Examples with SpeciesPattern org.vcell.model.rbm.SpeciesPattern used on opensource projects

Example 16 with SpeciesPattern

use of org.vcell.model.rbm.SpeciesPattern in project vcell by virtualcell.

the class ObservableTreeModel method valueForPathChanged.

@Override
public void valueForPathChanged(TreePath path, Object newValue) {
    Object obj = path.getLastPathComponent();
    if (obj == null || !(obj instanceof BioModelNode)) {
        return;
    }
    BioModelNode selectedNode = (BioModelNode) obj;
    BioModelNode parentNode = (BioModelNode) selectedNode.getParent();
    Object userObject = selectedNode.getUserObject();
    try {
        if (newValue instanceof String) {
            String inputString = (String) newValue;
            if (inputString == null || inputString.length() == 0) {
                return;
            }
            String mangled = TokenMangler.fixTokenStrict(inputString);
            if (!mangled.equals(inputString)) {
                String errMsg = ((Displayable) userObject).getDisplayType() + " '" + inputString + "' not legal identifier, try '" + mangled + "'";
                throw new RuntimeException(errMsg);
            }
            if (userObject instanceof RbmObservable) {
                // TODO: untested!!!
                ((RbmObservable) userObject).setName(inputString);
            }
        } else if (newValue instanceof MolecularComponentPattern) {
            MolecularComponentPattern newMcp = (MolecularComponentPattern) newValue;
            Object parentObject = parentNode == null ? null : parentNode.getUserObject();
            if (parentObject instanceof MolecularTypePattern) {
                MolecularTypePattern mtp = (MolecularTypePattern) parentObject;
                MolecularComponent mc = newMcp.getMolecularComponent();
                MolecularComponentPattern mcp = mtp.getMolecularComponentPattern(mc);
                mcp.setComponentStatePattern(newMcp.getComponentStatePattern());
                BondType bp = mcp.getBondType();
                BondType newbp = newMcp.getBondType();
                mcp.setBondType(newbp);
                // specified -> specified
                if (bp == BondType.Specified && newbp == BondType.Specified) {
                // bond didn't change
                } else if (bp == BondType.Specified && newbp != BondType.Specified) {
                    // specified -> non specified
                    // change the partner to possible
                    mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
                    mcp.setBond(null);
                } else if (bp != BondType.Specified && newbp == BondType.Specified) {
                    // non specified -> specified
                    int newBondId = newMcp.getBondId();
                    mcp.setBondId(newBondId);
                    mcp.setBond(newMcp.getBond());
                    mcp.getBond().molecularComponentPattern.setBondId(newBondId);
                    for (SpeciesPattern sp : observable.getSpeciesPatternList()) {
                        sp.resolveBonds();
                    }
                } else {
                }
            }
        }
    } catch (Exception ex) {
        DialogUtils.showErrorDialog(ownerTree, ex.getMessage());
    }
}

Example 17 with SpeciesPattern

use of org.vcell.model.rbm.SpeciesPattern 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();
            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();
            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 = bngReaction.getRuleName();
            } else {
                reactionName = bngReaction.getRuleName() + "_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);
                    }
                }
                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);
                }
                // String fieldParameterName = kforward.getName();
                // fieldParameterName += "_" + r.getRuleName();
                // kforward.setName(fieldParameterName);
                reactionStepMap.put(reactionName, sr);
            } else if (reverseBNGReactionsMap.containsValue(bngReaction) && !directBNGReactionsMap.containsKey(bngReaction.getKey())) {
                // reverse only (must be irreversible)
                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);
}

Example 18 with SpeciesPattern

use of org.vcell.model.rbm.SpeciesPattern in project vcell by virtualcell.

the class RulebasedMathMapping method addSpeciesPatterns.

private HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> addSpeciesPatterns(Domain domain, List<ReactionRule> rrList) throws MathException {
    // Particle Molecular Types
    // 
    Model model = getSimulationContext().getModel();
    List<RbmObservable> observableList = model.getRbmModelContainer().getObservableList();
    List<MolecularType> molecularTypeList = model.getRbmModelContainer().getMolecularTypeList();
    for (MolecularType molecularType : molecularTypeList) {
        ParticleMolecularType particleMolecularType = new ParticleMolecularType(molecularType.getName());
        for (MolecularComponent molecularComponent : molecularType.getComponentList()) {
            String pmcName = molecularComponent.getName();
            String pmcId = particleMolecularType.getName() + "_" + molecularComponent.getName();
            ParticleMolecularComponent particleMolecularComponent = new ParticleMolecularComponent(pmcId, pmcName);
            for (ComponentStateDefinition componentState : molecularComponent.getComponentStateDefinitions()) {
                ParticleComponentStateDefinition pcsd = particleMolecularComponent.getComponentStateDefinition(componentState.getName());
                if (pcsd == null) {
                    particleMolecularComponent.addComponentStateDefinition(new ParticleComponentStateDefinition(componentState.getName()));
                }
            }
            particleMolecularType.addMolecularComponent(particleMolecularComponent);
        }
        if (!molecularType.isAnchorAll()) {
            List<String> anchorList = new ArrayList<>();
            for (Structure struct : molecularType.getAnchors()) {
                anchorList.add(struct.getName());
            }
            particleMolecularType.setAnchorList(anchorList);
        }
        mathDesc.addParticleMolecularType(particleMolecularType);
    }
    // 
    // Assemble list of all Species Patterns (from observables, reaction rules, and seed species).
    // 
    // linked hash set maintains insertion order
    LinkedHashMap<SpeciesPattern, Structure> speciesPatternStructureMap = new LinkedHashMap<SpeciesPattern, Structure>();
    for (RbmObservable observable : observableList) {
        for (SpeciesPattern speciesPattern : observable.getSpeciesPatternList()) {
            speciesPatternStructureMap.put(speciesPattern, observable.getStructure());
        }
    }
    for (ReactionRule reactionRule : rrList) {
        for (ReactantPattern rp : reactionRule.getReactantPatterns()) {
            speciesPatternStructureMap.put(rp.getSpeciesPattern(), rp.getStructure());
        }
        for (ProductPattern pp : reactionRule.getProductPatterns()) {
            speciesPatternStructureMap.put(pp.getSpeciesPattern(), pp.getStructure());
        }
    }
    for (SpeciesContext sc : model.getSpeciesContexts()) {
        if (!sc.hasSpeciesPattern()) {
            continue;
        }
        speciesPatternStructureMap.put(sc.getSpeciesPattern(), sc.getStructure());
    }
    // 
    // add list of unique speciesPatterns
    // 
    HashMap<String, VolumeParticleSpeciesPattern> speciesPatternVCMLMap = new HashMap<String, VolumeParticleSpeciesPattern>();
    HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> speciesPatternMap = new HashMap<SpeciesPattern, VolumeParticleSpeciesPattern>();
    String speciesPatternName = "speciesPattern0";
    for (SpeciesPattern speciesPattern : speciesPatternStructureMap.keySet()) {
        VolumeParticleSpeciesPattern volumeParticleSpeciesPattern = new VolumeParticleSpeciesPattern(speciesPatternName, domain, speciesPatternStructureMap.get(speciesPattern).getName());
        for (MolecularTypePattern molecularTypePattern : speciesPattern.getMolecularTypePatterns()) {
            ParticleMolecularType particleMolecularType = mathDesc.getParticleMolecularType(molecularTypePattern.getMolecularType().getName());
            ParticleMolecularTypePattern particleMolecularTypePattern = new ParticleMolecularTypePattern(particleMolecularType);
            String participantMatchLabel = molecularTypePattern.getParticipantMatchLabel();
            if (molecularTypePattern.getParticipantMatchLabel() != null) {
                particleMolecularTypePattern.setMatchLabel(participantMatchLabel);
            }
            for (MolecularComponentPattern molecularComponentPattern : molecularTypePattern.getComponentPatternList()) {
                MolecularComponent molecularComponent = molecularComponentPattern.getMolecularComponent();
                ParticleMolecularComponent particleMolecularComponent = particleMolecularType.getMolecularComponent(molecularComponent.getName());
                ParticleMolecularComponentPattern particleMolecularComponentPattern = new ParticleMolecularComponentPattern(particleMolecularComponent);
                ComponentStatePattern componentState = molecularComponentPattern.getComponentStatePattern();
                if (componentState != null) {
                    if (componentState.isAny()) {
                        ParticleComponentStatePattern pcsp = new ParticleComponentStatePattern();
                        particleMolecularComponentPattern.setComponentStatePattern(pcsp);
                    } else {
                        String name = componentState.getComponentStateDefinition().getName();
                        ParticleComponentStateDefinition pcsd = particleMolecularComponent.getComponentStateDefinition(name);
                        // ParticleComponentStateDefinition pcsd = new ParticleComponentStateDefinition(componentState.getComponentStateDefinition().getName());
                        // particleMolecularComponent.addComponentStateDefinition(pcsd);
                        ParticleComponentStatePattern pcsp = new ParticleComponentStatePattern(pcsd);
                        particleMolecularComponentPattern.setComponentStatePattern(pcsp);
                    }
                } else {
                    ParticleComponentStatePattern pcsp = new ParticleComponentStatePattern();
                    particleMolecularComponentPattern.setComponentStatePattern(pcsp);
                }
                switch(molecularComponentPattern.getBondType()) {
                    case Specified:
                        {
                            particleMolecularComponentPattern.setBondType(ParticleBondType.Specified);
                            particleMolecularComponentPattern.setBondId(molecularComponentPattern.getBondId());
                            break;
                        }
                    case Exists:
                        {
                            particleMolecularComponentPattern.setBondType(ParticleBondType.Exists);
                            particleMolecularComponentPattern.setBondId(-1);
                            break;
                        }
                    case None:
                        {
                            particleMolecularComponentPattern.setBondType(ParticleBondType.None);
                            particleMolecularComponentPattern.setBondId(-1);
                            break;
                        }
                    case Possible:
                        {
                            particleMolecularComponentPattern.setBondType(ParticleBondType.Possible);
                            particleMolecularComponentPattern.setBondId(-1);
                            break;
                        }
                }
                particleMolecularTypePattern.addMolecularComponentPattern(particleMolecularComponentPattern);
            }
            volumeParticleSpeciesPattern.addMolecularTypePattern(particleMolecularTypePattern);
        }
        String speciesPatternVCML = volumeParticleSpeciesPattern.getVCML("tempName");
        VolumeParticleSpeciesPattern uniqueVolumeParticleSpeciesPattern = speciesPatternVCMLMap.get(speciesPatternVCML);
        if (uniqueVolumeParticleSpeciesPattern == null) {
            speciesPatternVCMLMap.put(speciesPatternVCML, volumeParticleSpeciesPattern);
            speciesPatternName = TokenMangler.getNextEnumeratedToken(speciesPatternName);
            speciesPatternMap.put(speciesPattern, volumeParticleSpeciesPattern);
        } else {
            speciesPatternMap.put(speciesPattern, uniqueVolumeParticleSpeciesPattern);
        }
    }
    return speciesPatternMap;
}

Example 19 with SpeciesPattern

use of org.vcell.model.rbm.SpeciesPattern in project vcell by virtualcell.

the class RulebasedMathMapping method refreshMathDescription.

/**
 * This method was created in VisualAge.
 */
@Override
protected void refreshMathDescription() throws MappingException, MatrixException, MathException, ExpressionException, ModelException {
    // use local variable instead of using getter all the time.
    SimulationContext simContext = getSimulationContext();
    GeometryClass geometryClass = simContext.getGeometry().getGeometrySpec().getSubVolumes()[0];
    Domain domain = new Domain(geometryClass);
    // local structure mapping list
    StructureMapping[] structureMappings = simContext.getGeometryContext().getStructureMappings();
    // We have to check if all the reactions are able to transform to stochastic jump processes before generating the math.
    String stochChkMsg = simContext.getModel().isValidForStochApp();
    if (!(stochChkMsg.equals(""))) {
        throw new ModelException("Problem updating math description: " + simContext.getName() + "\n" + stochChkMsg);
    }
    simContext.checkValidity();
    // 
    if (simContext.getGeometry().getDimension() > 0) {
        throw new MappingException("rule-based particle math mapping not implemented for spatial geometry - dimension >= 1");
    }
    // 
    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 = simContext.getBioEvents();
    if (bioEvents != null && bioEvents.length > 0) {
        throw new MappingException("events not yet supported for particle-based models");
    }
    // 
    // verify that all structures are mapped to subvolumes and all subvolumes are mapped to a structure
    // 
    Structure[] structures = simContext.getGeometryContext().getModel().getStructures();
    for (int i = 0; i < structures.length; i++) {
        StructureMapping sm = simContext.getGeometryContext().getStructureMapping(structures[i]);
        if (sm == null || (sm instanceof FeatureMapping && ((FeatureMapping) sm).getGeometryClass() == null)) {
            throw new MappingException("model structure '" + structures[i].getName() + "' not mapped to a geometry subVolume");
        }
        if (sm != null && (sm instanceof MembraneMapping) && ((MembraneMapping) sm).getVolumeFractionParameter() != null) {
            Expression volFractExp = ((MembraneMapping) sm).getVolumeFractionParameter().getExpression();
            try {
                if (volFractExp != null) {
                    double volFract = volFractExp.evaluateConstant();
                    if (volFract >= 1.0) {
                        throw new MappingException("model structure '" + (getSimulationContext().getModel().getStructureTopology().getInsideFeature(((MembraneMapping) sm).getMembrane()).getName() + "' has volume fraction >= 1.0"));
                    }
                }
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
            }
        }
    }
    SubVolume[] subVolumes = simContext.getGeometryContext().getGeometry().getGeometrySpec().getSubVolumes();
    for (int i = 0; i < subVolumes.length; i++) {
        Structure[] mappedStructures = simContext.getGeometryContext().getStructuresFromGeometryClass(subVolumes[i]);
        if (mappedStructures == null || mappedStructures.length == 0) {
            throw new MappingException("geometry subVolume '" + subVolumes[i].getName() + "' not mapped from a model structure");
        }
    }
    // 
    // gather only those reactionRules that are not "excluded"
    // 
    ArrayList<ReactionRule> rrList = new ArrayList<ReactionRule>();
    for (ReactionRuleSpec reactionRuleSpec : simContext.getReactionContext().getReactionRuleSpecs()) {
        if (!reactionRuleSpec.isExcluded()) {
            rrList.add(reactionRuleSpec.getReactionRule());
        }
    }
    // 
    for (ReactionRule reactionRule : rrList) {
        UnresolvedParameter[] unresolvedParameters = reactionRule.getKineticLaw().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("In Application '" + simContext.getName() + "', " + reactionRule.getDisplayType() + " '" + reactionRule.getName() + "' contains unresolved identifier(s): " + buffer);
        }
    }
    // 
    // create new MathDescription (based on simContext's previous MathDescription if possible)
    // 
    MathDescription oldMathDesc = simContext.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(simContext.getName() + "_generated");
    }
    // 
    // temporarily place all variables in a hashtable (before binding) and discarding duplicates
    // 
    VariableHash varHash = new VariableHash();
    // 
    // conversion factors
    // 
    Model model = simContext.getModel();
    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.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(simContext.getTemperatureKelvin()), model.getTEMPERATURE().getUnitDefinition(), null)));
    Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        if (scm.getVariable() instanceof StochVolVariable) {
            varHash.addVariable(scm.getVariable());
        }
    }
    // deals with model parameters
    ModelParameter[] modelParameters = simContext.getModel().getModelParameters();
    for (int j = 0; j < modelParameters.length; j++) {
        Expression expr = getSubstitutedExpr(modelParameters[j].getExpression(), true, false);
        expr = getIdentifierSubstitutions(expr, modelParameters[j].getUnitDefinition(), geometryClass);
        varHash.addVariable(newFunctionOrConstant(getMathSymbol(modelParameters[j], geometryClass), expr, geometryClass));
    }
    // added July 2009, ElectricalStimulusParameter electric mapping tab
    ElectricalStimulus[] elecStimulus = simContext.getElectricalStimuli();
    if (elecStimulus.length > 0) {
        throw new MappingException("Modles with electrophysiology are not supported for stochastic applications.");
    }
    for (int j = 0; j < structureMappings.length; j++) {
        if (structureMappings[j] instanceof MembraneMapping) {
            MembraneMapping memMapping = (MembraneMapping) structureMappings[j];
            Parameter initialVoltageParm = memMapping.getInitialVoltageParameter();
            try {
                Expression exp = initialVoltageParm.getExpression();
                exp.evaluateConstant();
                varHash.addVariable(newFunctionOrConstant(getMathSymbol(memMapping.getMembrane().getMembraneVoltage(), memMapping.getGeometryClass()), getIdentifierSubstitutions(memMapping.getInitialVoltageParameter().getExpression(), memMapping.getInitialVoltageParameter().getUnitDefinition(), memMapping.getGeometryClass()), memMapping.getGeometryClass()));
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new MappingException("Membrane initial voltage: " + initialVoltageParm.getName() + " cannot be evaluated as constant.");
            }
        }
    }
    // 
    for (ReactionRule reactionRule : rrList) {
        // if (reactionRule.getKineticLaw() instanceof LumpedKinetics){
        // throw new RuntimeException("Lumped Kinetics not yet supported for RuleBased Modeling");
        // }
        LocalParameter[] parameters = reactionRule.getKineticLaw().getLocalParameters();
        for (LocalParameter parameter : parameters) {
            // 
            if ((parameter.getRole() == RbmKineticLawParameterType.RuleRate)) {
                continue;
            }
            // 
            if (!reactionRule.isReversible() && parameter.getRole() == RbmKineticLawParameterType.MassActionReverseRate) {
                continue;
            }
            Expression expr = getSubstitutedExpr(parameter.getExpression(), true, false);
            varHash.addVariable(newFunctionOrConstant(getMathSymbol(parameter, geometryClass), getIdentifierSubstitutions(expr, parameter.getUnitDefinition(), geometryClass), geometryClass));
        }
    }
    // the parameter "Size" is already put into mathsymbolmapping in refreshSpeciesContextMapping()
    for (int i = 0; i < structureMappings.length; i++) {
        StructureMapping sm = structureMappings[i];
        StructureMapping.StructureMappingParameter parm = sm.getParameterFromRole(StructureMapping.ROLE_Size);
        if (parm.getExpression() != null) {
            try {
                double value = parm.getExpression().evaluateConstant();
                varHash.addVariable(new Constant(getMathSymbol(parm, sm.getGeometryClass()), new Expression(value)));
            } catch (ExpressionException e) {
                // varHash.addVariable(new Function(getMathSymbol0(parm,sm),getIdentifierSubstitutions(parm.getExpression(),parm.getUnitDefinition(),sm)));
                e.printStackTrace(System.out);
                throw new MappingException("Size of structure:" + sm.getNameScope().getName() + " cannot be evaluated as constant.");
            }
        }
    }
    SpeciesContextSpec[] speciesContextSpecs = getSimulationContext().getReactionContext().getSpeciesContextSpecs();
    addInitialConditions(domain, speciesContextSpecs, varHash);
    // 
    if (simContext.getGeometryContext().getGeometry() != null) {
        try {
            mathDesc.setGeometry(simContext.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 in Application " + simContext.getName());
    }
    // 
    // create subDomains
    // 
    SubVolume subVolume = simContext.getGeometry().getGeometrySpec().getSubVolumes()[0];
    SubDomain subDomain = new CompartmentSubDomain(subVolume.getName(), 0);
    mathDesc.addSubDomain(subDomain);
    // 
    // define all molecules and unique species patterns (add molecules to mathDesc and speciesPatterns to varHash).
    // 
    HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> speciesPatternMap = addSpeciesPatterns(domain, rrList);
    HashSet<VolumeParticleSpeciesPattern> uniqueParticleSpeciesPatterns = new HashSet<>(speciesPatternMap.values());
    for (VolumeParticleSpeciesPattern volumeParticleSpeciesPattern : uniqueParticleSpeciesPatterns) {
        varHash.addVariable(volumeParticleSpeciesPattern);
    }
    // 
    // define observables (those explicitly declared and those corresponding to seed species.
    // 
    List<ParticleObservable> observables = addObservables(geometryClass, domain, speciesPatternMap);
    for (ParticleObservable particleObservable : observables) {
        varHash.addVariable(particleObservable);
    }
    try {
        addParticleJumpProcesses(varHash, geometryClass, subDomain, speciesPatternMap);
    } catch (PropertyVetoException e1) {
        e1.printStackTrace();
        throw new MappingException(e1.getMessage(), e1);
    }
    // 
    for (int i = 0; i < fieldMathMappingParameters.length; i++) {
        if (fieldMathMappingParameters[i] instanceof UnitFactorParameter || fieldMathMappingParameters[i] instanceof ObservableConcentrationParameter) {
            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());
    // 
    for (SpeciesContext sc : model.getSpeciesContexts()) {
        if (!sc.hasSpeciesPattern()) {
            throw new MappingException("species " + sc.getName() + " has no molecular pattern");
        }
        VolumeParticleSpeciesPattern volumeParticleSpeciesPattern = speciesPatternMap.get(sc.getSpeciesPattern());
        ArrayList<ParticleInitialCondition> particleInitialConditions = new ArrayList<ParticleProperties.ParticleInitialCondition>();
        // initial conditions from scs
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(sc);
        Parameter initialCountParameter = scs.getInitialCountParameter();
        Expression e = getIdentifierSubstitutions(new Expression(initialCountParameter, getNameScope()), initialCountParameter.getUnitDefinition(), geometryClass);
        particleInitialConditions.add(new ParticleInitialConditionCount(e, new Expression(0.0), new Expression(0.0), new Expression(0.0)));
        ParticleProperties particleProperies = new ParticleProperties(volumeParticleSpeciesPattern, new Expression(0.0), new Expression(0.0), new Expression(0.0), new Expression(0.0), particleInitialConditions);
        subDomain.addParticleProperties(particleProperies);
    }
    // 
    for (int i = 0; i < fieldMathMappingParameters.length; i++) {
        if (fieldMathMappingParameters[i] instanceof UnitFactorParameter) {
            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 (fieldMathMappingParameters[i] instanceof ObservableConcentrationParameter) {
            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()) {
        System.out.println(mathDesc.getVCML_database());
        throw new MappingException("generated an invalid mathDescription: " + mathDesc.getWarning());
    }
}

Example 20 with SpeciesPattern

use of org.vcell.model.rbm.SpeciesPattern 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.");
}