Examples with ReactionStep cbit.vcell.model.ReactionStep used on opensource projects

Example 46 with ReactionStep

use of cbit.vcell.model.ReactionStep in project vcell by virtualcell.

the class SBMLImporter method addReactions.

/**
 * addReactions:
 */
protected void addReactions(VCMetaData metaData, Map<String, String> vcToSbmlNameMap, Map<String, String> sbmlToVcNameMap) {
    if (sbmlModel == null) {
        throw new SBMLImportException("SBML model is NULL");
    }
    ListOf<Reaction> reactions = sbmlModel.getListOfReactions();
    final int numReactions = reactions.size();
    if (numReactions == 0) {
        lg.info("No Reactions");
        return;
    }
    // all reactions
    ArrayList<ReactionStep> vcReactionList = new ArrayList<>();
    // just the fast ones
    ArrayList<ReactionStep> fastReactionList = new ArrayList<>();
    Model vcModel = vcBioModel.getSimulationContext(0).getModel();
    ModelUnitSystem vcModelUnitSystem = vcModel.getUnitSystem();
    SpeciesContext[] vcSpeciesContexts = vcModel.getSpeciesContexts();
    try {
        for (Reaction sbmlRxn : reactions) {
            ReactionStep vcReaction = null;
            String rxnSbmlId = sbmlRxn.getId();
            String rxnSbmlName = sbmlRxn.getName();
            if (isRestrictedXYZT(rxnSbmlId)) {
                // simply rename any x,y,z reaction if non-spatial model
                rxnSbmlId = "r_" + rxnSbmlId;
                vcToSbmlNameMap.put(rxnSbmlId, sbmlRxn.getId());
                sbmlToVcNameMap.put(sbmlRxn.getId(), rxnSbmlId);
            }
            boolean bReversible = true;
            if (sbmlRxn.isSetReversible()) {
                bReversible = sbmlRxn.getReversible();
            }
            // Check of reaction annotation is present; if so, does it have
            // an embedded element (flux or simpleRxn).
            // Create a fluxReaction or simpleReaction accordingly.
            Element sbmlImportRelatedElement = sbmlAnnotationUtil.readVCellSpecificAnnotation(sbmlRxn);
            Structure reactionStructure = getReactionStructure(sbmlRxn, vcSpeciesContexts, sbmlImportRelatedElement);
            if (sbmlImportRelatedElement != null) {
                Element embeddedRxnElement = getEmbeddedElementInAnnotation(sbmlImportRelatedElement, REACTION);
                if (embeddedRxnElement != null) {
                    if (embeddedRxnElement.getName().equals(XMLTags.FluxStepTag)) {
                        // If embedded element is a flux reaction, set flux
                        // reaction's strucure, flux carrier, physicsOption
                        // from the element attributes.
                        String structName = embeddedRxnElement.getAttributeValue(XMLTags.StructureAttrTag);
                        CastInfo<Membrane> ci = SBMLHelper.getTypedStructure(Membrane.class, vcModel, structName);
                        if (!ci.isGood()) {
                            throw new SBMLImportException("Appears that the flux reaction is occuring on " + ci.actualName() + ", not a membrane.");
                        }
                        vcReaction = new FluxReaction(vcModel, ci.get(), null, rxnSbmlId, bReversible);
                        vcReaction.setModel(vcModel);
                        // Set the fluxOption on the flux reaction based on
                        // whether it is molecular, molecular & electrical,
                        // electrical.
                        String fluxOptionStr = embeddedRxnElement.getAttributeValue(XMLTags.FluxOptionAttrTag);
                        if (fluxOptionStr.equals(XMLTags.FluxOptionMolecularOnly)) {
                            ((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_MOLECULAR_ONLY);
                        } else if (fluxOptionStr.equals(XMLTags.FluxOptionMolecularAndElectrical)) {
                            ((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_MOLECULAR_AND_ELECTRICAL);
                        } else if (fluxOptionStr.equals(XMLTags.FluxOptionElectricalOnly)) {
                            ((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_ELECTRICAL_ONLY);
                        } else {
                            localIssueList.add(new Issue(vcReaction, issueContext, IssueCategory.SBMLImport_Reaction, "Unknown FluxOption : " + fluxOptionStr + " for SBML reaction : " + rxnSbmlId, Issue.SEVERITY_WARNING));
                        // logger.sendMessage(VCLogger.Priority.MediumPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Unknown FluxOption : " + fluxOptionStr +
                        // " for SBML reaction : " + rxnName);
                        }
                    } else if (embeddedRxnElement.getName().equals(XMLTags.SimpleReactionTag)) {
                        // if embedded element is a simple reaction, set
                        // simple reaction's structure from element attributes
                        vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnSbmlId, bReversible);
                    }
                } else {
                    vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnSbmlId, bReversible);
                }
            } else {
                vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnSbmlId, bReversible);
            }
            if (rxnSbmlName != null && !rxnSbmlName.isEmpty()) {
                vcReaction.setSbmlName(rxnSbmlName);
            }
            // set annotations and notes on vcReactions[i]
            sbmlAnnotationUtil.readAnnotation(vcReaction, sbmlRxn);
            sbmlAnnotationUtil.readNotes(vcReaction, sbmlRxn);
            // the limit on the reactionName length.
            if (rxnSbmlId.length() > 64) {
                String freeTextAnnotation = metaData.getFreeTextAnnotation(vcReaction);
                if (freeTextAnnotation == null) {
                    freeTextAnnotation = "";
                }
                StringBuffer oldRxnAnnotation = new StringBuffer(freeTextAnnotation);
                oldRxnAnnotation.append("\n\n" + rxnSbmlId);
                metaData.setFreeTextAnnotation(vcReaction, oldRxnAnnotation.toString());
            }
            // Now add the reactants, products, modifiers as specified by
            // the sbmlRxn
            addReactionParticipants(sbmlRxn, vcReaction, sbmlToVcNameMap);
            KineticLaw kLaw = sbmlRxn.getKineticLaw();
            Kinetics kinetics = null;
            if (kLaw != null) {
                // Convert the formula from kineticLaw into MathML and then
                // to an expression (infix) to be used in VCell kinetics
                ASTNode sbmlRateMath = kLaw.getMath();
                Expression kLawRateExpr = getExpressionFromFormula(sbmlRateMath);
                // we don't need to make sure it's not spatial here, we checked before renaming the variables
                for (Map.Entry<String, String> entry : sbmlToVcNameMap.entrySet()) {
                    String sbmlName = entry.getKey();
                    String vcName = entry.getValue();
                    kLawRateExpr.substituteInPlace(new Expression(sbmlName), new Expression(vcName));
                }
                Expression vcRateExpression = new Expression(kLawRateExpr);
                // modifier (catalyst) to the reaction.
                for (int k = 0; k < vcSpeciesContexts.length; k++) {
                    SpeciesContext sc = vcSpeciesContexts[k];
                    if (vcRateExpression.hasSymbol(sc.getName())) {
                        ReactionParticipant r = vcReaction.getReactant(sc.getName());
                        ReactionParticipant p = vcReaction.getProduct(sc.getName());
                        ReactionParticipant c = vcReaction.getCatalyst(sc.getName());
                        if ((r == null) && (p == null) && (c == null)) {
                            // This means that the speciesContext is not a
                            // reactant, product or modifier : it has to be
                            // added to the VC Rxn as a catalyst
                            vcReaction.addCatalyst(sc);
                        }
                    }
                }
                // set kinetics on VCell reaction
                if (bSpatial) {
                    // if spatial SBML ('isSpatial' attribute set), create
                    // DistributedKinetics)
                    SpatialReactionPlugin ssrplugin = (SpatialReactionPlugin) sbmlRxn.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
                    // (a) the requiredElements attributes should be 'spatial'
                    if (ssrplugin != null && ssrplugin.getIsLocal()) {
                        kinetics = new GeneralKinetics(vcReaction);
                    } else {
                        kinetics = new GeneralLumpedKinetics(vcReaction);
                    }
                } else {
                    kinetics = new GeneralLumpedKinetics(vcReaction);
                }
                // set kinetics on vcReaction
                vcReaction.setKinetics(kinetics);
                // If the name of the rate parameter has been changed by
                // user, or matches with global/local param, it has to be changed.
                resolveRxnParameterNameConflicts(sbmlRxn, kinetics, sbmlImportRelatedElement);
                /**
                 * Now, based on the kinetic law expression, see if the rate
                 * is expressed in concentration/time or substance/time : If
                 * the compartment_id of the compartment corresponding to
                 * the structure in which the reaction takes place occurs in
                 * the rate law expression, it is in concentration/time;
                 * divide it by the compartment size and bring in the rate
                 * law as 'Distributed' kinetics. If not, the rate law is in
                 * substance/time; bring it in (as is) as 'Lumped' kinetics.
                 */
                ListOf<LocalParameter> localParameters = kLaw.getListOfLocalParameters();
                for (LocalParameter p : localParameters) {
                    String paramName = p.getId();
                    KineticsParameter kineticsParameter = kinetics.getKineticsParameter(paramName);
                    if (kineticsParameter == null) {
                        // add unresolved for now to prevent errors in kinetics.setParameterValue(kp,vcRateExpression) below
                        kinetics.addUnresolvedParameter(paramName);
                    }
                }
                KineticsParameter kp = kinetics.getAuthoritativeParameter();
                if (lg.isDebugEnabled()) {
                    lg.debug("Setting " + kp.getName() + ":  " + vcRateExpression.infix());
                }
                kinetics.setParameterValue(kp, vcRateExpression);
                // If there are any global parameters used in the kinetics,
                // and if they have species,
                // check if the species are already reactionParticipants in
                // the reaction. If not, add them as catalysts.
                KineticsProxyParameter[] kpps = kinetics.getProxyParameters();
                for (int j = 0; j < kpps.length; j++) {
                    if (kpps[j].getTarget() instanceof ModelParameter) {
                        ModelParameter mp = (ModelParameter) kpps[j].getTarget();
                        HashSet<String> refSpeciesNameHash = new HashSet<String>();
                        getReferencedSpeciesInExpr(mp.getExpression(), refSpeciesNameHash);
                        java.util.Iterator<String> refSpIterator = refSpeciesNameHash.iterator();
                        while (refSpIterator.hasNext()) {
                            String spName = refSpIterator.next();
                            org.sbml.jsbml.Species sp = sbmlModel.getSpecies(spName);
                            String spId = sp.getId();
                            String vcSpeciesName = spId;
                            if (sbmlToVcNameMap.get(spId) != null) {
                                vcSpeciesName = sbmlToVcNameMap.get(spId);
                            }
                            ArrayList<ReactionParticipant> rpArray = getVCReactionParticipantsFromSymbol(vcReaction, vcSpeciesName);
                            if (rpArray == null || rpArray.size() == 0) {
                                // This means that the speciesContext is not a reactant,
                                // product or modifier : it has to be added as a catalyst
                                vcReaction.addCatalyst(vcModel.getSpeciesContext(vcSpeciesName));
                            }
                        }
                    }
                }
                // model - local params cannot be defined by rules.
                for (LocalParameter param : localParameters) {
                    String paramName = param.getId();
                    Expression exp = new Expression(param.getValue());
                    String unitString = param.getUnits();
                    VCUnitDefinition paramUnit = sbmlUnitIdentifierHash.get(unitString);
                    if (paramUnit == null) {
                        paramUnit = vcModelUnitSystem.getInstance_TBD();
                    }
                    // check if sbml local param is in kinetic params list;
                    // if so, add its value.
                    boolean lpSet = false;
                    KineticsParameter kineticsParameter = kinetics.getKineticsParameter(paramName);
                    if (kineticsParameter != null) {
                        if (lg.isDebugEnabled()) {
                            lg.debug("Setting local " + kineticsParameter.getName() + ":  " + exp.infix());
                        }
                        kineticsParameter.setExpression(exp);
                        kineticsParameter.setUnitDefinition(paramUnit);
                        lpSet = true;
                    } else {
                        UnresolvedParameter ur = kinetics.getUnresolvedParameter(paramName);
                        if (ur != null) {
                            kinetics.addUserDefinedKineticsParameter(paramName, exp, paramUnit);
                            lpSet = true;
                        }
                    }
                    if (!lpSet) {
                        // check if it is a proxy parameter (specifically,
                        // speciesContext or model parameter (structureSize
                        // too)).
                        KineticsProxyParameter kpp = kinetics.getProxyParameter(paramName);
                        // and units to local param values
                        if (kpp != null && kpp.getTarget() instanceof ModelParameter) {
                            kinetics.convertParameterType(kpp, false);
                            kineticsParameter = kinetics.getKineticsParameter(paramName);
                            kinetics.setParameterValue(kineticsParameter, exp);
                            kineticsParameter.setUnitDefinition(paramUnit);
                        }
                    }
                }
            } else {
                // sbmlKLaw was null, so creating a GeneralKinetics with 0.0
                // as rate.
                kinetics = new GeneralKinetics(vcReaction);
            }
            // end - if-else KLaw != null
            // set the reaction kinetics, and add reaction to the vcell
            // model.
            kinetics.resolveUndefinedUnits();
            // System.out.println("ADDED SBML REACTION : \"" + rxnName +
            // "\" to VCModel");
            vcReactionList.add(vcReaction);
            if (sbmlRxn.isSetFast() && sbmlRxn.getFast()) {
                fastReactionList.add(vcReaction);
            }
        }
        // end - for vcReactions
        ReactionStep[] array = vcReactionList.toArray(new ReactionStep[vcReactionList.size()]);
        vcModel.setReactionSteps(array);
        final ReactionContext rc = vcBioModel.getSimulationContext(0).getReactionContext();
        for (ReactionStep frs : fastReactionList) {
            final ReactionSpec rs = rc.getReactionSpec(frs);
            rs.setReactionMapping(ReactionSpec.FAST);
        }
    } catch (ModelPropertyVetoException mpve) {
        throw new SBMLImportException(mpve.getMessage(), mpve);
    } catch (Exception e1) {
        e1.printStackTrace(System.out);
        throw new SBMLImportException(e1.getMessage(), e1);
    }
}

Example 47 with ReactionStep

use of cbit.vcell.model.ReactionStep in project vcell by virtualcell.

the class SBMLImporter method getBioModel.

// /**
// * @ TODO: This method doesn't take care of adjusting species in nested
// parameter rules with the species_concetration_factor.
// * @param kinetics
// * @param paramExpr
// * @throws ExpressionException
// */
// private void substituteOtherGlobalParams(Kinetics kinetics, Expression
// paramExpr) throws ExpressionException, PropertyVetoException {
// String[] exprSymbols = paramExpr.getSymbols();
// if (exprSymbols == null || exprSymbols.length == 0) {
// return;
// }
// Model vcModel = vcBioModel.getSimulationContext(0).getModel();
// for (int kk = 0; kk < exprSymbols.length; kk++) {
// ModelParameter mp = vcModel.getModelParameter(exprSymbols[kk]);
// if (mp != null) {
// Expression expr = mp.getExpression();
// if (expr != null) {
// Expression newExpr = new Expression(expr);
// substituteGlobalParamRulesInPlace(newExpr, false);
// // param has constant value, add it as a kinetic parameter if it is not
// already in the kinetics
// kinetics.setParameterValue(exprSymbols[kk], newExpr.infix());
// kinetics.getKineticsParameter(exprSymbols[kk]).setUnitDefinition(getSBMLUnit(sbmlModel.getParameter(exprSymbols[kk]).getUnits(),
// null));
// if (newExpr.getSymbols() != null) {
// substituteOtherGlobalParams(kinetics, newExpr);
// }
// }
// }
// }
// }
/**
 * parse SBML file into biomodel logs errors to log4j if present in source
 * document
 *
 * @return new Biomodel
 * @throws IOException
 * @throws XMLStreamException
 */
public BioModel getBioModel() throws XMLStreamException, IOException {
    if (sbmlFileName == null && sbmlModel == null) {
        throw new IllegalStateException("Expected non-null SBML model");
    }
    SBMLDocument document;
    String defaultErrorPrefix = "Unable to read SBML file";
    if (sbmlFileName != null) {
        try {
            // Read SBML model into libSBML SBMLDocument and create an SBML model
            List<String> readLines = FileUtils.readLines(new File(sbmlFileName), Charset.defaultCharset());
            StringBuffer sb = new StringBuffer();
            // throws NPE when "<sbml ... xmlns:render... " is defined in input document
            for (String line : readLines) {
                String str = "xmlns:render=\"http://www.sbml.org/sbml/level3/version1/render/version1\"";
                int indexOf = line.indexOf(str);
                if (indexOf != -1) {
                    line = line.substring(0, indexOf - 1) + line.substring(indexOf + str.length());
                }
                str = "render:required=\"false\"";
                indexOf = line.indexOf(str);
                if (indexOf != -1) {
                    line = line.substring(0, indexOf - 1) + line.substring(indexOf + str.length());
                }
                sb.append(line + "\n");
            }
            SBMLReader reader = new SBMLReader();
            document = reader.readSBMLFromString(sb.toString());
            // check for VCell origin
            String topNotes = document.getNotesString();
            if (topNotes != null && topNotes.contains("VCell")) {
                isFromVCell = true;
            }
            // document.checkConsistencyOffline();
            // long numProblems = document.getNumErrors();
            // 
            // System.out.println("\n\nSBML Import Error Report");
            // ByteArrayOutputStream os = new ByteArrayOutputStream();
            // PrintStream ps = new PrintStream(os);
            // document.printErrors(ps);
            // String output = os.toString();
            // if (numProblems > 0 && lg.isEnabledFor(Level.WARN)) {
            // lg.warn("Num problems in original SBML document : " + numProblems);
            // lg.warn(output);
            // }
            sbmlModel = document.getModel();
        } catch (Exception e) {
            throw new SBMLImportException(defaultErrorPrefix + ": \n" + sbmlFileName, e);
        }
        if (sbmlModel == null) {
            throw new SBMLImportException(defaultErrorPrefix + ": \n" + sbmlFileName);
        }
    } else {
        // sbmlModel != null
        try {
            document = sbmlModel.getSBMLDocument();
        } catch (Exception e) {
            throw new SBMLImportException(defaultErrorPrefix + ".\n", e);
        }
    }
    if (document == null) {
        throw new SBMLImportException(defaultErrorPrefix + ".\n");
    }
    int numPackages = 0;
    String msgPackages = "";
    try {
        boolean b = document.getPackageRequired("comp");
        if (document.isPackageEnabled("comp")) {
            numPackages++;
            msgPackages += "'comp', ";
            CompSBMLDocumentPlugin cdp = null;
            CompModelPlugin cmp = null;
            CompSBasePlugin csp = null;
            CompFlatteningConverter ccc = null;
        }
        if (document.isPackageEnabled("fbc")) {
            numPackages++;
            msgPackages += "'fbc', ";
        }
        if (document.isPackageEnabled("multi")) {
            numPackages++;
            msgPackages += "'multi', ";
        }
        if (document.isPackageEnabled("qual")) {
            numPackages++;
            msgPackages += "'qual', ";
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Unable to check the SBML file package requirements.");
    }
    String ext = "extension";
    String is = "is";
    String has = "has";
    if (numPackages > 0) {
        if (numPackages > 1) {
            ext += "s";
            is = "are";
        }
        msgPackages = msgPackages.substring(0, msgPackages.length() - 1);
        msgPackages = "The model includes elements of SBML " + ext + " " + msgPackages + " which " + is + " required for simulating the model but " + is + " not supported.";
        throw new SBMLImportException("Unable to import the SBML file.\n" + msgPackages);
    }
    try {
        if (document.isPackageEnabled("groups")) {
            numPackages++;
            msgPackages += "'groups', ";
        }
        if (document.isPackageEnabled("layout")) {
            numPackages++;
            msgPackages += "'layout', ";
        }
        if (document.isPackageEnabled("render")) {
            numPackages++;
            msgPackages += "'render', ";
        }
    } catch (Exception e) {
        // we're going to ignore these packages anyway
        e.printStackTrace(System.out);
    }
    if (numPackages > 0) {
        if (numPackages > 1) {
            ext += "s";
            is = "are";
            has = "have";
        }
        msgPackages = "The model includes elements of SBML " + ext + " " + msgPackages + " which " + is + " not required for simulating the model and " + has + " been ignored.";
        localIssueList.add(new Issue(vcBioModel, issueContext, IssueCategory.SBMLImport_UnsupportedFeature, msgPackages, Issue.Severity.WARNING));
    }
    // Convert SBML Model to VCell model
    // An SBML model will correspond to a simcontext - which needs a Model and a Geometry
    // SBML handles only nonspatial geometries at this time, hence creating a non-spatial default geometry
    // get namespace based on SBML model level and version to use in SBMLAnnotationUtil
    this.level = sbmlModel.getLevel();
    // this.version = sbmlModel.getVersion();
    String ns = document.getNamespace();
    // create SBML unit system for the model and create the bioModel.
    ModelUnitSystem modelUnitSystem;
    try {
        modelUnitSystem = createSBMLUnitSystemForVCModel();
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Inconsistent unit system. Cannot import SBML model into VCell.", Category.INCONSISTENT_UNIT, e);
    }
    try {
        Geometry geometry = new Geometry(BioModelChildSummary.COMPARTMENTAL_GEO_STR, 0);
        vcBioModel = new BioModel(null, modelUnitSystem);
        SimulationContext simulationContext = new SimulationContext(vcBioModel.getModel(), geometry, null, null, Application.NETWORK_DETERMINISTIC);
        vcBioModel.addSimulationContext(simulationContext);
        simulationContext.setName(vcBioModel.getSimulationContext(0).getModel().getName());
    // vcBioModel.getSimulationContext(0).setName(vcBioModel.getSimulationContext(0).getModel().getName()+"_"+vcBioModel.getSimulationContext(0).getGeometry().getName());
    } catch (Exception e) {
        // PropertyVetoException
        e.printStackTrace(System.out);
        throw new SBMLImportException("Could not create simulation context corresponding to the input SBML model.\n", e);
    }
    try {
        String biomodelName = sbmlModel.getName();
        if ((biomodelName == null) || biomodelName.trim().equals("")) {
            biomodelName = sbmlModel.getId();
        }
        if ((biomodelName == null) || biomodelName.trim().equals("")) {
            biomodelName = "newBioModel";
        }
        vcBioModel.setName(biomodelName);
        sbmlAnnotationUtil = new SBMLAnnotationUtil(vcBioModel.getVCMetaData(), vcBioModel, ns);
        sbmlAnnotationUtil.readAnnotation(vcBioModel, sbmlModel);
        sbmlAnnotationUtil.readNotes(vcBioModel, sbmlModel);
        // vcBioModel.getVCMetaData().printRdfPretty();
        // vcBioModel.getVCMetaData().printRdfStatements();
        translateSBMLModel();
        vcBioModel.refreshDependencies();
        ReactionStep[] reax = vcBioModel.getModel().getReactionSteps();
        for (int i = 0; i < reax.length; i++) {
            if (reax[i].getKinetics().getKineticsDescription().isLumped()) {
                DistributedKinetics.toDistributedKinetics((LumpedKinetics) reax[i].getKinetics());
            }
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Could not create Biomodel corresponding to the input SBML model.\n", e);
    }
    Issue[] warnings = localIssueList.toArray(new Issue[localIssueList.size()]);
    if (warnings != null && warnings.length > 0) {
        StringBuffer messageBuffer = new StringBuffer("Issues encountered during SBML Import:\n");
        int issueCount = 0;
        for (int i = 0; i < warnings.length; i++) {
            if (warnings[i].getSeverity() == Issue.Severity.WARNING || warnings[i].getSeverity() == Issue.Severity.INFO) {
                // messageBuffer.append("- " + warnings[i].getMessage() + " (" + warnings[i].getCategory() + ", " + warnings[i].getSeverity().name() + ")\n");
                messageBuffer.append("- " + warnings[i].getMessage() + "\n");
                issueCount++;
            }
        }
        if (issueCount > 0) {
            try {
                logger.sendMessage(VCLogger.Priority.MediumPriority, VCLogger.ErrorType.OverallWarning, messageBuffer.toString());
            } catch (Exception e) {
                e.printStackTrace(System.out);
            }
        }
    }
    // if called from GUI application convert if VCell origin, otherwise ask user
    if (isFromVCell) {
        ModelUnitSystem vcUnitSystem = ModelUnitSystem.createDefaultVCModelUnitSystem();
        try {
            BioModel convertedBioModel = ModelUnitConverter.createBioModelWithNewUnitSystem(vcBioModel, vcUnitSystem);
            return convertedBioModel;
        } catch (ExpressionException | XmlParseException e) {
            // TODO maybe alert user? for now fail silently...
            e.printStackTrace();
            return vcBioModel;
        }
    }
    return vcBioModel;
}

Example 48 with ReactionStep

use of cbit.vcell.model.ReactionStep in project vcell by virtualcell.

the class SBMLExporter method addInitialAssignments.

protected void addInitialAssignments() throws ExpressionException, MappingException, MathException, MatrixException, ModelException {
    // for species, the initial assignments are done in addSpecies()
    if (vcSelectedSimJob == null) {
        return;
    }
    int index = vcSelectedSimJob.getJobIndex();
    System.out.println("Simulation Job index = " + index);
    MathOverrides mo = vcSelectedSimJob.getSimulation().getMathOverrides();
    if (mo == null || !mo.hasOverrides()) {
        return;
    }
    // 
    // TODO: SEDMLExporter is doing it differently, much more complicated
    // 
    MathMapping mm = vcSelectedSimContext.createNewMathMapping();
    MathSymbolMapping msm = mm.getMathSymbolMapping();
    String[] ocns = mo.getOverridenConstantNames();
    for (String ocn : ocns) {
        SymbolTableEntry ste = SEDMLExporter.getSymbolTableEntryForModelEntity(msm, ocn);
        ModelParameter mp = vcSelectedSimContext.getModel().getModelParameter(ocn);
        Expression exp = mo.getActualExpression(ocn, index);
        String name = "";
        if (ste != null && ste instanceof SpeciesContextSpecParameter) {
            SpeciesContextSpecParameter scsp = (SpeciesContextSpecParameter) ste;
            SpeciesContext sc = scsp.getSpeciesContext();
            name = sc.getName();
        } else if (ste != null && ste instanceof ModelParameter) {
            name = ste.getName();
        } else if (ste != null && ste instanceof KineticsParameter) {
            // note: if we call this before adding the reactions, we can't verify that the name we use
            // here will match the name we assign when we actually add the reaction
            KineticsParameter kp = (KineticsParameter) ste;
            Kinetics ks = kp.getKinetics();
            ReactionStep rs = ks.getReactionStep();
            name = TokenMangler.mangleToSName(kp.getName() + "_" + rs.getName());
        } else {
            name = ocn;
            System.out.println("Unexpected override or parameter scan entity: " + ocn);
        }
        // System.out.println("  symbol: " + name + ", overriden constant: " + ocn + ", expression: " + exp.infix());
        org.sbml.jsbml.InitialAssignment ia = sbmlModel.createInitialAssignment();
        // String id = TokenMangler.mangleToSName("initialAssignment_" + name "_" + index);	// no point in defining id or name for initial assignment
        // ia.setId(id);
        // ia.setName(id);
        ia.setVariable(name);
        ASTNode math = getFormulaFromExpression(exp);
        ia.setMath(math);
    }
}

Example 49 with ReactionStep

use of cbit.vcell.model.ReactionStep in project vcell by virtualcell.

the class SBMLExporter method addReactions.

/**
 * addReactions comment.
 * @throws SbmlException
 * @throws XMLStreamException
 */
protected void addReactions() throws SbmlException, XMLStreamException {
    // Check if any reaction has electrical mapping
    boolean bCalculatePotential = false;
    StructureMapping[] structureMappings = getSelectedSimContext().getGeometryContext().getStructureMappings();
    for (int i = 0; i < structureMappings.length; i++) {
        if (structureMappings[i] instanceof MembraneMapping) {
            if (((MembraneMapping) structureMappings[i]).getCalculateVoltage()) {
                bCalculatePotential = true;
            }
        }
    }
    // If it does, VCell doesn't export it to SBML (no representation).
    if (bCalculatePotential) {
        throw new RuntimeException("This VCell model has Electrical mapping; cannot be exported to SBML at this time");
    }
    l2gMap.clear();
    ReactionSpec[] vcReactionSpecs = getSelectedSimContext().getReactionContext().getReactionSpecs();
    for (int i = 0; i < vcReactionSpecs.length; i++) {
        if (vcReactionSpecs[i].isExcluded()) {
            continue;
        }
        ReactionStep vcReactionStep = vcReactionSpecs[i].getReactionStep();
        // Create sbml reaction
        String rxnName = vcReactionStep.getName();
        org.sbml.jsbml.Reaction sbmlReaction = sbmlModel.createReaction();
        sbmlReaction.setId(org.vcell.util.TokenMangler.mangleToSName(rxnName));
        sbmlReaction.setName(rxnName);
        String rxnSbmlName = vcReactionStep.getSbmlName();
        if (rxnSbmlName != null && !rxnSbmlName.isEmpty()) {
            sbmlReaction.setName(rxnSbmlName);
        }
        // If the reactionStep is a flux reaction, add the details to the annotation (structure, carrier valence, flux carrier, fluxOption, etc.)
        // If reactionStep is a simple reaction, add annotation to indicate the structure of reaction.
        // Useful when roundtripping ...
        Element sbmlImportRelatedElement = null;
        // try {
        // sbmlImportRelatedElement = getAnnotationElement(vcReactionStep);
        // } catch (XmlParseException e1) {
        // e1.printStackTrace(System.out);
        // //			throw new RuntimeException("Error ");
        // }
        // Get annotation (RDF and non-RDF) for reactionStep from SBMLAnnotationUtils
        sbmlAnnotationUtil.writeAnnotation(vcReactionStep, sbmlReaction, sbmlImportRelatedElement);
        // Now set notes,
        sbmlAnnotationUtil.writeNotes(vcReactionStep, sbmlReaction);
        // Get reaction kineticLaw
        Kinetics vcRxnKinetics = vcReactionStep.getKinetics();
        org.sbml.jsbml.KineticLaw sbmlKLaw = sbmlReaction.createKineticLaw();
        try {
            // Convert expression from kinetics rate parameter into MathML and use libSBMl utilities to convert it to formula
            // (instead of directly using rate parameter's expression infix) to maintain integrity of formula :
            // for example logical and inequalities are not handled gracefully by libSBMl if expression.infix is used.
            final Expression localRateExpr;
            final Expression lumpedRateExpr;
            if (vcRxnKinetics instanceof DistributedKinetics) {
                localRateExpr = ((DistributedKinetics) vcRxnKinetics).getReactionRateParameter().getExpression();
                lumpedRateExpr = null;
            } else if (vcRxnKinetics instanceof LumpedKinetics) {
                localRateExpr = null;
                lumpedRateExpr = ((LumpedKinetics) vcRxnKinetics).getLumpedReactionRateParameter().getExpression();
            } else {
                throw new RuntimeException("unexpected Rate Law '" + vcRxnKinetics.getClass().getSimpleName() + "', not distributed or lumped type");
            }
            // if (vcRxnKinetics instanceof DistributedKinetics)
            // Expression correctedRateExpr = kineticsAdapter.getExpression();
            // Add parameters, if any, to the kineticLaw
            Kinetics.KineticsParameter[] vcKineticsParams = vcRxnKinetics.getKineticsParameters();
            // In the first pass thro' the kinetic params, store the non-numeric param names and expressions in arrays
            String[] kinParamNames = new String[vcKineticsParams.length];
            Expression[] kinParamExprs = new Expression[vcKineticsParams.length];
            for (int j = 0; j < vcKineticsParams.length; j++) {
                if (true) {
                    // Since local reaction parameters cannot be defined by a rule, such parameters (with rules) are exported as global parameters.
                    if ((vcKineticsParams[j].getRole() == Kinetics.ROLE_CurrentDensity && (!vcKineticsParams[j].getExpression().isZero())) || (vcKineticsParams[j].getRole() == Kinetics.ROLE_LumpedCurrent && (!vcKineticsParams[j].getExpression().isZero()))) {
                        throw new RuntimeException("Electric current not handled by SBML export; failed to export reaction \"" + vcReactionStep.getName() + "\" at this time");
                    }
                    if (!vcKineticsParams[j].getExpression().isNumeric()) {
                        // NON_NUMERIC KINETIC PARAM
                        // Create new name for kinetic parameter and store it in kinParamNames, store corresponding exprs in kinParamExprs
                        // Will be used later to add this param as global.
                        String newParamName = TokenMangler.mangleToSName(vcKineticsParams[j].getName() + "_" + vcReactionStep.getName());
                        kinParamNames[j] = newParamName;
                        kinParamExprs[j] = new Expression(vcKineticsParams[j].getExpression());
                    }
                }
            }
            // If so, these need to be added as global param (else the SBML doc will not be valid)
            for (int j = 0; j < vcKineticsParams.length; j++) {
                final KineticsParameter vcKParam = vcKineticsParams[j];
                if ((vcKParam.getRole() != Kinetics.ROLE_ReactionRate) && (vcKParam.getRole() != Kinetics.ROLE_LumpedReactionRate)) {
                    // if expression of kinetic param evaluates to a double, the parameter value is set
                    if ((vcKParam.getRole() == Kinetics.ROLE_CurrentDensity && (!vcKParam.getExpression().isZero())) || (vcKParam.getRole() == Kinetics.ROLE_LumpedCurrent && (!vcKParam.getExpression().isZero()))) {
                        throw new RuntimeException("Electric current not handled by SBML export; failed to export reaction \"" + vcReactionStep.getName() + "\" at this time");
                    }
                    if (vcKParam.getExpression().isNumeric()) {
                        // NUMERIC KINETIC PARAM
                        // check if it is used in other parameters that have expressions,
                        boolean bAddedParam = false;
                        String origParamName = vcKParam.getName();
                        String newParamName = TokenMangler.mangleToSName(origParamName + "_" + vcReactionStep.getName());
                        VCUnitDefinition vcUnit = vcKParam.getUnitDefinition();
                        for (int k = 0; k < vcKineticsParams.length; k++) {
                            if (kinParamExprs[k] != null) {
                                // The param could be in the expression for any other param
                                if (kinParamExprs[k].hasSymbol(origParamName)) {
                                    // mangle its name to avoid conflict with other globals
                                    if (globalParamNamesHash.get(newParamName) == null) {
                                        globalParamNamesHash.put(newParamName, newParamName);
                                        org.sbml.jsbml.Parameter sbmlKinParam = sbmlModel.createParameter();
                                        sbmlKinParam.setId(newParamName);
                                        sbmlKinParam.setValue(vcKParam.getConstantValue());
                                        final boolean constValue = vcKParam.isConstant();
                                        sbmlKinParam.setConstant(true);
                                        // Set SBML units for sbmlParam using VC units from vcParam
                                        if (!vcUnit.isTBD()) {
                                            UnitDefinition unitDefn = getOrCreateSBMLUnit(vcUnit);
                                            sbmlKinParam.setUnits(unitDefn);
                                        }
                                        Pair<String, String> origParam = new Pair<String, String>(rxnName, origParamName);
                                        l2gMap.put(origParam, newParamName);
                                        bAddedParam = true;
                                    } else {
                                    // need to get another name for param and need to change all its refereces in the other kinParam euqations.
                                    }
                                    // update the expression to contain new name, since the globalparam has new name
                                    kinParamExprs[k].substituteInPlace(new Expression(origParamName), new Expression(newParamName));
                                }
                            }
                        }
                        // If the param hasn't been added yet, it is definitely a local param. add it to kineticLaw now.
                        if (!bAddedParam) {
                            org.sbml.jsbml.LocalParameter sbmlKinParam = sbmlKLaw.createLocalParameter();
                            sbmlKinParam.setId(origParamName);
                            sbmlKinParam.setValue(vcKParam.getConstantValue());
                            System.out.println("tis constant " + sbmlKinParam.isExplicitlySetConstant());
                            // Set SBML units for sbmlParam using VC units from vcParam
                            if (!vcUnit.isTBD()) {
                                UnitDefinition unitDefn = getOrCreateSBMLUnit(vcUnit);
                                sbmlKinParam.setUnits(unitDefn);
                            }
                        } else {
                            // hence change its occurance in rate expression if it contains that param name
                            if (localRateExpr != null && localRateExpr.hasSymbol(origParamName)) {
                                localRateExpr.substituteInPlace(new Expression(origParamName), new Expression(newParamName));
                            }
                            if (lumpedRateExpr != null && lumpedRateExpr.hasSymbol(origParamName)) {
                                lumpedRateExpr.substituteInPlace(new Expression(origParamName), new Expression(newParamName));
                            }
                        }
                    }
                }
            }
            // (using the kinParamNames and kinParamExprs above) to ensure uniqueness in the global parameter names.
            for (int j = 0; j < vcKineticsParams.length; j++) {
                if (((vcKineticsParams[j].getRole() != Kinetics.ROLE_ReactionRate) && (vcKineticsParams[j].getRole() != Kinetics.ROLE_LumpedReactionRate)) && !(vcKineticsParams[j].getExpression().isNumeric())) {
                    String oldName = vcKineticsParams[j].getName();
                    String newName = kinParamNames[j];
                    // change the name of this parameter in the rate expression
                    if (localRateExpr != null && localRateExpr.hasSymbol(oldName)) {
                        localRateExpr.substituteInPlace(new Expression(oldName), new Expression(newName));
                    }
                    if (lumpedRateExpr != null && lumpedRateExpr.hasSymbol(oldName)) {
                        lumpedRateExpr.substituteInPlace(new Expression(oldName), new Expression(newName));
                    }
                    // Change the occurence of this param in other param expressions
                    for (int k = 0; k < vcKineticsParams.length; k++) {
                        if (((vcKineticsParams[k].getRole() != Kinetics.ROLE_ReactionRate) && (vcKineticsParams[j].getRole() != Kinetics.ROLE_LumpedReactionRate)) && !(vcKineticsParams[k].getExpression().isNumeric())) {
                            if (k != j && vcKineticsParams[k].getExpression().hasSymbol(oldName)) {
                                // for all params except the current param represented by index j (whose name was changed)
                                kinParamExprs[k].substituteInPlace(new Expression(oldName), new Expression(newName));
                            }
                            if (k == j && vcKineticsParams[k].getExpression().hasSymbol(oldName)) {
                                throw new RuntimeException("A parameter cannot refer to itself in its expression");
                            }
                        }
                    }
                // end for - k
                }
            }
            // In the fifth pass thro' the kinetic params, the non-numeric params are added to the global params of the model
            for (int j = 0; j < vcKineticsParams.length; j++) {
                if (((vcKineticsParams[j].getRole() != Kinetics.ROLE_ReactionRate) && (vcKineticsParams[j].getRole() != Kinetics.ROLE_LumpedReactionRate)) && !(vcKineticsParams[j].getExpression().isNumeric())) {
                    // Now, add this param to the globalParamNamesHash and add a global parameter to the sbmlModel
                    String paramName = kinParamNames[j];
                    if (globalParamNamesHash.get(paramName) == null) {
                        globalParamNamesHash.put(paramName, paramName);
                    } else {
                    // need to get another name for param and need to change all its refereces in the other kinParam euqations.
                    }
                    Pair<String, String> origParam = new Pair<String, String>(rxnName, paramName);
                    // keeps its name but becomes a global (?)
                    l2gMap.put(origParam, paramName);
                    ASTNode paramFormulaNode = getFormulaFromExpression(kinParamExprs[j]);
                    AssignmentRule sbmlParamAssignmentRule = sbmlModel.createAssignmentRule();
                    sbmlParamAssignmentRule.setVariable(paramName);
                    sbmlParamAssignmentRule.setMath(paramFormulaNode);
                    org.sbml.jsbml.Parameter sbmlKinParam = sbmlModel.createParameter();
                    sbmlKinParam.setId(paramName);
                    if (!vcKineticsParams[j].getUnitDefinition().isTBD()) {
                        sbmlKinParam.setUnits(getOrCreateSBMLUnit(vcKineticsParams[j].getUnitDefinition()));
                    }
                    // Since the parameter is being specified by a Rule, its 'constant' field shoud be set to 'false' (default - true).
                    sbmlKinParam.setConstant(false);
                }
            }
            // end for (j) - fifth pass
            // After making all necessary adjustments to the rate expression, now set the sbmlKLaw.
            final ASTNode exprFormulaNode;
            if (lumpedRateExpr != null) {
                exprFormulaNode = getFormulaFromExpression(lumpedRateExpr);
            } else {
                if (bSpatial) {
                    exprFormulaNode = getFormulaFromExpression(localRateExpr);
                } else {
                    exprFormulaNode = getFormulaFromExpression(Expression.mult(localRateExpr, new Expression(vcReactionStep.getStructure().getName())));
                }
            }
            sbmlKLaw.setMath(exprFormulaNode);
        } catch (cbit.vcell.parser.ExpressionException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error getting value of parameter : " + e.getMessage());
        }
        // Add kineticLaw to sbmlReaction - not needed now, since we use sbmlRxn.createKLaw() ??
        // sbmlReaction.setKineticLaw(sbmlKLaw);
        // Add reactants, products, modifiers
        // Simple reactions have catalysts, fluxes have 'flux'
        cbit.vcell.model.ReactionParticipant[] rxnParticipants = vcReactionStep.getReactionParticipants();
        for (ReactionParticipant rxnParticpant : rxnParticipants) {
            SimpleSpeciesReference ssr = null;
            SpeciesReference sr = null;
            // to get unique ID when the same species is both a reactant and a product
            String rolePostfix = "";
            if (rxnParticpant instanceof cbit.vcell.model.Reactant) {
                rolePostfix = "r";
                ssr = sr = sbmlReaction.createReactant();
            } else if (rxnParticpant instanceof cbit.vcell.model.Product) {
                rolePostfix = "p";
                ssr = sr = sbmlReaction.createProduct();
            }
            if (rxnParticpant instanceof cbit.vcell.model.Catalyst) {
                rolePostfix = "c";
                ssr = sbmlReaction.createModifier();
            }
            if (ssr != null) {
                ssr.setSpecies(rxnParticpant.getSpeciesContext().getName());
            }
            if (sr != null) {
                sr.setStoichiometry(Double.parseDouble(Integer.toString(rxnParticpant.getStoichiometry())));
                String modelUniqueName = vcReactionStep.getName() + '_' + rxnParticpant.getName() + rolePostfix;
                sr.setId(TokenMangler.mangleToSName(modelUniqueName));
                // SBML-REVIEW
                sr.setConstant(true);
            // int rcode = sr.appendNotes("<
            // we know that in VCell we can't override stoichiometry anywhere, below is no longer questionable
            // try {
            // SBMLHelper.addNote(sr, "VCELL guess: how do we know if reaction is constant?");
            // } catch (Exception e) {
            // e.printStackTrace();
            // }
            }
        }
        sbmlReaction.setFast(vcReactionSpecs[i].isFast());
        // this attribute is mandatory for L3, optional for L2. So explicitly setting value.
        sbmlReaction.setReversible(true);
        if (bSpatial) {
            // set compartment for reaction if spatial
            sbmlReaction.setCompartment(vcReactionStep.getStructure().getName());
            // CORE  HAS ALT MATH true
            // set the "isLocal" attribute = true (in 'spatial' namespace) for each species
            SpatialReactionPlugin srplugin = (SpatialReactionPlugin) sbmlReaction.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
            srplugin.setIsLocal(vcRxnKinetics instanceof DistributedKinetics);
        }
    }
}

Example 50 with ReactionStep

use of cbit.vcell.model.ReactionStep in project vcell by virtualcell.

the class AnnotationMapping method annotation2BioPaxObject.

public String annotation2BioPaxObject(BioModel bioModel, Identifiable identifiable) {
    String name = "";
    String type = "";
    ArrayList<String> componentInfo = getComponentInfo(bioModel, identifiable);
    if (componentInfo.size() > 0) {
        name = componentInfo.get(0);
        type = componentInfo.get(1);
    }
    String info = type + " : " + name;
    HashMap<String, String> refInfo = getRefInfo(bioModel, identifiable);
    // otherwise, create object and add link
    if (type.equals(VCID.CLASS_SPECIES)) {
        // lookup name by speciesContext
        ArrayList<SpeciesContext> speciesContextArrList = new ArrayList<SpeciesContext>(Arrays.asList(new SpeciesContext[] { bioModel.getModel().getSpeciesContext(name) }));
        if (speciesContextArrList.get(0) == null) {
            speciesContextArrList.clear();
            // lookup name by species
            for (int i = 0; i < bioModel.getModel().getSpeciesContexts().length; i++) {
                if (bioModel.getModel().getSpeciesContexts()[i].getSpecies().getCommonName().equals(name)) {
                    speciesContextArrList.add(bioModel.getModel().getSpeciesContexts()[i]);
                }
            }
        }
        for (int i = 0; i < speciesContextArrList.size(); i++) {
            SpeciesContext speciesContext = speciesContextArrList.get(i);
            if (bioModel.getRelationshipModel().getRelationshipObjects(speciesContext).size() == 0) {
                ArrayList<Xref> xRef = getXrefs(bioModel, refInfo);
                ArrayList<String> refName = getNameRef(xRef, name);
                BioPaxObject bpObject = bioModel.getPathwayModel().findFromNameAndType(refName.get(0), EntityImpl.TYPE_PHYSICALENTITY);
            // 
            // Commenting out legacy code from the times when we didn't have proper annotation visualization
            // What we were doing below was to create a bioPax object, link it to the species and create
            // copies of the annotations in order to be able to navigate to external databases through XRef
            // Commenting out this code since we can now navigate to external databases from the annotation panel
            // 
            // if(bpObject == null){
            // bpObject = createPhysicalEntity(xRef, refName, name);
            // bioModel.getPathwayModel().add(bpObject);
            // }
            // if(bpObject != null && !isLinked(bioModel, bpObject, speciesContext)) {
            // // create linkage
            // RelationshipObject newRelationship = new RelationshipObject(speciesContext, bpObject);
            // bioModel.getRelationshipModel().addRelationshipObject(newRelationship);
            // return info;
            // }
            }
        }
    } else if (type.equals(VCID.CLASS_BIOMODEL)) {
    // BioPaxObject bpObject = bioModel.getPathwayModel().findFromName(refName.get(0), "Pathway");
    // if(bpObject == null){
    // bpObject = createPathway(componentInfo, refInfo);
    // bioModel.getPathwayModel().add(bpObject);
    // return info;
    // }
    } else if (type.equals(VCID.CLASS_REACTION_STEP)) {
        ReactionStep reactionStep = bioModel.getModel().getReactionStep(name);
        ArrayList<Xref> xRef = getXrefs(bioModel, refInfo);
        ArrayList<String> refName = getNameRef(xRef, name);
        if (bioModel.getRelationshipModel().getRelationshipObjects(reactionStep).size() == 0) {
            BioPaxObject bpObject = bioModel.getPathwayModel().findFromNameAndType(refName.get(0), EntityImpl.TYPE_INTERACTION);
        // 
        // We are eliminating some obsolete code, see above the species context comment
        // 
        // if(bpObject == null){
        // bpObject = createInteraction(reactionStep, xRef, refName);
        // bioModel.getPathwayModel().add(bpObject);
        // }
        // if(bpObject != null && !isLinked(bioModel, bpObject, reactionStep)) {
        // // create linkage
        // RelationshipObject newRelationship = new RelationshipObject(reactionStep, bpObject);
        // bioModel.getRelationshipModel().addRelationshipObject(newRelationship);
        // return info;
        // }
        }
    }
    return null;
}