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

Example 6 with Catalyst

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

the class StructureAnalyzer method getReactionRateExpression.

public Expression getReactionRateExpression(ReactionStep reactionStep, ReactionParticipant reactionParticipant) throws Exception {
    if (reactionParticipant instanceof Catalyst) {
        throw new Exception("Catalyst " + reactionParticipant + " doesn't have a rate for this reaction");
    // return new Expression(0.0);
    }
    double stoich = reactionStep.getStoichiometry(reactionParticipant.getSpeciesContext());
    if (stoich == 0.0) {
        return new Expression(0.0);
    }
    if (reactionStep.getKinetics() instanceof DistributedKinetics) {
        DistributedKinetics distributedKinetics = (DistributedKinetics) reactionStep.getKinetics();
        if (stoich != 1) {
            Expression exp = Expression.mult(new Expression(stoich), new Expression(distributedKinetics.getReactionRateParameter(), mathMapping_4_8.getNameScope()));
            return exp;
        } else {
            Expression exp = new Expression(distributedKinetics.getReactionRateParameter(), mathMapping_4_8.getNameScope());
            return exp;
        }
    } else if (reactionStep.getKinetics() instanceof LumpedKinetics) {
        Structure.StructureSize structureSize = reactionStep.getStructure().getStructureSize();
        // 
        // need to put this into concentration/time with respect to structure for reaction.
        // 
        LumpedKinetics lumpedKinetics = (LumpedKinetics) reactionStep.getKinetics();
        Expression factor = null;
        ModelUnitSystem unitSystem = mathMapping_4_8.getSimulationContext().getModel().getUnitSystem();
        if (reactionStep.getStructure() instanceof Feature || ((reactionStep.getStructure() instanceof Membrane) && reactionStep instanceof FluxReaction)) {
            VCUnitDefinition lumpedToVolumeSubstance = unitSystem.getVolumeSubstanceUnit().divideBy(unitSystem.getLumpedReactionSubstanceUnit());
            factor = Expression.div(new Expression(lumpedToVolumeSubstance.getDimensionlessScale()), new Expression(structureSize, mathMapping_4_8.getNameScope()));
        } else if (reactionStep.getStructure() instanceof Membrane && reactionStep instanceof SimpleReaction) {
            VCUnitDefinition lumpedToVolumeSubstance = unitSystem.getMembraneSubstanceUnit().divideBy(unitSystem.getLumpedReactionSubstanceUnit());
            factor = Expression.div(new Expression(lumpedToVolumeSubstance.getDimensionlessScale()), new Expression(structureSize, mathMapping_4_8.getNameScope()));
        } else {
            throw new RuntimeException("failed to create reaction rate expression for reaction " + reactionStep.getName() + ", with kinetic type of " + reactionStep.getKinetics().getClass().getName());
        }
        if (stoich != 1) {
            Expression exp = Expression.mult(new Expression(stoich), Expression.mult(new Expression(lumpedKinetics.getLumpedReactionRateParameter(), mathMapping_4_8.getNameScope()), factor));
            return exp;
        } else {
            Expression exp = Expression.mult(new Expression(lumpedKinetics.getLumpedReactionRateParameter(), mathMapping_4_8.getNameScope()), factor);
            return exp;
        }
    } else {
        throw new RuntimeException("unexpected kinetic type " + reactionStep.getKinetics().getClass().getName());
    }
}

Example 7 with Catalyst

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

the class DBReactionWizardPanel method bfnActionPerformed.

/**
 * Comment
 */
private void bfnActionPerformed(java.awt.event.ActionEvent actionEvent) {
    try {
        // 
        javax.swing.DefaultListModel pndlm = (javax.swing.DefaultListModel) getParameterNamesJList().getModel();
        // 
        if (actionEvent.getSource().equals(getBackJButton())) {
            if (getResolverJPanel().isVisible() && pndlm.size() == 0 && getSearchDictionaryJRadioButton().isSelected() == false) {
                // skip Parameters if there are none
                ((java.awt.CardLayout) getCardLayoutJPanel().getLayout()).previous(getCardLayoutJPanel());
            }
            ((java.awt.CardLayout) getCardLayoutJPanel().getLayout()).previous(getCardLayoutJPanel());
        } else if (actionEvent.getSource().equals(getNextJButton())) {
            if (getSearchCriteriaJPanel().isVisible()) {
                if (getSearchDictionaryJRadioButton().isSelected()) {
                    getParameterJPanel().setVisible(false);
                } else {
                    getParameterJPanel().setVisible(true);
                }
                if (!lastSearchIsSameAsCurrent()) {
                    search();
                    lastReactionSelection = null;
                    return;
                }
            } else if (getParameterJPanel().isVisible()) {
                if (lastReactStepSelection == null || !lastReactStepSelection.equals(getReactionStep0())) {
                    lastReactStepSelection = getReactionStep0();
                    ReactionType rxType = null;
                    if (getReactionStep0() instanceof FluxReaction) {
                        if (getReactionStep0().isReversible()) {
                            rxType = ReactionType.REACTTYPE_FLUX_REVERSIBLE;
                        } else {
                            rxType = ReactionType.REACTTYPE_FLUX_IRREVERSIBLE;
                        }
                    } else {
                        if (getReactionStep0().isReversible()) {
                            rxType = ReactionType.REACTTYPE_SIMPLE_REVERSIBLE;
                        } else {
                            rxType = ReactionType.REACTTYPE_SIMPLE_IRREVERSIBLE;
                        }
                    }
                    KeyValue bmid = mapRXIDtoBMIDs.get(lastReactStepSelection.getKey());
                    KeyValue structRef = mapRXIDtoStructRefIDs.get(lastReactStepSelection.getKey());
                    ReactionDescription dbfr = new ReactionDescription(getReactionStep0().getName(), rxType, getReactionStep0().getKey(), bmid, structRef);
                    // 
                    ReactionParticipant[] rpArr = getReactionStep0().getReactionParticipants();
                    for (int i = 0; i < rpArr.length; i += 1) {
                        DBNonFormalUnboundSpecies dbnfu = new DBNonFormalUnboundSpecies(rpArr[i].getSpecies().getCommonName());
                        char role;
                        if (rpArr[i] instanceof Reactant) {
                            role = ReactionDescription.RX_ELEMENT_REACTANT;
                        } else if (rpArr[i] instanceof Product) {
                            role = ReactionDescription.RX_ELEMENT_PRODUCT;
                        } else if (rpArr[i] instanceof Catalyst) {
                            role = ReactionDescription.RX_ELEMENT_CATALYST;
                        } else {
                            throw new RuntimeException("Unsupported ReationParticiapnt=" + rpArr[i].getClass().getName());
                        }
                        dbfr.addReactionElement(dbnfu, rpArr[i].getSpeciesContext().getName(), rpArr[i].getStoichiometry(), role);
                    }
                    if (dbfr.isFluxReaction()) {
                        // make sure flux is in right direction
                        Structure outsideStruct = getModel().getStructureTopology().getOutsideFeature((Membrane) getReactionStep0().getStructure());
                        String defaultOutsideSCName = dbfr.getOrigSpeciesContextName(dbfr.getFluxIndexOutside());
                        for (int i = 0; i < rpArr.length; i += 1) {
                            if (rpArr[i].getSpeciesContext().getName().equals(defaultOutsideSCName)) {
                                if (!rpArr[i].getStructure().equals(outsideStruct)) {
                                    dbfr.swapFluxSCNames();
                                }
                                break;
                            }
                        }
                    }
                    setupRX(dbfr);
                }
            }
            // 
            ((java.awt.CardLayout) getCardLayoutJPanel().getLayout()).next(getCardLayoutJPanel());
        } else if (actionEvent.getSource().equals(getFinishJButton())) {
            applySelectedReactionElements();
        }
        // 
        configureBFN();
    } catch (Exception e) {
        e.printStackTrace();
        DialogUtils.showErrorDialog(this, "DBReactionWizard failed\n" + e.getMessage(), e);
    }
}

Example 8 with Catalyst

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

the class ITextWriter method writeReactions.

// each reaction has its own table, ordered by the structures.
protected void writeReactions(Chapter physioChapter, Model model) throws DocumentException {
    if (model == null) {
        return;
    }
    Paragraph reactionParagraph = new Paragraph();
    reactionParagraph.add(new Chunk("Structures and Reactions Diagram").setLocalDestination(model.getName()));
    Section reactionDiagramSection = physioChapter.addSection(reactionParagraph, physioChapter.numberDepth() + 1);
    try {
        addImage(reactionDiagramSection, encodeJPEG(generateDocReactionsImage(model, null)));
    } catch (Exception e) {
        e.printStackTrace();
        throw new DocumentException(e.getClass().getName() + ": " + e.getMessage());
    }
    for (int i = 0; i < model.getNumStructures(); i++) {
        ReactionStep[] reactionSteps = model.getReactionSteps();
        ReactionStep rs = null;
        Table modifierTable = null;
        Table reactionTable = null;
        boolean firstTime = true;
        Section reactStructSection = null;
        for (int j = 0; j < reactionSteps.length; j++) {
            if (reactionSteps[j].getStructure() == model.getStructure(i)) {
                // can also use structureName1.equals(structureName2)
                if (firstTime) {
                    Paragraph linkParagraph = new Paragraph();
                    linkParagraph.add(new Chunk("Reaction(s) in " + model.getStructure(i).getName()).setLocalDestination(model.getStructure(i).getName()));
                    reactStructSection = physioChapter.addSection(linkParagraph, physioChapter.numberDepth() + 1);
                    firstTime = false;
                }
                rs = reactionSteps[j];
                String type;
                if (rs instanceof SimpleReaction) {
                    type = "Reaction";
                } else {
                    type = "Flux";
                }
                // write Reaction equation as a table
                // Get the image arrow cell depending on type of reactionStep : MassAction => double arrow, otherwise, forward arrow
                boolean bReversible = false;
                if (rs.getKinetics() instanceof MassActionKinetics) {
                    bReversible = true;
                }
                Cell arrowImageCell = getReactionArrowImageCell(bReversible);
                // Get reactants and products strings
                ReactionCanvas rc = new ReactionCanvas();
                rc.setReactionStep(rs);
                ReactionCanvasDisplaySpec rcdSpec = rc.getReactionCanvasDisplaySpec();
                String reactants = rcdSpec.getLeftText();
                String products = rcdSpec.getRightText();
                // Create table and add cells for reactants, arrow(s) images, products
                int[] widths = { 8, 1, 8 };
                reactionTable = getTable(3, 100, 0, 2, 2);
                // Add reactants as cell
                Cell tableCell = createCell(reactants, getBold());
                tableCell.setHorizontalAlignment(Cell.ALIGN_RIGHT);
                tableCell.setBorderColor(Color.white);
                reactionTable.addCell(tableCell);
                // add arrow(s) image as cell
                if (arrowImageCell != null) {
                    arrowImageCell.setHorizontalAlignment(Cell.ALIGN_CENTER);
                    arrowImageCell.setBorderColor(Color.white);
                    reactionTable.addCell(arrowImageCell);
                }
                // add products as cell
                tableCell = createCell(products, getBold());
                tableCell.setBorderColor(Color.white);
                reactionTable.addCell(tableCell);
                // reactionTable.setBorderColor(Color.white);
                reactionTable.setWidths(widths);
                // Identify modifiers,
                ReactionParticipant[] rpArr = rs.getReactionParticipants();
                Vector<ReactionParticipant> modifiersVector = new Vector<ReactionParticipant>();
                for (int k = 0; k < rpArr.length; k += 1) {
                    if (rpArr[k] instanceof Catalyst) {
                        modifiersVector.add(rpArr[k]);
                    }
                }
                // Write the modifiers in a separate table, if present
                if (modifiersVector.size() > 0) {
                    modifierTable = getTable(1, 50, 0, 1, 1);
                    modifierTable.addCell(createCell("Modifiers List", getBold(DEF_HEADER_FONT_SIZE), 1, 1, Element.ALIGN_CENTER, true));
                    StringBuffer modifierNames = new StringBuffer();
                    for (int k = 0; k < modifiersVector.size(); k++) {
                        modifierNames.append(((Catalyst) modifiersVector.elementAt(k)).getName() + "\n");
                    }
                    modifierTable.addCell(createCell(modifierNames.toString().trim(), getFont()));
                    modifiersVector.removeAllElements();
                }
                Section reactionSection = reactStructSection.addSection(type + " " + rs.getName(), reactStructSection.numberDepth() + 1);
                // Annotation
                VCMetaData vcMetaData = rs.getModel().getVcMetaData();
                if (vcMetaData.getFreeTextAnnotation(rs) != null) {
                    Table annotTable = getTable(1, 100, 1, 3, 3);
                    annotTable.addCell(createCell("Reaction Annotation", getBold(DEF_HEADER_FONT_SIZE), 1, 1, Element.ALIGN_CENTER, true));
                    annotTable.addCell(createCell(vcMetaData.getFreeTextAnnotation(rs), getFont()));
                    reactionSection.add(annotTable);
                // reactionSection.add(new Paragraph("\""+rs.getAnnotation()+"\""));
                }
                // reaction table
                if (reactionTable != null) {
                    reactionSection.add(reactionTable);
                    // re-set reactionTable
                    reactionTable = null;
                }
                if (modifierTable != null) {
                    reactionSection.add(modifierTable);
                    modifierTable = null;
                }
                // Write kinetics parameters, etc. in a table
                writeKineticsParams(reactionSection, rs);
            }
        }
    }
}

Example 9 with Catalyst

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

the class ReactionCartoonTool method getLineTypeFromAttachment.

private LineType getLineTypeFromAttachment(SpeciesContext speciesContext, Point worldPoint) throws Exception {
    Shape mouseOverShape = getReactionCartoon().pickWorld(worldPoint);
    if (mouseOverShape instanceof ReactionStepShape) {
        // check if the ReactionStep already has a ReactionParticipant for
        // this SpeciesContext
        ReactionStep reactionStep = (ReactionStep) mouseOverShape.getModelObject();
        ReactionParticipant[] rps = reactionStep.getReactionParticipants();
        if (mouseOverShape instanceof SimpleReactionShape) {
            switch(mouseOverShape.getAttachmentFromAbs(worldPoint)) {
                case Shape.ATTACH_LEFT:
                    {
                        for (int i = 0; i < rps.length; i++) {
                            if (rps[i] instanceof Reactant && rps[i].getSpeciesContext() == speciesContext) {
                                return LineType.NULL;
                            }
                        }
                        return LineType.REACTANT;
                    }
                case Shape.ATTACH_CENTER:
                    {
                        for (int i = 0; i < rps.length; i++) {
                            if (rps[i] instanceof Catalyst && rps[i].getSpeciesContext() == speciesContext) {
                                return LineType.NULL;
                            }
                        }
                        return LineType.CATALYST;
                    }
                case Shape.ATTACH_RIGHT:
                    {
                        for (int i = 0; i < rps.length; i++) {
                            if (rps[i] instanceof Product && rps[i].getSpeciesContext() == speciesContext) {
                                return LineType.NULL;
                            }
                        }
                        return LineType.PRODUCT;
                    }
            }
        } else if (mouseOverShape instanceof FluxReactionShape) {
            switch(mouseOverShape.getAttachmentFromAbs(worldPoint)) {
                case Shape.ATTACH_LEFT:
                    {
                        // return LineType.FLUX;
                        for (int i = 0; i < rps.length; i++) {
                            if (rps[i] instanceof Reactant && rps[i].getSpeciesContext() == speciesContext) {
                                return LineType.NULL;
                            }
                        }
                        return LineType.REACTANT;
                    }
                case Shape.ATTACH_CENTER:
                    {
                        for (int i = 0; i < rps.length; i++) {
                            if (rps[i] instanceof Catalyst && rps[i].getSpeciesContext() == speciesContext) {
                                return LineType.NULL;
                            }
                        }
                        return LineType.CATALYST;
                    }
                case Shape.ATTACH_RIGHT:
                    {
                        for (int i = 0; i < rps.length; i++) {
                            // return LineType.FLUX;
                            if (rps[i] instanceof Product && rps[i].getSpeciesContext() == speciesContext) {
                                return LineType.NULL;
                            }
                        }
                        return LineType.PRODUCT;
                    }
            }
        }
    }
    return LineType.NULL;
}

Example 10 with Catalyst

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

the class BioCartoonTool method pasteReactionSteps0.

/**
 * pasteReactionSteps0 : does the actual pasting. First called with a cloned model, to track issues. If user still wants to proceed, the paste
 * is performed on the original model.
 *
 * Insert the method's description here.
 * Creation date: (5/10/2003 3:55:25 PM)
 * @param pasteToModel cbit.vcell.model.Model
 * @param pasteToStructure cbit.vcell.model.Structure
 * @param bNew boolean
 */
private static final PasteHelper pasteReactionSteps0(HashMap<String, HashMap<ReactionParticipant, Structure>> rxPartMapStructure, Component parent, IssueContext issueContext, ReactionStep[] copyFromRxSteps, Model pasteToModel, Structure pasteToStructure, boolean bNew, /*boolean bUseDBSpecies,*/
UserResolvedRxElements userResolvedRxElements) throws Exception {
    HashMap<BioModelEntityObject, BioModelEntityObject> reactionsAndSpeciesContexts = new HashMap<>();
    if (copyFromRxSteps == null || copyFromRxSteps.length == 0 || pasteToModel == null || pasteToStructure == null) {
        throw new IllegalArgumentException("CartoonTool.pasteReactionSteps Error " + (copyFromRxSteps == null || copyFromRxSteps.length == 0 ? "reactionStepsArr empty " : "") + (pasteToModel == null ? "model is null " : "") + (pasteToStructure == null ? "struct is null " : ""));
    }
    if (!pasteToModel.contains(pasteToStructure)) {
        throw new IllegalArgumentException("CartoonTool.pasteReactionSteps model " + pasteToModel.getName() + " does not contain structure " + pasteToStructure.getName());
    }
    // Check PasteToModel has preferred targets if set
    if (userResolvedRxElements != null) {
        for (int i = 0; i < userResolvedRxElements.toSpeciesArr.length; i++) {
            if (userResolvedRxElements.toSpeciesArr[i] != null) {
                if (!pasteToModel.contains(userResolvedRxElements.toSpeciesArr[i])) {
                    throw new RuntimeException("PasteToModel does not contain preferred Species " + userResolvedRxElements.toSpeciesArr[i]);
                }
            }
            if (userResolvedRxElements.toStructureArr[i] != null) {
                if (!pasteToModel.contains(userResolvedRxElements.toStructureArr[i])) {
                    throw new RuntimeException("PasteToModel does not contain preferred Structure " + userResolvedRxElements.toStructureArr[i]);
                }
            }
        }
    }
    int counter = 0;
    Structure currentStruct = pasteToStructure;
    String copiedStructName = copyFromRxSteps[counter].getStructure().getName();
    StructureTopology structTopology = (copyFromRxSteps[counter].getModel() == null ? pasteToModel.getStructureTopology() : copyFromRxSteps[counter].getModel().getStructureTopology());
    IdentityHashMap<Species, Species> speciesHash = new IdentityHashMap<Species, Species>();
    IdentityHashMap<SpeciesContext, SpeciesContext> speciesContextHash = new IdentityHashMap<SpeciesContext, SpeciesContext>();
    Vector<Issue> issueVector = new Vector<Issue>();
    do {
        // create a new reaction, instead of cloning the old one; set struc
        ReactionStep copyFromReactionStep = copyFromRxSteps[counter];
        String newName = copyFromReactionStep.getName();
        while (pasteToModel.getReactionStep(newName) != null) {
            newName = org.vcell.util.TokenMangler.getNextEnumeratedToken(newName);
        }
        ReactionStep newReactionStep = null;
        if (copyFromReactionStep instanceof SimpleReaction) {
            newReactionStep = new SimpleReaction(pasteToModel, currentStruct, newName, copyFromReactionStep.isReversible());
        } else if (copyFromReactionStep instanceof FluxReaction && currentStruct instanceof Membrane) {
            newReactionStep = new FluxReaction(pasteToModel, (Membrane) currentStruct, null, newName, copyFromReactionStep.isReversible());
        }
        pasteToModel.addReactionStep(newReactionStep);
        reactionsAndSpeciesContexts.put(newReactionStep, copyFromReactionStep);
        Structure toRxnStruct = newReactionStep.getStructure();
        Structure fromRxnStruct = copyFromReactionStep.getStructure();
        if (!fromRxnStruct.getClass().equals(pasteToStructure.getClass())) {
            throw new Exception("Cannot copy reaction from " + fromRxnStruct.getTypeName() + " to " + pasteToStructure.getTypeName() + ".");
        }
        // add appropriate reactionParticipants to newReactionStep.
        StructureTopology toStructureTopology = pasteToModel.getStructureTopology();
        ReactionParticipant[] copyFromRxParticipantArr = copyFromReactionStep.getReactionParticipants();
        if (rxPartMapStructure == null) {
            // null during 'issues' trial
            rxPartMapStructure = new HashMap<String, HashMap<ReactionParticipant, Structure>>();
        }
        if (rxPartMapStructure.get(copyFromReactionStep.getName()) == null) {
            // Ask user to assign species to compartments for each reaction to be pasted
            rxPartMapStructure.put(copyFromReactionStep.getName(), askUserResolveMembraneConnections(parent, pasteToModel.getStructures(), currentStruct, fromRxnStruct, toRxnStruct, copyFromRxParticipantArr, toStructureTopology, structTopology));
        }
        for (int i = 0; i < copyFromRxParticipantArr.length; i += 1) {
            Structure pasteToStruct = currentStruct;
            // if(toRxnStruct instanceof Membrane){
            pasteToStruct = rxPartMapStructure.get(copyFromReactionStep.getName()).get(copyFromRxParticipantArr[i]);
            // if(pasteToStruct == null){
            // for(ReactionParticipant myRXPart:rxPartMapStructure.get(copyFromReactionStep.getName()).keySet()){
            // if(myRXPart.getSpeciesContext().getName().equals(copyFromRxParticipantArr[i].getSpeciesContext().getName())){
            // pasteToStruct = rxPartMapStructure.get(copyFromReactionStep.getName()).get(myRXPart);
            // break;
            // }
            // }
            // }
            // }
            // this adds the speciesContexts and species (if any) to the model)
            String rootSC = ReactionCartoonTool.speciesContextRootFinder(copyFromRxParticipantArr[i].getSpeciesContext());
            SpeciesContext newSc = null;
            SpeciesContext[] matchSC = pasteToModel.getSpeciesContexts();
            for (int j = 0; matchSC != null && j < matchSC.length; j++) {
                String matchRoot = ReactionCartoonTool.speciesContextRootFinder(matchSC[j]);
                if (matchRoot != null && matchRoot.equals(rootSC) && matchSC[j].getStructure().getName().equals(pasteToStruct.getName())) {
                    newSc = matchSC[j];
                    reactionsAndSpeciesContexts.put(newSc, matchSC[j]);
                    break;
                }
            }
            if (newSc == null) {
                newSc = pasteSpecies(parent, copyFromRxParticipantArr[i].getSpecies(), rootSC, pasteToModel, pasteToStruct, bNew, /*bUseDBSpecies,*/
                speciesHash, UserResolvedRxElements.getPreferredReactionElement(userResolvedRxElements, copyFromRxParticipantArr[i]));
                reactionsAndSpeciesContexts.put(newSc, copyFromRxParticipantArr[i].getSpeciesContext());
            }
            // record the old-new speciesContexts (reactionparticipants) in the IdHashMap, this is useful, esp for 'Paste new', while replacing proxyparams.
            SpeciesContext oldSc = copyFromRxParticipantArr[i].getSpeciesContext();
            if (speciesContextHash.get(oldSc) == null) {
                speciesContextHash.put(oldSc, newSc);
            }
            if (copyFromRxParticipantArr[i] instanceof Reactant) {
                newReactionStep.addReactionParticipant(new Reactant(null, newReactionStep, newSc, copyFromRxParticipantArr[i].getStoichiometry()));
            } else if (copyFromRxParticipantArr[i] instanceof Product) {
                newReactionStep.addReactionParticipant(new Product(null, newReactionStep, newSc, copyFromRxParticipantArr[i].getStoichiometry()));
            } else if (copyFromRxParticipantArr[i] instanceof Catalyst) {
                newReactionStep.addCatalyst(newSc);
            }
        }
        // // If 'newReactionStep' is a fluxRxn, set its fluxCarrier
        // if (newReactionStep instanceof FluxReaction) {
        // if (fluxCarrierSp != null) {
        // ((FluxReaction)newReactionStep).setFluxCarrier(fluxCarrierSp, pasteToModel);
        // } else {
        // throw new RuntimeException("Could not set FluxCarrier species for the flux reaction to be pasted");
        // }
        // }
        // For each kinetic parameter expression for new kinetics, replace the proxyParams from old kinetics with proxyParams in new kinetics
        // i.e., if the proxyParams are speciesContexts, replace with corresponding speciesContext in newReactionStep;
        // if the proxyParams are structureSizes or MembraneVoltages, replace with corresponding structure quantity in newReactionStep
        Kinetics oldKinetics = copyFromReactionStep.getKinetics();
        KineticsParameter[] oldKps = oldKinetics.getKineticsParameters();
        KineticsProxyParameter[] oldKprps = oldKinetics.getProxyParameters();
        Hashtable<String, Expression> paramExprHash = new Hashtable<String, Expression>();
        for (int i = 0; oldKps != null && i < oldKps.length; i++) {
            Expression newExpression = new Expression(oldKps[i].getExpression());
            for (int j = 0; oldKprps != null && j < oldKprps.length; j++) {
                // check if kinetic proxy parameter is in kinetic parameter expression
                if (newExpression.hasSymbol(oldKprps[j].getName())) {
                    SymbolTableEntry ste = oldKprps[j].getTarget();
                    Model pasteFromModel = copyFromReactionStep.getModel();
                    if (ste instanceof SpeciesContext) {
                        // if newRxnStruct is a feature/membrane, get matching spContexts from old reaction and replace them in new rate expr.
                        SpeciesContext oldSC = (SpeciesContext) ste;
                        SpeciesContext newSC = speciesContextHash.get(oldSC);
                        if (newSC == null) {
                            // check if oldSc is present in paste-model; if not, add it.
                            if (!pasteToModel.equals(pasteFromModel)) {
                                if (pasteToModel.getSpeciesContext(oldSC.getName()) == null) {
                                    // if paste-model has oldSc struct, paste it there,
                                    Structure newSCStruct = pasteToModel.getStructure(oldSC.getStructure().getName());
                                    if (newSCStruct != null) {
                                        newSC = pasteSpecies(parent, oldSC.getSpecies(), null, pasteToModel, newSCStruct, bNew, /*bUseDBSpecies,*/
                                        speciesHash, UserResolvedRxElements.getPreferredReactionElement(userResolvedRxElements, oldSC));
                                        speciesContextHash.put(oldSC, newSC);
                                    } else {
                                        // oldStruct wasn't found in paste-model, paste it in newRxnStruct and add warning to issues list
                                        newSC = pasteSpecies(parent, oldSC.getSpecies(), null, pasteToModel, toRxnStruct, bNew, /*bUseDBSpecies,*/
                                        speciesHash, UserResolvedRxElements.getPreferredReactionElement(userResolvedRxElements, oldSC));
                                        speciesContextHash.put(oldSC, newSC);
                                        Issue issue = new Issue(oldSC, issueContext, IssueCategory.CopyPaste, "SpeciesContext '" + oldSC.getSpecies().getCommonName() + "' was not found in compartment '" + oldSC.getStructure().getName() + "' in the model; the species was added to the compartment '" + toRxnStruct.getName() + "' where the reaction was pasted.", Issue.SEVERITY_WARNING);
                                        issueVector.add(issue);
                                    }
                                }
                            }
                        // if models are the same and newSc is null, then oldSc is not a rxnParticipant. Leave it as is in the expr.
                        }
                        if (newSC != null) {
                            reactionsAndSpeciesContexts.put(newSC, oldSC);
                            newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(newSC.getName()));
                        }
                    // SpeciesContext sc = null;
                    // Species newSp = model.getSpecies(oldSc.getSpecies().getCommonName());
                    // if  (oldSc.getStructure() == (oldRxnStruct)) {
                    // sc = model.getSpeciesContext(newSp, newRxnStruct);
                    // } else {
                    // if (newRxnStruct instanceof Membrane) {
                    // // for a membrane, we need to make sure that inside-outside spContexts used are appropriately replaced.
                    // if (oldSc.getStructure() == ((Membrane)oldRxnStruct).getOutsideFeature()) {
                    // // old speciesContext is outside (old) membrane, new spContext should be outside new membrane
                    // sc = model.getSpeciesContext(newSp, ((Membrane)newRxnStruct).getOutsideFeature());
                    // } else if (oldSc.getStructure() == ((Membrane)oldRxnStruct).getInsideFeature()) {
                    // // old speciesContext is inside (old) membrane, new spContext should be inside new membrane
                    // sc = model.getSpeciesContext(newSp, ((Membrane)newRxnStruct).getInsideFeature());
                    // }
                    // }
                    // }
                    // if (sc != null) {
                    // newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(sc.getName()));
                    // }
                    } else if (ste instanceof StructureSize) {
                        Structure str = ((StructureSize) ste).getStructure();
                        // if the structure size used is same as the structure in which the reaction is present, change the structSize to appropriate new struct
                        if (str.compareEqual(fromRxnStruct)) {
                            newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(toRxnStruct.getStructureSize().getName()));
                        } else {
                            if (fromRxnStruct instanceof Membrane) {
                                if (str.equals(structTopology.getOutsideFeature((Membrane) fromRxnStruct))) {
                                    newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(structTopology.getOutsideFeature((Membrane) toRxnStruct).getStructureSize().getName()));
                                } else if (str.equals(structTopology.getInsideFeature((Membrane) fromRxnStruct))) {
                                    newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(structTopology.getInsideFeature((Membrane) toRxnStruct).getStructureSize().getName()));
                                }
                            }
                        }
                    } else if (ste instanceof MembraneVoltage) {
                        Membrane membr = ((MembraneVoltage) ste).getMembrane();
                        // if the MembraneVoltage used is same as that of the membrane in which the reaction is present, change the MemVoltage
                        if ((fromRxnStruct instanceof Membrane) && (membr.compareEqual(fromRxnStruct))) {
                            newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(((Membrane) toRxnStruct).getMembraneVoltage().getName()));
                        }
                    } else if (ste instanceof ModelParameter) {
                        // see if model has this global parameter (if rxn is being pasted into another model, it won't)
                        if (!pasteToModel.equals(pasteFromModel)) {
                            ModelParameter oldMp = (ModelParameter) ste;
                            ModelParameter mp = pasteToModel.getModelParameter(oldMp.getName());
                            boolean bNonNumeric = false;
                            String newMpName = oldMp.getName();
                            if (mp != null) {
                                // new model has a model parameter with same name - are they the same param?
                                if (!mp.getExpression().equals(oldMp.getExpression())) {
                                    // no, they are not the same param, so mangle the 'ste' name and add as global in the other model
                                    while (pasteToModel.getModelParameter(newMpName) != null) {
                                        newMpName = TokenMangler.getNextEnumeratedToken(newMpName);
                                    }
                                    // if expression if numeric, add it as such. If not, set it to 0.0 and add it as global
                                    Expression exp = oldMp.getExpression();
                                    if (!exp.flatten().isNumeric()) {
                                        exp = new Expression(0.0);
                                        bNonNumeric = true;
                                    }
                                    ModelParameter newMp = pasteToModel.new ModelParameter(newMpName, exp, Model.ROLE_UserDefined, oldMp.getUnitDefinition());
                                    String annotation = "Copied from model : " + pasteFromModel.getNameScope();
                                    newMp.setModelParameterAnnotation(annotation);
                                    pasteToModel.addModelParameter(newMp);
                                    // if global param name had to be changed, make sure newExpr is updated as well.
                                    if (!newMpName.equals(oldMp.getName())) {
                                        newExpression.substituteInPlace(new Expression(oldMp.getName()), new Expression(newMpName));
                                    }
                                }
                            } else {
                                // no global param with same name was found in other model, so add it to other model.
                                // if expression if numeric, add it as such. If not, set it to 0.0 and add it as global
                                Expression exp = oldMp.getExpression();
                                if (!exp.flatten().isNumeric()) {
                                    exp = new Expression(0.0);
                                    bNonNumeric = true;
                                }
                                ModelParameter newMp = pasteToModel.new ModelParameter(newMpName, exp, Model.ROLE_UserDefined, oldMp.getUnitDefinition());
                                String annotation = "Copied from model : " + pasteFromModel.getNameScope();
                                newMp.setModelParameterAnnotation(annotation);
                                pasteToModel.addModelParameter(newMp);
                            }
                            // if a non-numeric parameter was encountered in the old model, it was added as a numeric (0.0), warn user of change.
                            if (bNonNumeric) {
                                Issue issue = new Issue(oldMp, issueContext, IssueCategory.CopyPaste, "Global parameter '" + oldMp.getName() + "' was non-numeric; it has been added " + "as global parameter '" + newMpName + "' in the new model with value = 0.0. " + "Please update its value, if required, before using it.", Issue.SEVERITY_WARNING);
                                issueVector.add(issue);
                            }
                        }
                    }
                }
            // end - if newExpr.hasSymbol(ProxyParam)
            }
            // now if store <param names, new expression> in hashTable
            if (paramExprHash.get(oldKps[i].getName()) == null) {
                paramExprHash.put(oldKps[i].getName(), newExpression);
            }
        }
        // end for - oldKps (old kinetic parameters)
        // use this new expression to generate 'vcml' for the (new) kinetics (easier way to transfer all kinetic parameters)
        String newKineticsStr = oldKinetics.writeTokensWithReplacingProxyParams(paramExprHash);
        // convert the kinetics 'vcml' to tokens.
        CommentStringTokenizer kineticsTokens = new CommentStringTokenizer(newKineticsStr);
        // skip the first token;
        kineticsTokens.nextToken();
        // second token is the kinetic type; use this to create a dummy kinetics
        String kineticType = kineticsTokens.nextToken();
        Kinetics newkinetics = KineticsDescription.fromVCMLKineticsName(kineticType).createKinetics(newReactionStep);
        // use the remaining tokens to construct the new kinetics
        newkinetics.fromTokens(newKineticsStr);
        // bind newkinetics to newReactionStep and add it to newReactionStep
        newkinetics.bind(newReactionStep);
        newReactionStep.setKinetics(newkinetics);
        counter += 1;
        if (counter == copyFromRxSteps.length) {
            break;
        }
        if (!copiedStructName.equals(fromRxnStruct.getName())) {
            if (currentStruct instanceof Feature) {
                currentStruct = structTopology.getMembrane((Feature) currentStruct);
            } else if (currentStruct instanceof Membrane) {
                currentStruct = structTopology.getInsideFeature((Membrane) currentStruct);
            }
        }
        copiedStructName = fromRxnStruct.getName();
    } while (true);
    return new PasteHelper(issueVector, rxPartMapStructure, reactionsAndSpeciesContexts);
}