieldMathMappingParameters[i] instanceof UnitFactorParameter) {
GeometryClass geometryClass = fieldMathMappingParameters[i].getGeometryClass();
varHash.addVariable(newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], geometryClass), getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), geometryClass), fieldMathMappingParameters[i].getGeometryClass()));
}
}
//
// set Variables to MathDescription all at once with the order resolved by "VariableHash"
//
mathDesc.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
//
if (getSimulationContext().getGeometryContext().getGeometry() != null) {
try {
mathDesc.setGeometry(getSimulationContext().getGeometryContext().getGeometry());
} catch (java.beans.PropertyVetoException e) {
e.printStackTrace(System.out);
throw new MappingException("failure setting geometry " + e.getMessage());
}
} else {
throw new MappingException("geometry must be defined");
}
//
// create subdomains (volume and surfaces)
//
GeometryClass[] geometryClasses = getSimulationContext().getGeometryContext().getGeometry().getGeometryClasses();
for (int k = 0; k < geometryClasses.length; k++) {
if (geometryClasses[k] instanceof SubVolume) {
SubVolume subVolume = (SubVolume) geometryClasses[k];
//
// get priority of subDomain
//
// now does not have to match spatial feature, *BUT* needs to be unique
int priority = k;
//
// create subDomain
//
CompartmentSubDomain subDomain = new CompartmentSubDomain(subVolume.getName(), priority);
mathDesc.addSubDomain(subDomain);
//
// assign boundary condition types
//
StructureMapping[] mappedSMs = getSimulationContext().getGeometryContext().getStructureMappings(subVolume);
FeatureMapping mappedFM = null;
for (int i = 0; i < mappedSMs.length; i++) {
if (mappedSMs[i] instanceof FeatureMapping) {
if (mappedFM != null) {
lg.warn("WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique");
}
mappedFM = (FeatureMapping) mappedSMs[i];
}
}
if (mappedFM != null) {
subDomain.setBoundaryConditionXm(mappedFM.getBoundaryConditionTypeXm());
subDomain.setBoundaryConditionXp(mappedFM.getBoundaryConditionTypeXp());
if (getSimulationContext().getGeometry().getDimension() > 1) {
subDomain.setBoundaryConditionYm(mappedFM.getBoundaryConditionTypeYm());
subDomain.setBoundaryConditionYp(mappedFM.getBoundaryConditionTypeYp());
}
if (getSimulationContext().getGeometry().getDimension() > 2) {
subDomain.setBoundaryConditionZm(mappedFM.getBoundaryConditionTypeZm());
subDomain.setBoundaryConditionZp(mappedFM.getBoundaryConditionTypeZp());
}
}
} else if (geometryClasses[k] instanceof SurfaceClass) {
SurfaceClass surfaceClass = (SurfaceClass) geometryClasses[k];
// determine membrane inside and outside subvolume
// this preserves backward compatibility so that membrane subdomain
// inside and outside correspond to structure hierarchy when present
Pair<SubVolume, SubVolume> ret = DiffEquMathMapping.computeBoundaryConditionSource(model, simContext, surfaceClass);
SubVolume innerSubVolume = ret.one;
SubVolume outerSubVolume = ret.two;
//
// create subDomain
//
CompartmentSubDomain outerCompartment = mathDesc.getCompartmentSubDomain(outerSubVolume.getName());
CompartmentSubDomain innerCompartment = mathDesc.getCompartmentSubDomain(innerSubVolume.getName());
MembraneSubDomain memSubDomain = new MembraneSubDomain(innerCompartment, outerCompartment, surfaceClass.getName());
mathDesc.addSubDomain(memSubDomain);
}
}
//
// create Particle Contexts for all Particle Variables
//
Enumeration<SpeciesContextMapping> enumSCM = getSpeciesContextMappings();
Expression unitFactor = getUnitFactor(modelUnitSystem.getStochasticSubstanceUnit().divideBy(modelUnitSystem.getVolumeSubstanceUnit()));
while (enumSCM.hasMoreElements()) {
SpeciesContextMapping scm = enumSCM.nextElement();
SpeciesContext sc = scm.getSpeciesContext();
StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(sc.getStructure());
SpeciesContextSpec scs = getSimulationContext().getReactionContext().getSpeciesContextSpec(sc);
if (scm.getVariable() instanceof ParticleVariable && scm.getDependencyExpression() == null) {
ParticleVariable particleVariable = (ParticleVariable) scm.getVariable();
//
// initial distribution of particles
//
ArrayList<ParticleInitialCondition> particleInitialConditions = new ArrayList<ParticleInitialCondition>();
ParticleInitialCondition pic = null;
if (getSimulationContext().isUsingConcentration()) {
Expression initialDistribution = scs.getInitialConcentrationParameter().getExpression() == null ? null : new Expression(getMathSymbol(scs.getInitialConcentrationParameter(), sm.getGeometryClass()));
if (particleVariable instanceof VolumeParticleVariable) {
initialDistribution = Expression.mult(initialDistribution, unitFactor);
}
pic = new ParticleInitialConditionConcentration(initialDistribution);
} else {
Expression initialCount = scs.getInitialCountParameter().getExpression() == null ? null : new Expression(getMathSymbol(scs.getInitialCountParameter(), sm.getGeometryClass()));
if (initialCount == null) {
throw new MappingException("initialCount not defined for speciesContext " + scs.getSpeciesContext().getName());
}
Expression locationX = new Expression("u");
Expression locationY = new Expression("u");
Expression locationZ = new Expression("u");
pic = new ParticleInitialConditionCount(initialCount, locationX, locationY, locationZ);
}
particleInitialConditions.add(pic);
//
// diffusion
//
Expression diffusion = new Expression(getMathSymbol(scs.getDiffusionParameter(), sm.getGeometryClass()));
Expression driftXExp = null;
if (scs.getVelocityXParameter().getExpression() != null) {
driftXExp = new Expression(getMathSymbol(scs.getVelocityXParameter(), sm.getGeometryClass()));
} else {
SpatialQuantity[] velX_quantities = scs.getVelocityQuantities(QuantityComponent.X);
if (velX_quantities.length > 0) {
int numRegions = simContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions(sm.getGeometryClass()).length;
if (velX_quantities.length == 1 && numRegions == 1) {
driftXExp = new Expression(getMathSymbol(velX_quantities[0], sm.getGeometryClass()));
} else {
throw new MappingException("multiple advection velocities enabled set for multiple volume domains ");
}
}
}
Expression driftYExp = null;
if (scs.getVelocityYParameter().getExpression() != null) {
driftYExp = new Expression(getMathSymbol(scs.getVelocityYParameter(), sm.getGeometryClass()));
} else {
SpatialQuantity[] velY_quantities = scs.getVelocityQuantities(QuantityComponent.Y);
if (velY_quantities.length > 0) {
int numRegions = simContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions(sm.getGeometryClass()).length;
if (velY_quantities.length == 1 && numRegions == 1) {
driftYExp = new Expression(getMathSymbol(velY_quantities[0], sm.getGeometryClass()));
} else {
throw new MappingException("multiple advection velocities enabled set for multiple volume domains ");
}
}
}
Expression driftZExp = null;
if (scs.getVelocityZParameter().getExpression() != null) {
driftZExp = new Expression(getMathSymbol(scs.getVelocityZParameter(), sm.getGeometryClass()));
} else {
SpatialQuantity[] velZ_quantities = scs.getVelocityQuantities(QuantityComponent.Z);
if (velZ_quantities.length > 0) {
int numRegions = simContext.getGeometry().getGeometrySurfaceDescription().getGeometricRegions(sm.getGeometryClass()).length;
if (velZ_quantities.length == 1 && numRegions == 1) {
driftZExp = new Expression(getMathSymbol(velZ_quantities[0], sm.getGeometryClass()));
} else {
throw new MappingException("multiple advection velocities enabled set for multiple volume domains ");
}
}
}
ParticleProperties particleProperties = new ParticleProperties(particleVariable, diffusion, driftXExp, driftYExp, driftZExp, particleInitialConditions);
GeometryClass myGC = sm.getGeometryClass();
if (myGC == null) {
throw new MappingException("Application '" + getSimulationContext().getName() + "'\nGeometry->StructureMapping->(" + sm.getStructure().getTypeName() + ")'" + sm.getStructure().getName() + "' must be mapped to geometry domain.\n(see 'Problems' tab)");
}
SubDomain subDomain = mathDesc.getSubDomain(myGC.getName());
subDomain.addParticleProperties(particleProperties);
}
}
for (ReactionStep reactionStep : reactionSteps) {
Kinetics kinetics = reactionStep.getKinetics();
StructureMapping sm = getSimulationContext().getGeometryContext().getStructureMapping(reactionStep.getStructure());
GeometryClass reactionStepGeometryClass = sm.getGeometryClass();
SubDomain subdomain = mathDesc.getSubDomain(reactionStepGeometryClass.getName());
KineticsParameter reactionRateParameter = null;
if (kinetics instanceof LumpedKinetics) {
reactionRateParameter = ((LumpedKinetics) kinetics).getLumpedReactionRateParameter();
} else {
reactionRateParameter = ((DistributedKinetics) kinetics).getReactionRateParameter();
}
// macroscopic_irreversible/Microscopic_irreversible for bimolecular membrane reactions. They will NOT go through MassAction solver.
if (kinetics.getKineticsDescription().equals(KineticsDescription.Macroscopic_irreversible) || kinetics.getKineticsDescription().equals(KineticsDescription.Microscopic_irreversible)) {
Expression radiusExp = getIdentifierSubstitutions(reactionStep.getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_Binding_Radius).getExpression(), modelUnitSystem.getBindingRadiusUnit(), reactionStepGeometryClass);
if (radiusExp != null) {
Expression expCopy = new Expression(radiusExp);
try {
MassActionSolver.substituteParameters(expCopy, true).evaluateConstant();
} catch (ExpressionException e) {
throw new MathException(VCellErrorMessages.getMassActionSolverMessage(reactionStep.getName(), "Problem in binding radius of " + reactionStep.getName() + ": '" + radiusExp.infix() + "', " + e.getMessage()));
}
} else {
throw new MathException(VCellErrorMessages.getMassActionSolverMessage(reactionStep.getName(), "Binding radius of " + reactionStep.getName() + " is null."));
}
List<ParticleVariable> reactantParticles = new ArrayList<ParticleVariable>();
List<ParticleVariable> productParticles = new ArrayList<ParticleVariable>();
List<Action> forwardActions = new ArrayList<Action>();
for (ReactionParticipant rp : reactionStep.getReactionParticipants()) {
SpeciesContext sc = rp.getSpeciesContext();
SpeciesContextSpec scs = getSimulationContext().getReactionContext().getSpeciesContextSpec(sc);
GeometryClass scGeometryClass = getSimulationContext().getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass();
String varName = getMathSymbol(sc, scGeometryClass);
Variable var = mathDesc.getVariable(varName);
if (var instanceof ParticleVariable) {
ParticleVariable particle = (ParticleVariable) var;
if (rp instanceof Reactant) {
reactantParticles.add(particle);
if (!scs.isConstant() && !scs.isForceContinuous()) {
for (int i = 0; i < Math.abs(rp.getStoichiometry()); i++) {
if (radiusExp != null) {
forwardActions.add(Action.createDestroyAction(particle));
}
}
}
} else if (rp instanceof Product) {
productParticles.add(particle);
if (!scs.isConstant() && !scs.isForceContinuous()) {
for (int i = 0; i < Math.abs(rp.getStoichiometry()); i++) {
if (radiusExp != null) {
forwardActions.add(Action.createCreateAction(particle));
}
}
}
}
} else {
throw new MappingException("particle variable '" + varName + "' not found");
}
}
JumpProcessRateDefinition bindingRadius = new InteractionRadius(radiusExp);
// get jump process name
String jpName = TokenMangler.mangleToSName(reactionStep.getName());
// only for NFSim/Rules for now.
ProcessSymmetryFactor processSymmetryFactor = null;
if (forwardActions.size() > 0) {
ParticleJumpProcess forwardProcess = new ParticleJumpProcess(jpName, reactantParticles, bindingRadius, forwardActions, processSymmetryFactor);
subdomain.addParticleJumpProcess(forwardProcess);
}
} else // other type of reactions
{
/* check the reaction rate law to see if we need to decompose a reaction(reversible) into two jump processes.
rate constants are important in calculating the probability rate.
for Mass Action, we use KForward and KReverse,
for General Kinetics we parse reaction rate J to see if it is in Mass Action form.
*/
Expression forwardRate = null;
Expression reverseRate = null;
// Using the MassActionFunction to write out the math description
MassActionSolver.MassActionFunction maFunc = null;
if (kinetics.getKineticsDescription().equals(KineticsDescription.MassAction) || kinetics.getKineticsDescription().equals(KineticsDescription.General) || kinetics.getKineticsDescription().equals(KineticsDescription.GeneralPermeability)) {
Expression rateExp = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_ReactionRate).getExpression();
Parameter forwardRateParameter = null;
Parameter reverseRateParameter = null;
if (kinetics.getKineticsDescription().equals(KineticsDescription.MassAction)) {
forwardRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KForward);
reverseRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_KReverse);
} else if (kinetics.getKineticsDescription().equals(KineticsDescription.GeneralPermeability)) {
forwardRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_Permeability);
reverseRateParameter = kinetics.getKineticsParameterFromRole(Kinetics.ROLE_Permeability);
}
maFunc = MassActionSolver.solveMassAction(forwardRateParameter, reverseRateParameter, rateExp, reactionStep);
if (maFunc.getForwardRate() == null && maFunc.getReverseRate() == null) {
throw new MappingException("Cannot generate stochastic math mapping for the reaction:" + reactionStep.getName() + "\nLooking for the rate function according to the form of k1*Reactant1^Stoir1*Reactant2^Stoir2...-k2*Product1^Stoip1*Product2^Stoip2.");
} else {
if (maFunc.getForwardRate() != null) {
forwardRate = maFunc.getForwardRate();
}
if (maFunc.getReverseRate() != null) {
reverseRate = maFunc.getReverseRate();
}
}
}
if (maFunc != null) {
// if the reaction has forward rate (Mass action,HMMs), or don't have either forward or reverse rate (some other rate laws--like general)
// we process it as forward reaction
List<ParticleVariable> reactantParticles = new ArrayList<ParticleVariable>();
List<ParticleVariable> productParticles = new ArrayList<ParticleVariable>();
List<Action> forwardActions = new ArrayList<Action>();
List<Action> reverseActions = new ArrayList<Action>();
List<ReactionParticipant> reactants = maFunc.getReactants();
List<ReactionParticipant> products = maFunc.getProducts();
for (ReactionParticipant rp : reactants) {
SpeciesContext sc = rp.getSpeciesContext();
SpeciesContextSpec scs = getSimulationContext().getReactionContext().getSpeciesContextSpec(sc);
GeometryClass scGeometryClass = getSimulationContext().getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass();
String varName = getMathSymbol(sc, scGeometryClass);
Variable var = mathDesc.getVariable(varName);
if (var instanceof ParticleVariable) {
ParticleVariable particle = (ParticleVariable) var;
reactantParticles.add(particle);
if (!scs.isConstant() && !scs.isForceContinuous()) {
for (int i = 0; i < Math.abs(rp.getStoichiometry()); i++) {
if (forwardRate != null) {
forwardActions.add(Action.createDestroyAction(particle));
}
if (reverseRate != null) {
reverseActions.add(Action.createCreateAction(particle));
}
}
}
} else {
throw new MappingException("particle variable '" + varName + "' not found");
}
}
for (ReactionParticipant rp : products) {
SpeciesContext sc = rp.getSpeciesContext();
SpeciesContextSpec scs = getSimulationContext().getReactionContext().getSpeciesContextSpec(sc);
GeometryClass scGeometryClass = getSimulationContext().getGeometryContext().getStructureMapping(sc.getStructure()).getGeometryClass();
String varName = getMathSymbol(sc, scGeometryClass);
Variable var = mathDesc.getVariable(varName);
if (var instanceof ParticleVariable) {
ParticleVariable particle = (ParticleVariable) var;
productParticles.add(particle);
if (!scs.isConstant() && !scs.isForceContinuous()) {
for (int i = 0; i < Math.abs(rp.getStoichiometry()); i++) {
if (forwardRate != null) {
forwardActions.add(Action.createCreateAction(particle));
}
if (reverseRate != null) {
reverseActions.add(Action.createDestroyAction(particle));
}
}
}
} else {
throw new MappingException("particle variable '" + varName + "' not found");
}
}
//
// There are two unit conversions required:
//
// 1) convert entire reaction rate from vcell reaction units to Smoldyn units (molecules/lengthunit^dim/timeunit)
// (where dim is 2 for membrane reactions and 3 for volume reactions)
//
// for forward rates:
// 2) convert each reactant from Smoldyn units (molecules/lengthunit^dim) to VCell units
// (where dim is 2 for membrane reactants and 3 for volume reactants)
//
// or
//
// for reverse rates:
// 2) convert each product from Smoldyn units (molecules/lengthunit^dim) to VCell units
// (where dim is 2 for membrane products and 3 for volume products)
//
RationalNumber reactionLocationDim = new RationalNumber(reactionStep.getStructure().getDimension());
VCUnitDefinition timeUnit = modelUnitSystem.getTimeUnit();
VCUnitDefinition smoldynReactionSizeUnit = modelUnitSystem.getLengthUnit().raiseTo(reactionLocationDim);
VCUnitDefinition smoldynSubstanceUnit = modelUnitSystem.getStochasticSubstanceUnit();
VCUnitDefinition smoldynReactionRateUnit = smoldynSubstanceUnit.divideBy(smoldynReactionSizeUnit).divideBy(timeUnit);
VCUnitDefinition vcellReactionRateUnit = reactionRateParameter.getUnitDefinition();
VCUnitDefinition reactionUnitFactor = smoldynReactionRateUnit.divideBy(vcellReactionRateUnit);
if (forwardRate != null) {
VCUnitDefinition smoldynReactantsUnit = modelUnitSystem.getInstance_DIMENSIONLESS();
// start with factor to translate entire reaction rate.
VCUnitDefinition forwardUnitFactor = reactionUnitFactor;
//
for (ReactionParticipant reactant : maFunc.getReactants()) {
VCUnitDefinition vcellReactantUnit = reactant.getSpeciesContext().getUnitDefinition();
boolean bForceContinuous = simContext.getReactionContext().getSpeciesContextSpec(reactant.getSpeciesContext()).isForceContinuous();
VCUnitDefinition smoldynReactantUnit = null;
if (bForceContinuous) {
// reactant is continuous (vcell units)
smoldynReactantUnit = reactant.getSpeciesContext().getUnitDefinition();
} else {
// reactant is a particle (smoldyn units)
RationalNumber reactantLocationDim = new RationalNumber(reactant.getStructure().getDimension());
VCUnitDefinition smoldynReactantSize = modelUnitSystem.getLengthUnit().raiseTo(reactantLocationDim);
smoldynReactantUnit = smoldynSubstanceUnit.divideBy(smoldynReactantSize);
}
// keep track of units of all reactants
smoldynReactantsUnit = smoldynReactantsUnit.multiplyBy(smoldynReactantUnit);
RationalNumber reactantStoichiometry = new RationalNumber(reactant.getStoichiometry());
VCUnitDefinition reactantUnitFactor = (vcellReactantUnit.divideBy(smoldynReactantUnit)).raiseTo(reactantStoichiometry);
// accumulate unit factors for all reactants
forwardUnitFactor = forwardUnitFactor.multiplyBy(reactantUnitFactor);
}
forwardRate = Expression.mult(forwardRate, getUnitFactor(forwardUnitFactor));
VCUnitDefinition smoldynExpectedForwardRateUnit = smoldynReactionRateUnit.divideBy(smoldynReactantsUnit);
// get probability
Expression exp = getIdentifierSubstitutions(forwardRate, smoldynExpectedForwardRateUnit, reactionStepGeometryClass).flatten();
JumpProcessRateDefinition partRateDef = new MacroscopicRateConstant(exp);
// create particle jump process
String jpName = TokenMangler.mangleToSName(reactionStep.getName());
// only for NFSim/Rules for now.
ProcessSymmetryFactor processSymmetryFactor = null;
if (forwardActions.size() > 0) {
ParticleJumpProcess forwardProcess = new ParticleJumpProcess(jpName, reactantParticles, partRateDef, forwardActions, processSymmetryFactor);
subdomain.addParticleJumpProcess(forwardProcess);
}
}
// end of forward rate not null
if (reverseRate != null) {
VCUnitDefinition smoldynProductsUnit = modelUnitSystem.getInstance_DIMENSIONLESS();
// start with factor to translate entire reaction rate.
VCUnitDefinition reverseUnitFactor = reactionUnitFactor;
//
for (ReactionParticipant product : maFunc.getProducts()) {
VCUnitDefinition vcellProductUnit = product.getSpeciesContext().getUnitDefinition();
boolean bForceContinuous = simContext.getReactionContext().getSpeciesContextSpec(product.getSpeciesContext()).isForceContinuous();
VCUnitDefinition smoldynProductUnit = null;
if (bForceContinuous) {
smoldynProductUnit = product.getSpeciesContext().getUnitDefinition();
} else {
RationalNumber productLocationDim = new RationalNumber(product.getStructure().getDimension());
VCUnitDefinition smoldynProductSize = modelUnitSystem.getLengthUnit().raiseTo(productLocationDim);
smoldynProductUnit = smoldynSubstanceUnit.divideBy(smoldynProductSize);
}
// keep track of units of all products
smoldynProductsUnit = smoldynProductsUnit.multiplyBy(smoldynProductUnit);
RationalNumber productStoichiometry = new RationalNumber(product.getStoichiometry());
VCUnitDefinition productUnitFactor = (vcellProductUnit.divideBy(smoldynProductUnit)).raiseTo(productStoichiometry);
// accumulate unit factors for all products
reverseUnitFactor = reverseUnitFactor.multiplyBy(productUnitFactor);
}
reverseRate = Expression.mult(reverseRate, getUnitFactor(reverseUnitFactor));
VCUnitDefinition smoldynExpectedReverseRateUnit = smoldynReactionRateUnit.divideBy(smoldynProductsUnit);
// get probability
Expression exp = getIdentifierSubstitutions(reverseRate, smoldynExpectedReverseRateUnit, reactionStepGeometryClass).flatten();
JumpProcessRateDefinition partProbRate = new MacroscopicRateConstant(exp);
// get jump process name
String jpName = TokenMangler.mangleToSName(reactionStep.getName() + "_reverse");
// only for NFSim/Rules for now.
ProcessSymmetryFactor processSymmetryFactor = null;
if (reverseActions.size() > 0) {
ParticleJumpProcess reverseProcess = new ParticleJumpProcess(jpName, productParticles, partProbRate, reverseActions, processSymmetryFactor);
subdomain.addParticleJumpProcess(reverseProcess);
}
}
// end of reverse rate not null
}
// end of maFunc not null
}
// end of reaction step for loop
}
//
for (int i = 0; i < fieldMathMappingParameters.length; i++) {
if (fieldMathMappingParameters[i] instanceof UnitFactorParameter) {
GeometryClass geometryClass = fieldMathMappingParameters[i].getGeometryClass();
Variable variable = newFunctionOrConstant(getMathSymbol(fieldMathMappingParameters[i], geometryClass), getIdentifierSubstitutions(fieldMathMappingParameters[i].getExpression(), fieldMathMappingParameters[i].getUnitDefinition(), geometryClass), fieldMathMappingParameters[i].getGeometryClass());
if (mathDesc.getVariable(variable.getName()) == null) {
mathDesc.addVariable(variable);
}
}
}
if (!mathDesc.isValid()) {
lg.warn(mathDesc.getVCML_database());
throw new MappingException("generated an invalid mathDescription: " + mathDesc.getWarning());
}
if (lg.isDebugEnabled()) {
System.out.println("]]]]]]]]]]]]]]]]]]]]]] VCML string begin ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]");
System.out.println(mathDesc.getVCML());
System.out.println("]]]]]]]]]]]]]]]]]]]]]] VCML string end ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]");
}
}
Also used :
MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)
LumpedKinetics(cbit.vcell.model.LumpedKinetics)
MathDescription(cbit.vcell.math.MathDescription)
ArrayList(java.util.ArrayList)
Product(cbit.vcell.model.Product)
SpeciesContext(cbit.vcell.model.SpeciesContext)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
Reactant(cbit.vcell.model.Reactant)
ExpressionException(cbit.vcell.parser.ExpressionException)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
SubDomain(cbit.vcell.math.SubDomain)
MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
SubVolume(cbit.vcell.geometry.SubVolume)
Vector(java.util.Vector)
SpatialQuantity(cbit.vcell.mapping.spatial.SpatialObject.SpatialQuantity)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
JumpProcessRateDefinition(cbit.vcell.math.JumpProcessRateDefinition)
InteractionRadius(cbit.vcell.math.InteractionRadius)
ParticleJumpProcess(cbit.vcell.math.ParticleJumpProcess)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
VCUnitDefinition(cbit.vcell.units.VCUnitDefinition)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
ParticleInitialCondition(cbit.vcell.math.ParticleProperties.ParticleInitialCondition)
ReactionStep(cbit.vcell.model.ReactionStep)
ParticleProperties(cbit.vcell.math.ParticleProperties)
Kinetics(cbit.vcell.model.Kinetics)
DistributedKinetics(cbit.vcell.model.DistributedKinetics)
LumpedKinetics(cbit.vcell.model.LumpedKinetics)
CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain)
SubDomain(cbit.vcell.math.SubDomain)
Domain(cbit.vcell.math.Variable.Domain)
MembraneSubDomain(cbit.vcell.math.MembraneSubDomain)
ReactionParticipant(cbit.vcell.model.ReactionParticipant)
GeometryClass(cbit.vcell.geometry.GeometryClass)
Action(cbit.vcell.math.Action)
VolumeParticleVariable(cbit.vcell.math.VolumeParticleVariable)
MembraneParticleVariable(cbit.vcell.math.MembraneParticleVariable)
ParticleVariable(cbit.vcell.math.ParticleVariable)
Variable(cbit.vcell.math.Variable)
SpeciesContextSpecProxyParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecProxyParameter)
SurfaceClass(cbit.vcell.geometry.SurfaceClass)
VariableHash(cbit.vcell.math.VariableHash)
VolumeParticleVariable(cbit.vcell.math.VolumeParticleVariable)
MembraneParticleVariable(cbit.vcell.math.MembraneParticleVariable)
ParticleVariable(cbit.vcell.math.ParticleVariable)
MacroscopicRateConstant(cbit.vcell.math.MacroscopicRateConstant)
Constant(cbit.vcell.math.Constant)
SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry)
MacroscopicRateConstant(cbit.vcell.math.MacroscopicRateConstant)
RationalNumber(ucar.units_vcell.RationalNumber)
ModelUnitSystem(cbit.vcell.model.ModelUnitSystem)
Pair(org.vcell.util.Pair)
ParticleInitialConditionConcentration(cbit.vcell.math.ParticleProperties.ParticleInitialConditionConcentration)
ProcessSymmetryFactor(cbit.vcell.math.ParticleJumpProcess.ProcessSymmetryFactor)
Expression(cbit.vcell.parser.Expression)
VolumeParticleVariable(cbit.vcell.math.VolumeParticleVariable)
MathException(cbit.vcell.math.MathException)
Model(cbit.vcell.model.Model)
StructureMappingParameter(cbit.vcell.mapping.StructureMapping.StructureMappingParameter)
Parameter(cbit.vcell.model.Parameter)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
SpeciesContextSpecProxyParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecProxyParameter)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
SpeciesContextSpecParameter(cbit.vcell.mapping.SpeciesContextSpec.SpeciesContextSpecParameter)
MassActionSolver(cbit.vcell.model.MassActionSolver)
ParticleInitialConditionCount(cbit.vcell.math.ParticleProperties.ParticleInitialConditionCount)
Example 10 with Kinetics
use of cbit.vcell.model.Kinetics in project vcell by virtualcell.
the class RulebasedTransformer method transform.
private void transform(SimulationContext originalSimContext, SimulationContext transformedSimulationContext, ArrayList<ModelEntityMapping> entityMappings, MathMappingCallback mathMappingCallback) throws PropertyVetoException {
Model newModel = transformedSimulationContext.getModel();
Model originalModel = originalSimContext.getModel();
ModelEntityMapping em = null;
// list of rules created from the reactions; we apply the symmetry factor computed by bionetgen only to these
Set<ReactionRule> fromReactions = new HashSet<>();
for (SpeciesContext newSpeciesContext : newModel.getSpeciesContexts()) {
final SpeciesContext originalSpeciesContext = originalModel.getSpeciesContext(newSpeciesContext.getName());
// map new and old species contexts
em = new ModelEntityMapping(originalSpeciesContext, newSpeciesContext);
entityMappings.add(em);
if (newSpeciesContext.hasSpeciesPattern()) {
// it's perfect already and can't be improved
continue;
}
try {
MolecularType newmt = newModel.getRbmModelContainer().createMolecularType();
newModel.getRbmModelContainer().addMolecularType(newmt, false);
MolecularTypePattern newmtp_sc = new MolecularTypePattern(newmt);
SpeciesPattern newsp_sc = new SpeciesPattern();
newsp_sc.addMolecularTypePattern(newmtp_sc);
newSpeciesContext.setSpeciesPattern(newsp_sc);
RbmObservable newo = new RbmObservable(newModel, "O0_" + newmt.getName() + "_tot", newSpeciesContext.getStructure(), RbmObservable.ObservableType.Molecules);
MolecularTypePattern newmtp_ob = new MolecularTypePattern(newmt);
SpeciesPattern newsp_ob = new SpeciesPattern();
newsp_ob.addMolecularTypePattern(newmtp_ob);
newo.addSpeciesPattern(newsp_ob);
newModel.getRbmModelContainer().addObservable(newo);
// map new observable to old species context
em = new ModelEntityMapping(originalSpeciesContext, newo);
entityMappings.add(em);
} catch (ModelException e) {
e.printStackTrace();
throw new RuntimeException("unable to transform species context: " + e.getMessage());
} catch (PropertyVetoException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
ReactionSpec[] reactionSpecs = transformedSimulationContext.getReactionContext().getReactionSpecs();
for (ReactionSpec reactionSpec : reactionSpecs) {
if (reactionSpec.isExcluded()) {
// we create rules only from those reactions which are not excluded
continue;
}
ReactionStep rs = reactionSpec.getReactionStep();
String name = rs.getName();
String mangled = TokenMangler.fixTokenStrict(name);
mangled = newModel.getReactionName(mangled);
Kinetics k = rs.getKinetics();
if (!(k instanceof MassActionKinetics)) {
throw new RuntimeException("Only Mass Action Kinetics supported at this time, reaction \"" + rs.getName() + "\" uses kinetic law type \"" + rs.getKinetics().getName() + "\"");
}
boolean bReversible = rs.isReversible();
ReactionRule rr = new ReactionRule(newModel, mangled, rs.getStructure(), bReversible);
fromReactions.add(rr);
MassActionKinetics massActionKinetics = (MassActionKinetics) k;
List<Reactant> rList = rs.getReactants();
List<Product> pList = rs.getProducts();
// counting the stoichiometry - 2A+B means 3 reactants
int numReactants = 0;
for (Reactant r : rList) {
numReactants += r.getStoichiometry();
if (numReactants > 2) {
String message = "NFSim doesn't support more than 2 reactants within a reaction: " + name;
throw new RuntimeException(message);
}
}
int numProducts = 0;
for (Product p : pList) {
numProducts += p.getStoichiometry();
if (bReversible && numProducts > 2) {
String message = "NFSim doesn't support more than 2 products within a reversible reaction: " + name;
throw new RuntimeException(message);
}
}
RateLawType rateLawType = RateLawType.MassAction;
RbmKineticLaw kineticLaw = new RbmKineticLaw(rr, rateLawType);
try {
String forwardRateName = massActionKinetics.getForwardRateParameter().getName();
Expression forwardRateExp = massActionKinetics.getForwardRateParameter().getExpression();
String reverseRateName = massActionKinetics.getReverseRateParameter().getName();
Expression reverseRateExp = massActionKinetics.getReverseRateParameter().getExpression();
LocalParameter fR = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate);
fR.setName(forwardRateName);
LocalParameter rR = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate);
rR.setName(reverseRateName);
if (rs.hasReactant()) {
kineticLaw.setParameterValue(fR, forwardRateExp, true);
}
if (rs.hasProduct()) {
kineticLaw.setParameterValue(rR, reverseRateExp, true);
}
//
for (KineticsParameter reaction_p : massActionKinetics.getKineticsParameters()) {
if (reaction_p.getRole() == Kinetics.ROLE_UserDefined) {
LocalParameter rule_p = kineticLaw.getLocalParameter(reaction_p.getName());
if (rule_p == null) {
//
// after lazy parameter creation we didn't find a user-defined rule parameter with this same name.
//
// there must be a global symbol with the same name, that the local reaction parameter has overridden.
//
ParameterContext.LocalProxyParameter rule_proxy_parameter = null;
for (ProxyParameter proxyParameter : kineticLaw.getProxyParameters()) {
if (proxyParameter.getName().equals(reaction_p.getName())) {
rule_proxy_parameter = (LocalProxyParameter) proxyParameter;
}
}
if (rule_proxy_parameter != null) {
// we want to convert to local
boolean bConvertToGlobal = false;
kineticLaw.convertParameterType(rule_proxy_parameter, bConvertToGlobal);
} else {
// could find neither local parameter nor proxy parameter
throw new RuntimeException("user defined parameter " + reaction_p.getName() + " from reaction " + rs.getName() + " didn't map to a reactionRule parameter");
}
} else if (rule_p.getRole() == RbmKineticLawParameterType.UserDefined) {
kineticLaw.setParameterValue(rule_p, reaction_p.getExpression(), true);
rule_p.setUnitDefinition(reaction_p.getUnitDefinition());
} else {
throw new RuntimeException("user defined parameter " + reaction_p.getName() + " from reaction " + rs.getName() + " mapped to a reactionRule parameter with unexpected role " + rule_p.getRole().getDescription());
}
}
}
} catch (ExpressionException e) {
e.printStackTrace();
throw new RuntimeException("Problem attempting to set RbmKineticLaw expression: " + e.getMessage());
}
rr.setKineticLaw(kineticLaw);
KineticsParameter[] kpList = k.getKineticsParameters();
ModelParameter[] mpList = rs.getModel().getModelParameters();
ModelParameter mp = rs.getModel().getModelParameter(kpList[0].getName());
ReactionParticipant[] rpList = rs.getReactionParticipants();
for (ReactionParticipant p : rpList) {
if (p instanceof Reactant) {
int stoichiometry = p.getStoichiometry();
for (int i = 0; i < stoichiometry; i++) {
SpeciesPattern speciesPattern = new SpeciesPattern(rs.getModel(), p.getSpeciesContext().getSpeciesPattern());
ReactantPattern reactantPattern = new ReactantPattern(speciesPattern, p.getStructure());
rr.addReactant(reactantPattern);
}
} else if (p instanceof Product) {
int stoichiometry = p.getStoichiometry();
for (int i = 0; i < stoichiometry; i++) {
SpeciesPattern speciesPattern = new SpeciesPattern(rs.getModel(), p.getSpeciesContext().getSpeciesPattern());
ProductPattern productPattern = new ProductPattern(speciesPattern, p.getStructure());
rr.addProduct(productPattern);
}
}
}
// commented code below is probably obsolete, we verify (above) in the reaction the number of participants,
// no need to do it again in the corresponding rule
// if(rr.getReactantPatterns().size() > 2) {
// String message = "NFSim doesn't support more than 2 reactants within a reaction: " + name;
// throw new RuntimeException(message);
// }
// if(rr.getProductPatterns().size() > 2) {
// String message = "NFSim doesn't support more than 2 products within a reaction: " + name;
// throw new RuntimeException(message);
// }
newModel.removeReactionStep(rs);
newModel.getRbmModelContainer().addReactionRule(rr);
}
for (ReactionRuleSpec rrs : transformedSimulationContext.getReactionContext().getReactionRuleSpecs()) {
if (rrs == null) {
continue;
}
ReactionRule rr = rrs.getReactionRule();
if (rrs.isExcluded()) {
// delete those rules which are disabled (excluded) in the Specifications / Reaction table
newModel.getRbmModelContainer().removeReactionRule(rr);
continue;
}
}
// now that we generated the rules we can delete the reaction steps they're coming from
for (ReactionStep rs : newModel.getReactionSteps()) {
newModel.removeReactionStep(rs);
}
try {
// we invoke bngl just for the purpose of generating the xml file, which we'll then use to extract the symmetry factor
generateNetwork(transformedSimulationContext, fromReactions, mathMappingCallback);
} catch (ClassNotFoundException | IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
System.out.println("Finished RuleBased Transformer.");
}
Also used :
Product(cbit.vcell.model.Product)
SpeciesContext(cbit.vcell.model.SpeciesContext)
Reactant(cbit.vcell.model.Reactant)
LocalProxyParameter(cbit.vcell.mapping.ParameterContext.LocalProxyParameter)
SpeciesPattern(org.vcell.model.rbm.SpeciesPattern)
ExpressionException(cbit.vcell.parser.ExpressionException)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
RateLawType(cbit.vcell.model.RbmKineticLaw.RateLawType)
HashSet(java.util.HashSet)
ReactantPattern(cbit.vcell.model.ReactantPattern)
ReactionRule(cbit.vcell.model.ReactionRule)
ModelException(cbit.vcell.model.ModelException)
ProductPattern(cbit.vcell.model.ProductPattern)
RbmObservable(cbit.vcell.model.RbmObservable)
RbmKineticLaw(cbit.vcell.model.RbmKineticLaw)
IOException(java.io.IOException)
MolecularType(org.vcell.model.rbm.MolecularType)
PropertyVetoException(java.beans.PropertyVetoException)
LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
ProxyParameter(cbit.vcell.model.ProxyParameter)
LocalProxyParameter(cbit.vcell.mapping.ParameterContext.LocalProxyParameter)
Expression(cbit.vcell.parser.Expression)
ReactionStep(cbit.vcell.model.ReactionStep)
Model(cbit.vcell.model.Model)
MassActionKinetics(cbit.vcell.model.MassActionKinetics)
Kinetics(cbit.vcell.model.Kinetics)
MassActionKinetics(cbit.vcell.model.MassActionKinetics)
MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern)
ReactionParticipant(cbit.vcell.model.ReactionParticipant)
Aggregations
Kinetics (cbit.vcell.model.Kinetics)31
KineticsParameter (cbit.vcell.model.Kinetics.KineticsParameter)21
ReactionStep (cbit.vcell.model.ReactionStep)17
Expression (cbit.vcell.parser.Expression)16
ModelParameter (cbit.vcell.model.Model.ModelParameter)11
ExpressionException (cbit.vcell.parser.ExpressionException)11
ReactionParticipant (cbit.vcell.model.ReactionParticipant)10
SpeciesContext (cbit.vcell.model.SpeciesContext)10
MassActionKinetics (cbit.vcell.model.MassActionKinetics)9
ModelUnitSystem (cbit.vcell.model.ModelUnitSystem)9
SimpleReaction (cbit.vcell.model.SimpleReaction)9
PropertyVetoException (java.beans.PropertyVetoException)9
LumpedKinetics (cbit.vcell.model.LumpedKinetics)8
VCUnitDefinition (cbit.vcell.units.VCUnitDefinition)8
Model (cbit.vcell.model.Model)7
Parameter (cbit.vcell.model.Parameter)7
Product (cbit.vcell.model.Product)7
Reactant (cbit.vcell.model.Reactant)7
FluxReaction (cbit.vcell.model.FluxReaction)6
StructureMapping (cbit.vcell.mapping.StructureMapping)5
