Example 1 with FakeReactionRuleRateParameter
use of org.vcell.model.rbm.FakeReactionRuleRateParameter in project vcell by virtualcell.
the class NetworkTransformer method transform.
private void transform(SimulationContext simContext, SimulationContext transformedSimulationContext, ArrayList<ModelEntityMapping> entityMappings, MathMappingCallback mathMappingCallback, NetworkGenerationRequirements networkGenerationRequirements) {
String msg = "Generating network: flattening...";
mathMappingCallback.setMessage(msg);
TaskCallbackMessage tcm = new TaskCallbackMessage(TaskCallbackStatus.Clean, "");
simContext.appendToConsole(tcm);
tcm = new TaskCallbackMessage(TaskCallbackStatus.TaskStart, msg);
simContext.appendToConsole(tcm);
long startTime = System.currentTimeMillis();
System.out.println("Convert to bngl, execute BNG, retrieve the results.");
try {
BNGOutputSpec outputSpec = generateNetwork(simContext, mathMappingCallback, networkGenerationRequirements);
if (mathMappingCallback.isInterrupted()) {
msg = "Canceled by user.";
tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
simContext.appendToConsole(tcm);
throw new UserCancelException(msg);
}
long endTime = System.currentTimeMillis();
long elapsedTime = endTime - startTime;
System.out.println(" " + elapsedTime + " milliseconds");
Model model = transformedSimulationContext.getModel();
ReactionContext reactionContext = transformedSimulationContext.getReactionContext();
// ---- Parameters -----------------------------------------------------------------------------------------------
startTime = System.currentTimeMillis();
for (int i = 0; i < outputSpec.getBNGParams().length; i++) {
BNGParameter p = outputSpec.getBNGParams()[i];
// System.out.println(i+1 + ":\t\t"+ p.toString());
if (model.getRbmModelContainer().getParameter(p.getName()) != null) {
// if it's already there we don't try to add it again; this should be true for all of them!
continue;
}
String s = p.getName();
if (NetworkConstraints.SPECIES_LIMIT_PARAMETER.equals(s)) {
System.out.println("found NetworkConstraints seciesLimit parameter.");
continue;
}
if (NetworkConstraints.REACTIONS_LIMIT_PARAMETER.equals(s)) {
System.out.println("found NetworkConstraints reactionsLimit parameter.");
continue;
}
FakeSeedSpeciesInitialConditionsParameter fakeICParam = FakeSeedSpeciesInitialConditionsParameter.fromString(s);
if (speciesEquivalenceMap.containsKey(fakeICParam)) {
// we get rid of the fake parameters we use as keys
continue;
}
FakeReactionRuleRateParameter fakeKineticParam = FakeReactionRuleRateParameter.fromString(s);
if (fakeKineticParam != null) {
System.out.println("found fakeKineticParam " + fakeKineticParam.fakeParameterName);
// we get rid of the fake parameters we use as keys
continue;
}
throw new RuntimeException("unexpected parameter " + p.getName() + " in internal BNG processing");
// Expression exp = new Expression(p.getValue());
// exp.bindExpression(model.getRbmModelContainer().getSymbolTable());
// model.getRbmModelContainer().addParameter(p.getName(), exp, model.getUnitSystem().getInstance_TBD());
}
endTime = System.currentTimeMillis();
elapsedTime = endTime - startTime;
msg = "Adding " + outputSpec.getBNGParams().length + " parameters to model, " + elapsedTime + " ms";
System.out.println(msg);
// ---- Species ------------------------------------------------------------------------------------------------------------
mathMappingCallback.setMessage("generating network: adding species...");
mathMappingCallback.setProgressFraction(progressFractionQuota / 4.0f);
startTime = System.currentTimeMillis();
System.out.println("\nSpecies :");
// the reactions will need this map to recover the names of species knowing only the networkFileIndex
HashMap<Integer, String> speciesMap = new HashMap<Integer, String>();
LinkedHashMap<String, Species> sMap = new LinkedHashMap<String, Species>();
LinkedHashMap<String, SpeciesContext> scMap = new LinkedHashMap<String, SpeciesContext>();
LinkedHashMap<String, BNGSpecies> crossMap = new LinkedHashMap<String, BNGSpecies>();
List<SpeciesContext> noMapForThese = new ArrayList<SpeciesContext>();
// final int decimalTickCount = Math.max(outputSpec.getBNGSpecies().length/10, 1);
for (int i = 0; i < outputSpec.getBNGSpecies().length; i++) {
BNGSpecies s = outputSpec.getBNGSpecies()[i];
// System.out.println(i+1 + ":\t\t"+ s.toString());
String key = s.getConcentration().infix();
FakeSeedSpeciesInitialConditionsParameter fakeParam = FakeSeedSpeciesInitialConditionsParameter.fromString(key);
if (fakeParam != null) {
Pair<SpeciesContext, Expression> value = speciesEquivalenceMap.get(fakeParam);
// the species context of the original model
SpeciesContext originalsc = value.one;
Expression initial = value.two;
// replace the fake initial condition with the real one
s.setConcentration(initial);
// we'll have to find the species context from the cloned model which correspond to the original species
SpeciesContext sc = model.getSpeciesContext(originalsc.getName());
// System.out.println(sc.getName() + ", " + sc.getSpecies().getCommonName() + " ...is one of the original seed species.");
// existing name
speciesMap.put(s.getNetworkFileIndex(), sc.getName());
sMap.put(sc.getName(), sc.getSpecies());
scMap.put(sc.getName(), sc);
crossMap.put(sc.getName(), s);
noMapForThese.add(sc);
continue;
}
// all these species are new!
// generate unique name for the species
int count = 0;
String speciesName = null;
String nameRoot = "s";
String speciesPatternNameString = s.extractName();
while (true) {
speciesName = nameRoot + count;
if (Model.isNameUnused(speciesName, model) && !sMap.containsKey(speciesName) && !scMap.containsKey(speciesName)) {
break;
}
count++;
}
// newly created name
speciesMap.put(s.getNetworkFileIndex(), speciesName);
SpeciesContext speciesContext;
if (s.hasCompartment()) {
String speciesPatternCompartmentString = s.extractCompartment();
speciesContext = new SpeciesContext(new Species(speciesName, s.getName()), model.getStructure(speciesPatternCompartmentString), null);
} else {
speciesContext = new SpeciesContext(new Species(speciesName, s.getName()), model.getStructure(0), null);
}
speciesContext.setName(speciesName);
try {
if (speciesPatternNameString != null) {
SpeciesPattern sp = RbmUtils.parseSpeciesPattern(speciesPatternNameString, model);
speciesContext.setSpeciesPattern(sp);
}
} catch (ParseException e) {
e.printStackTrace();
throw new RuntimeException("Bad format for species pattern string: " + e.getMessage());
}
// speciesContext.setSpeciesPatternString(speciesPatternString);
// model.addSpecies(speciesContext.getSpecies());
// model.addSpeciesContext(speciesContext);
sMap.put(speciesName, speciesContext.getSpecies());
scMap.put(speciesName, speciesContext);
crossMap.put(speciesName, s);
// }
if (mathMappingCallback.isInterrupted()) {
msg = "Canceled by user.";
tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
simContext.appendToConsole(tcm);
throw new UserCancelException(msg);
}
// if(i%50 == 0) {
// System.out.println(i+"");
// }
// if(i%decimalTickCount == 0) {
// int multiplier = i/decimalTickCount;
// float progress = progressFractionQuota/4.0f + progressFractionQuotaSpecies*multiplier;
// mathMappingCallback.setProgressFraction(progress);
// }
}
for (SpeciesContext sc1 : model.getSpeciesContexts()) {
boolean found = false;
for (Map.Entry<String, SpeciesContext> entry : scMap.entrySet()) {
SpeciesContext sc2 = entry.getValue();
if (sc1.getName().equals(sc2.getName())) {
found = true;
// System.out.println("found species context " + sc1.getName() + " of species " + sc1.getSpecies().getCommonName() + " // " + sc2.getSpecies().getCommonName());
break;
}
}
if (found == false) {
// we add to the map the species context and the species which exist in the model but which are not in the map yet
// the only ones in this situation should be plain species which were not given to bngl for flattening (they are flat already)
// System.out.println("species context " + sc1.getName() + " not found in the map. Adding it.");
scMap.put(sc1.getName(), sc1);
sMap.put(sc1.getName(), sc1.getSpecies());
noMapForThese.add(sc1);
}
}
for (Species s1 : model.getSpecies()) {
boolean found = false;
for (Map.Entry<String, Species> entry : sMap.entrySet()) {
Species s2 = entry.getValue();
if (s1.getCommonName().equals(s2.getCommonName())) {
found = true;
// System.out.println("found species " + s1.getCommonName());
break;
}
}
if (found == false) {
System.err.println("species " + s1.getCommonName() + " not found in the map!");
}
}
SpeciesContext[] sca = new SpeciesContext[scMap.size()];
scMap.values().toArray(sca);
Species[] sa = new HashSet<Species>(sMap.values()).toArray(new Species[0]);
model.setSpecies(sa);
model.setSpeciesContexts(sca);
boolean isSpatial = transformedSimulationContext.getGeometry().getDimension() > 0;
for (SpeciesContext sc : sca) {
if (noMapForThese.contains(sc)) {
continue;
}
SpeciesContextSpec scs = reactionContext.getSpeciesContextSpec(sc);
Parameter param = scs.getParameter(SpeciesContextSpec.ROLE_InitialConcentration);
BNGSpecies s = crossMap.get(sc.getName());
param.setExpression(s.getConcentration());
SpeciesContext origSpeciesContext = simContext.getModel().getSpeciesContext(s.getName());
if (origSpeciesContext != null) {
ModelEntityMapping em = new ModelEntityMapping(origSpeciesContext, sc);
entityMappings.add(em);
} else {
ModelEntityMapping em = new ModelEntityMapping(new GeneratedSpeciesSymbolTableEntry(sc), sc);
if (isSpatial) {
scs.initializeForSpatial();
}
entityMappings.add(em);
}
}
// for(SpeciesContext sc : sca) { // clean all the species patterns from the flattened species, we have no sp now
// sc.setSpeciesPattern(null);
// }
endTime = System.currentTimeMillis();
elapsedTime = endTime - startTime;
msg = "Adding " + outputSpec.getBNGSpecies().length + " species to model, " + elapsedTime + " ms";
System.out.println(msg);
// ---- Reactions -----------------------------------------------------------------------------------------------------
mathMappingCallback.setMessage("generating network: adding reactions...");
mathMappingCallback.setProgressFraction(progressFractionQuota / 4.0f * 3.0f);
startTime = System.currentTimeMillis();
System.out.println("\nReactions :");
Map<String, HashSet<String>> ruleKeyMap = new HashMap<String, HashSet<String>>();
Map<String, BNGReaction> directBNGReactionsMap = new HashMap<String, BNGReaction>();
Map<String, BNGReaction> reverseBNGReactionsMap = new HashMap<String, BNGReaction>();
for (int i = 0; i < outputSpec.getBNGReactions().length; i++) {
BNGReaction r = outputSpec.getBNGReactions()[i];
if (!r.isRuleReversed()) {
// direct
directBNGReactionsMap.put(r.getKey(), r);
} else {
reverseBNGReactionsMap.put(r.getKey(), r);
}
//
// for each rule name, store set of keySets (number of unique keysets are number of generated reactions from this ruleName).
//
HashSet<String> keySet = ruleKeyMap.get(r.getRuleName());
if (keySet == null) {
keySet = new HashSet<String>();
ruleKeyMap.put(r.getRuleName(), keySet);
}
keySet.add(r.getKey());
}
Map<String, ReactionStep> reactionStepMap = new HashMap<String, ReactionStep>();
for (int i = 0; i < outputSpec.getBNGReactions().length; i++) {
BNGReaction bngReaction = outputSpec.getBNGReactions()[i];
// System.out.println(i+1 + ":\t\t"+ r.writeReaction());
String baseName = bngReaction.getRuleName();
// which may never happen since we encountered this problem only one time in many years
if (baseName.contains(",") && (baseName.length() > 192)) {
int pos = baseName.indexOf(",");
baseName = baseName.substring(0, pos);
}
// System.out.println(i + ": " + baseName);
String reactionName = null;
HashSet<String> keySetsForThisRule = ruleKeyMap.get(bngReaction.getRuleName());
if (keySetsForThisRule.size() == 1 && model.getReactionStep(bngReaction.getRuleName()) == null && !reactionStepMap.containsKey(bngReaction.getRuleName())) {
// we can reuse the reaction rule labels
reactionName = baseName;
} else {
reactionName = baseName + "_0";
while (true) {
if (model.getReactionStep(reactionName) == null && !reactionStepMap.containsKey(reactionName)) {
// we can reuse the reaction rule labels
break;
}
reactionName = TokenMangler.getNextEnumeratedToken(reactionName);
}
}
//
if (directBNGReactionsMap.containsValue(bngReaction)) {
BNGReaction forwardBNGReaction = bngReaction;
BNGReaction reverseBNGReaction = reverseBNGReactionsMap.get(bngReaction.getKey());
String name = forwardBNGReaction.getRuleName();
if (name.endsWith(ReactionRule.DirectHalf)) {
name = name.substring(0, name.indexOf(ReactionRule.DirectHalf));
}
if (name.endsWith(ReactionRule.InverseHalf)) {
name = name.substring(0, name.indexOf(ReactionRule.InverseHalf));
}
ReactionRule rr = model.getRbmModelContainer().getReactionRule(name);
Structure structure = rr.getStructure();
boolean bReversible = reverseBNGReaction != null;
SimpleReaction sr = new SimpleReaction(model, structure, reactionName, bReversible);
for (int j = 0; j < forwardBNGReaction.getReactants().length; j++) {
BNGSpecies s = forwardBNGReaction.getReactants()[j];
String scName = speciesMap.get(s.getNetworkFileIndex());
SpeciesContext sc = model.getSpeciesContext(scName);
Reactant reactant = sr.getReactant(scName);
if (reactant == null) {
int stoichiometry = 1;
sr.addReactant(sc, stoichiometry);
} else {
int stoichiometry = reactant.getStoichiometry();
stoichiometry += 1;
reactant.setStoichiometry(stoichiometry);
}
}
for (int j = 0; j < forwardBNGReaction.getProducts().length; j++) {
BNGSpecies s = forwardBNGReaction.getProducts()[j];
String scName = speciesMap.get(s.getNetworkFileIndex());
SpeciesContext sc = model.getSpeciesContext(scName);
Product product = sr.getProduct(scName);
if (product == null) {
int stoichiometry = 1;
sr.addProduct(sc, stoichiometry);
} else {
int stoichiometry = product.getStoichiometry();
stoichiometry += 1;
product.setStoichiometry(stoichiometry);
}
}
if (!bngReaction.isMichaelisMenten()) {
// MassAction
MassActionKinetics targetKinetics = new MassActionKinetics(sr);
sr.setKinetics(targetKinetics);
KineticsParameter kforward = targetKinetics.getForwardRateParameter();
KineticsParameter kreverse = targetKinetics.getReverseRateParameter();
String kforwardNewName = rr.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate).getName();
if (!kforward.getName().equals(kforwardNewName)) {
targetKinetics.renameParameter(kforward.getName(), kforwardNewName);
kforward = targetKinetics.getForwardRateParameter();
}
final String kreverseNewName = rr.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate).getName();
if (!kreverse.getName().equals(kreverseNewName)) {
targetKinetics.renameParameter(kreverse.getName(), kreverseNewName);
kreverse = targetKinetics.getReverseRateParameter();
}
applyKineticsExpressions(forwardBNGReaction, kforward, targetKinetics);
if (reverseBNGReaction != null) {
applyKineticsExpressions(reverseBNGReaction, kreverse, targetKinetics);
}
} else {
// MichaelisMenten
HMM_IRRKinetics targetKinetics = new HMM_IRRKinetics(sr);
sr.setKinetics(targetKinetics);
KineticsParameter vmax = targetKinetics.getVmaxParameter();
KineticsParameter km = targetKinetics.getKmParameter();
String vmaxNewName = rr.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MichaelisMentenVmax).getName();
if (!vmax.getName().equals(vmaxNewName)) {
targetKinetics.renameParameter(vmax.getName(), vmaxNewName);
vmax = targetKinetics.getVmaxParameter();
}
applyKineticsExpressions(forwardBNGReaction, vmax, targetKinetics);
final String kmNewName = rr.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MichaelisMentenKm).getName();
if (!km.getName().equals(kmNewName)) {
targetKinetics.renameParameter(km.getName(), kmNewName);
km = targetKinetics.getKmParameter();
}
applyKineticsExpressions(forwardBNGReaction, km, targetKinetics);
}
reactionStepMap.put(reactionName, sr);
} else if (reverseBNGReactionsMap.containsValue(bngReaction) && !directBNGReactionsMap.containsKey(bngReaction.getKey())) {
// reverse only (must be irreversible, cannot be Michaelis-Menten)
BNGReaction reverseBNGReaction = reverseBNGReactionsMap.get(bngReaction.getKey());
ReactionRule rr = model.getRbmModelContainer().getReactionRule(reverseBNGReaction.extractRuleName());
Structure structure = rr.getStructure();
boolean bReversible = false;
SimpleReaction sr = new SimpleReaction(model, structure, reactionName, bReversible);
for (int j = 0; j < reverseBNGReaction.getReactants().length; j++) {
BNGSpecies s = reverseBNGReaction.getReactants()[j];
String scName = speciesMap.get(s.getNetworkFileIndex());
SpeciesContext sc = model.getSpeciesContext(scName);
Reactant reactant = sr.getReactant(scName);
if (reactant == null) {
int stoichiometry = 1;
sr.addReactant(sc, stoichiometry);
} else {
int stoichiometry = reactant.getStoichiometry();
stoichiometry += 1;
reactant.setStoichiometry(stoichiometry);
}
}
for (int j = 0; j < reverseBNGReaction.getProducts().length; j++) {
BNGSpecies s = reverseBNGReaction.getProducts()[j];
String scName = speciesMap.get(s.getNetworkFileIndex());
SpeciesContext sc = model.getSpeciesContext(scName);
Product product = sr.getProduct(scName);
if (product == null) {
int stoichiometry = 1;
sr.addProduct(sc, stoichiometry);
} else {
int stoichiometry = product.getStoichiometry();
stoichiometry += 1;
product.setStoichiometry(stoichiometry);
}
}
MassActionKinetics k = new MassActionKinetics(sr);
sr.setKinetics(k);
KineticsParameter kforward = k.getForwardRateParameter();
KineticsParameter kreverse = k.getReverseRateParameter();
String kforwardNewName = rr.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate).getName();
if (!kforward.getName().equals(kforwardNewName)) {
k.renameParameter(kforward.getName(), kforwardNewName);
kforward = k.getForwardRateParameter();
}
final String kreverseNewName = rr.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate).getName();
if (!kreverse.getName().equals(kreverseNewName)) {
k.renameParameter(kreverse.getName(), kreverseNewName);
kreverse = k.getReverseRateParameter();
}
applyKineticsExpressions(reverseBNGReaction, kforward, k);
// String fieldParameterName = kforward.getName();
// fieldParameterName += "_" + r.getRuleName();
// kforward.setName(fieldParameterName);
reactionStepMap.put(reactionName, sr);
}
}
for (ReactionStep rs : model.getReactionSteps()) {
reactionStepMap.put(rs.getName(), rs);
}
ReactionStep[] reactionSteps = new ReactionStep[reactionStepMap.size()];
reactionStepMap.values().toArray(reactionSteps);
model.setReactionSteps(reactionSteps);
if (mathMappingCallback.isInterrupted()) {
msg = "Canceled by user.";
tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
simContext.appendToConsole(tcm);
throw new UserCancelException(msg);
}
endTime = System.currentTimeMillis();
elapsedTime = endTime - startTime;
msg = "Adding " + outputSpec.getBNGReactions().length + " reactions to model, " + elapsedTime + " ms";
System.out.println(msg);
// clean all the reaction rules
model.getRbmModelContainer().getReactionRuleList().clear();
// ---- Observables -------------------------------------------------------------------------------------------------
mathMappingCallback.setMessage("generating network: adding observables...");
mathMappingCallback.setProgressFraction(progressFractionQuota / 8.0f * 7.0f);
startTime = System.currentTimeMillis();
System.out.println("\nObservables :");
RbmModelContainer rbmmc = model.getRbmModelContainer();
for (int i = 0; i < outputSpec.getObservableGroups().length; i++) {
ObservableGroup o = outputSpec.getObservableGroups()[i];
if (rbmmc.getParameter(o.getObservableGroupName()) != null) {
System.out.println(" ...already exists.");
// if it's already there we don't try to add it again; this should be true for all of them!
continue;
}
ArrayList<Expression> terms = new ArrayList<Expression>();
for (int j = 0; j < o.getListofSpecies().length; j++) {
Expression term = Expression.mult(new Expression(o.getSpeciesMultiplicity()[j]), new Expression(speciesMap.get(o.getListofSpecies()[j].getNetworkFileIndex())));
terms.add(term);
}
Expression exp = Expression.add(terms.toArray(new Expression[terms.size()])).flatten();
exp.bindExpression(rbmmc.getSymbolTable());
RbmObservable originalObservable = rbmmc.getObservable(o.getObservableGroupName());
VCUnitDefinition observableUnitDefinition = originalObservable.getUnitDefinition();
rbmmc.removeObservable(originalObservable);
Parameter newParameter = rbmmc.addParameter(o.getObservableGroupName(), exp, observableUnitDefinition);
RbmObservable origObservable = simContext.getModel().getRbmModelContainer().getObservable(o.getObservableGroupName());
ModelEntityMapping em = new ModelEntityMapping(origObservable, newParameter);
entityMappings.add(em);
}
if (mathMappingCallback.isInterrupted()) {
msg = "Canceled by user.";
tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
simContext.appendToConsole(tcm);
throw new UserCancelException(msg);
}
endTime = System.currentTimeMillis();
elapsedTime = endTime - startTime;
msg = "Adding " + outputSpec.getObservableGroups().length + " observables to model, " + elapsedTime + " ms";
System.out.println(msg);
} catch (PropertyVetoException ex) {
ex.printStackTrace(System.out);
throw new RuntimeException(ex.getMessage());
} catch (ExpressionBindingException ex) {
ex.printStackTrace(System.out);
throw new RuntimeException(ex.getMessage());
} catch (ModelException ex) {
ex.printStackTrace(System.out);
throw new RuntimeException(ex.getMessage());
} catch (ExpressionException ex) {
ex.printStackTrace(System.out);
throw new RuntimeException(ex.getMessage());
} catch (ClassNotFoundException ex) {
throw new RuntimeException(ex.getMessage());
} catch (IOException ex) {
throw new RuntimeException(ex.getMessage());
}
System.out.println("Done transforming");
msg = "Generating math...";
System.out.println(msg);
mathMappingCallback.setMessage(msg);
mathMappingCallback.setProgressFraction(progressFractionQuota);
}
Also used :
HashMap(java.util.HashMap)
LinkedHashMap(java.util.LinkedHashMap)
HMM_IRRKinetics(cbit.vcell.model.HMM_IRRKinetics)
UserCancelException(org.vcell.util.UserCancelException)
ArrayList(java.util.ArrayList)
Product(cbit.vcell.model.Product)
SpeciesContext(cbit.vcell.model.SpeciesContext)
FakeSeedSpeciesInitialConditionsParameter(org.vcell.model.rbm.FakeSeedSpeciesInitialConditionsParameter)
Reactant(cbit.vcell.model.Reactant)
BNGOutputSpec(cbit.vcell.bionetgen.BNGOutputSpec)
ExpressionException(cbit.vcell.parser.ExpressionException)
LinkedHashMap(java.util.LinkedHashMap)
FakeReactionRuleRateParameter(org.vcell.model.rbm.FakeReactionRuleRateParameter)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
RbmModelContainer(cbit.vcell.model.Model.RbmModelContainer)
Species(cbit.vcell.model.Species)
BNGSpecies(cbit.vcell.bionetgen.BNGSpecies)
HashSet(java.util.HashSet)
BNGParameter(cbit.vcell.bionetgen.BNGParameter)
ModelException(cbit.vcell.model.ModelException)
ObservableGroup(cbit.vcell.bionetgen.ObservableGroup)
RbmObservable(cbit.vcell.model.RbmObservable)
PropertyVetoException(java.beans.PropertyVetoException)
BNGReaction(cbit.vcell.bionetgen.BNGReaction)
VCUnitDefinition(cbit.vcell.units.VCUnitDefinition)
ReactionStep(cbit.vcell.model.ReactionStep)
Map(java.util.Map)
HashMap(java.util.HashMap)
LinkedHashMap(java.util.LinkedHashMap)
SpeciesPattern(org.vcell.model.rbm.SpeciesPattern)
Structure(cbit.vcell.model.Structure)
SimpleReaction(cbit.vcell.model.SimpleReaction)
ReactionRule(cbit.vcell.model.ReactionRule)
IOException(java.io.IOException)
ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException)
Expression(cbit.vcell.parser.Expression)
Model(cbit.vcell.model.Model)
FakeSeedSpeciesInitialConditionsParameter(org.vcell.model.rbm.FakeSeedSpeciesInitialConditionsParameter)
Parameter(cbit.vcell.model.Parameter)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter)
BNGParameter(cbit.vcell.bionetgen.BNGParameter)
FakeReactionRuleRateParameter(org.vcell.model.rbm.FakeReactionRuleRateParameter)
MassActionKinetics(cbit.vcell.model.MassActionKinetics)
ParseException(org.vcell.model.bngl.ParseException)
BNGSpecies(cbit.vcell.bionetgen.BNGSpecies)
Example 2 with FakeReactionRuleRateParameter
use of org.vcell.model.rbm.FakeReactionRuleRateParameter in project vcell by virtualcell.
the class NetworkTransformer method applyKineticsExpressions.
// private Expression substituteFakeParameters(Expression paramExpression) throws ExpressionException {
// Expression newExp = new Expression(paramExpression);
// String[] fakeSymbols = paramExpression.getSymbols();
// for (String fakeSymbol : fakeSymbols){
// FakeReactionRuleRateParameter fakeParameter = FakeReactionRuleRateParameter.fromString(fakeSymbol);
// if (fakeParameter == null){
// throw new RuntimeException("unexpected identifier "+fakeSymbol+" in kinetic law during network generation");
// }
// LocalParameter localParameter = this.kineticsParameterMap.get(fakeParameter);
// Expression ruleExpression = localParameter.getExpression();
// newExp.substituteInPlace(new Expression(fakeSymbol), new Expression(ruleExpression));
// }
// return newExp;
// }
private Expression applyKineticsExpressions(BNGReaction bngReaction, KineticsParameter rateParameter, DistributedKinetics targetKinetics) throws ExpressionException {
ReactionRule reactionRule = null;
Expression paramExpression = null;
if (!bngReaction.isMichaelisMenten()) {
paramExpression = bngReaction.getParamExpression();
} else {
paramExpression = bngReaction.getMichaelisMentenParamExpression(rateParameter);
}
Expression newExp = new Expression(paramExpression);
String[] fakeSymbols = paramExpression.getSymbols();
for (String fakeSymbol : fakeSymbols) {
FakeReactionRuleRateParameter fakeParameter = FakeReactionRuleRateParameter.fromString(fakeSymbol);
if (fakeParameter == null) {
throw new RuntimeException("unexpected identifier " + fakeSymbol + " in kinetic law during network generation");
}
LocalParameter localParameter = this.kineticsParameterMap.get(fakeParameter);
System.out.println(localParameter.getNameScope());
if (localParameter.getNameScope() instanceof ReactionRule.ReactionRuleNameScope) {
reactionRule = ((ReactionRule.ReactionRuleNameScope) localParameter.getNameScope()).getReactionRule();
}
Expression ruleExpression = localParameter.getExpression();
newExp.substituteInPlace(new Expression(fakeSymbol), new Expression(ruleExpression));
}
//
try {
targetKinetics.setParameterValue(rateParameter, newExp);
} catch (PropertyVetoException e) {
e.printStackTrace();
throw new RuntimeException("failed to set kinetics expression for reaction " + targetKinetics.getReactionStep().getName() + ": " + e.getMessage(), e);
}
//
if (reactionRule != null) {
// try to set values from user-defined parameters into the target kinetics
for (LocalParameter localParameter : reactionRule.getKineticLaw().getLocalParameters()) {
if (localParameter.getRole() == RbmKineticLawParameterType.UserDefined) {
KineticsParameter userDefinedParam = targetKinetics.getKineticsParameter(localParameter.getName());
if (userDefinedParam != null) {
try {
targetKinetics.setParameterValue(userDefinedParam, localParameter.getExpression());
} catch (PropertyVetoException e) {
e.printStackTrace();
throw new RuntimeException("failed to set kinetics expression for reaction " + targetKinetics.getReactionStep().getName() + ": " + e.getMessage(), e);
}
}
}
}
}
return newExp;
}
Also used :
LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter)
PropertyVetoException(java.beans.PropertyVetoException)
FakeReactionRuleRateParameter(org.vcell.model.rbm.FakeReactionRuleRateParameter)
ReactionRule(cbit.vcell.model.ReactionRule)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
Expression(cbit.vcell.parser.Expression)
Example 3 with FakeReactionRuleRateParameter
use of org.vcell.model.rbm.FakeReactionRuleRateParameter in project vcell by virtualcell.
the class NetworkTransformer method applyKineticsExpressions.
// private Expression substituteFakeParameters(Expression paramExpression) throws ExpressionException {
// Expression newExp = new Expression(paramExpression);
// String[] fakeSymbols = paramExpression.getSymbols();
// for (String fakeSymbol : fakeSymbols){
// FakeReactionRuleRateParameter fakeParameter = FakeReactionRuleRateParameter.fromString(fakeSymbol);
// if (fakeParameter == null){
// throw new RuntimeException("unexpected identifier "+fakeSymbol+" in kinetic law during network generation");
// }
// LocalParameter localParameter = this.kineticsParameterMap.get(fakeParameter);
// Expression ruleExpression = localParameter.getExpression();
// newExp.substituteInPlace(new Expression(fakeSymbol), new Expression(ruleExpression));
// }
// return newExp;
// }
private Expression applyKineticsExpressions(BNGReaction bngReaction, KineticsParameter rateParameter, MassActionKinetics targetKinetics) throws ExpressionException {
ReactionRule reactionRule = null;
Expression paramExpression = bngReaction.getParamExpression();
Expression newExp = new Expression(paramExpression);
String[] fakeSymbols = paramExpression.getSymbols();
for (String fakeSymbol : fakeSymbols) {
FakeReactionRuleRateParameter fakeParameter = FakeReactionRuleRateParameter.fromString(fakeSymbol);
if (fakeParameter == null) {
throw new RuntimeException("unexpected identifier " + fakeSymbol + " in kinetic law during network generation");
}
LocalParameter localParameter = this.kineticsParameterMap.get(fakeParameter);
System.out.println(localParameter.getNameScope());
if (localParameter.getNameScope() instanceof ReactionRule.ReactionRuleNameScope) {
reactionRule = ((ReactionRule.ReactionRuleNameScope) localParameter.getNameScope()).getReactionRule();
}
Expression ruleExpression = localParameter.getExpression();
newExp.substituteInPlace(new Expression(fakeSymbol), new Expression(ruleExpression));
}
//
try {
targetKinetics.setParameterValue(rateParameter, newExp);
} catch (PropertyVetoException e) {
e.printStackTrace();
throw new RuntimeException("failed to set kinetics expression for reaction " + targetKinetics.getReactionStep().getName() + ": " + e.getMessage(), e);
}
//
if (reactionRule != null) {
// try to set values from user-defined parameters into the target kinetics
for (LocalParameter localParameter : reactionRule.getKineticLaw().getLocalParameters()) {
if (localParameter.getRole() == RbmKineticLawParameterType.UserDefined) {
KineticsParameter userDefinedParam = targetKinetics.getKineticsParameter(localParameter.getName());
if (userDefinedParam != null) {
try {
targetKinetics.setParameterValue(userDefinedParam, localParameter.getExpression());
} catch (PropertyVetoException e) {
e.printStackTrace();
throw new RuntimeException("failed to set kinetics expression for reaction " + targetKinetics.getReactionStep().getName() + ": " + e.getMessage(), e);
}
}
}
}
}
return newExp;
}
Also used :
LocalParameter(cbit.vcell.mapping.ParameterContext.LocalParameter)
PropertyVetoException(java.beans.PropertyVetoException)
FakeReactionRuleRateParameter(org.vcell.model.rbm.FakeReactionRuleRateParameter)
ReactionRule(cbit.vcell.model.ReactionRule)
KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter)
Expression(cbit.vcell.parser.Expression)
Aggregations
LocalParameter (cbit.vcell.mapping.ParameterContext.LocalParameter)3
KineticsParameter (cbit.vcell.model.Kinetics.KineticsParameter)3
ReactionRule (cbit.vcell.model.ReactionRule)3
Expression (cbit.vcell.parser.Expression)3
PropertyVetoException (java.beans.PropertyVetoException)3
FakeReactionRuleRateParameter (org.vcell.model.rbm.FakeReactionRuleRateParameter)3
BNGOutputSpec (cbit.vcell.bionetgen.BNGOutputSpec)1
BNGParameter (cbit.vcell.bionetgen.BNGParameter)1
BNGReaction (cbit.vcell.bionetgen.BNGReaction)1
BNGSpecies (cbit.vcell.bionetgen.BNGSpecies)1
ObservableGroup (cbit.vcell.bionetgen.ObservableGroup)1
HMM_IRRKinetics (cbit.vcell.model.HMM_IRRKinetics)1
MassActionKinetics (cbit.vcell.model.MassActionKinetics)1
Model (cbit.vcell.model.Model)1
RbmModelContainer (cbit.vcell.model.Model.RbmModelContainer)1
ModelException (cbit.vcell.model.ModelException)1
Parameter (cbit.vcell.model.Parameter)1
Product (cbit.vcell.model.Product)1
RbmObservable (cbit.vcell.model.RbmObservable)1
Reactant (cbit.vcell.model.Reactant)1
