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

Example 26 with Product

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

the class Xmlproducer method getXML.

/**
 * This method returns a XML representation of a Flux Reaction object.
 * Creation date: (2/26/2001 12:30:13 PM)
 * @return Element
 * @param param cbit.vcell.model.FluxReaction
 */
private Element getXML(FluxReaction param) throws XmlParseException {
    Element fluxreaction = new Element(XMLTags.FluxStepTag);
    // get Attributes
    String versionName = (param.getName() != null) ? mangle(param.getName()) : "unnamed_fluxReaction";
    fluxreaction.setAttribute(XMLTags.NameAttrTag, versionName);
    fluxreaction.setAttribute(XMLTags.StructureAttrTag, mangle(param.getStructure().getName()));
    fluxreaction.setAttribute(XMLTags.ReversibleAttrTag, mangle(Boolean.valueOf(param.isReversible()).toString()));
    if (param.getPhysicsOptions() == FluxReaction.PHYSICS_ELECTRICAL_ONLY) {
        fluxreaction.setAttribute(XMLTags.FluxOptionAttrTag, XMLTags.FluxOptionElectricalOnly);
    } else if (param.getPhysicsOptions() == FluxReaction.PHYSICS_MOLECULAR_AND_ELECTRICAL) {
        fluxreaction.setAttribute(XMLTags.FluxOptionAttrTag, XMLTags.FluxOptionMolecularAndElectrical);
    } else if (param.getPhysicsOptions() == FluxReaction.PHYSICS_MOLECULAR_ONLY) {
        fluxreaction.setAttribute(XMLTags.FluxOptionAttrTag, XMLTags.FluxOptionMolecularOnly);
    }
    // If keyFlag is on print the Keyvalue
    if (param.getKey() != null && this.printKeysFlag) {
        fluxreaction.setAttribute(XMLTags.KeyValueAttrTag, param.getKey().toString());
    }
    // Add subelements: Reactants/Products/Catalysts
    // separate the order of the reactants, products, and modifiers.
    ReactionParticipant[] rpArray = param.getReactionParticipants();
    ArrayList<Element> products = new ArrayList<Element>();
    ArrayList<Element> modifiers = new ArrayList<Element>();
    for (int i = 0; i < rpArray.length; i++) {
        Element rp = getXML(rpArray[i]);
        if (rp != null) {
            if (rpArray[i] instanceof Reactant)
                fluxreaction.addContent(rp);
            else if (rpArray[i] instanceof Product)
                products.add(rp);
            else if (rpArray[i] instanceof Catalyst)
                modifiers.add(rp);
        }
    }
    for (int i = 0; i < products.size(); i++) fluxreaction.addContent((Element) products.get(i));
    for (int i = 0; i < modifiers.size(); i++) fluxreaction.addContent((Element) modifiers.get(i));
    // Add Kinetics
    fluxreaction.addContent(getXML(param.getKinetics()));
    return fluxreaction;
}

Example 27 with Product

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

the class ModelProcessEquation method computeEquationString.

private void computeEquationString() {
    if (modelProcess instanceof ReactionStep) {
        ReactionStep reactionStep = (ReactionStep) modelProcess;
        ReactionParticipant[] reactantParticipants = reactionStep.getReactionParticipants();
        ArrayList<ReactionParticipant> reactantList = new ArrayList<ReactionParticipant>();
        ArrayList<ReactionParticipant> productList = new ArrayList<ReactionParticipant>();
        // if (reactionStep instanceof SimpleReaction) {
        for (ReactionParticipant rp : reactantParticipants) {
            if (rp instanceof Reactant) {
                reactantList.add(rp);
            } else if (rp instanceof Product) {
                productList.add(rp);
            }
        }
        // } else {
        // Membrane membrane = (Membrane) ((FluxReaction)reactionStep).getStructure();
        // StructureTopology structTopology = reactionStep.getModel().getStructureTopology();
        // for (ReactionParticipant rp : reactantParticipants) {
        // if (rp instanceof Flux) {
        // Flux flux = (Flux)rp;
        // Feature scf = (Feature) flux.getSpeciesContext().getStructure();
        // if (structTopology.getInsideFeature(membrane) == scf) {
        // productList.add(rp);
        // } else {
        // reactantList.add(rp);
        // }
        // }
        // }
        // }
        StringBuffer sb = new StringBuffer();
        for (ReactionParticipant r : reactantList) {
            if (sb.length() > 0) {
                sb.append(" + ");
            }
            int stoichiometry = r.getStoichiometry();
            sb.append((stoichiometry > 1 ? stoichiometry : "") + r.getName());
        }
        equationleftHand = sb.toString();
        sb = new StringBuffer();
        for (ReactionParticipant p : productList) {
            if (sb.length() > 0) {
                sb.append(" + ");
            }
            int stoichiometry = p.getStoichiometry();
            sb.append((stoichiometry > 1 ? stoichiometry : "") + p.getName());
        }
        equationRightHand = sb.toString();
        equationString = equationleftHand + " " + REACTION_GOESTO + " " + equationRightHand;
    } else if (modelProcess instanceof ReactionRule) {
        ReactionRule reactionRuleEmbedded = (ReactionRule) modelProcess;
        equationString = RbmUtils.toBnglStringShort(reactionRuleEmbedded, CompartmentMode.hide);
    }
}

Example 28 with Product

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

the class PathwayMapping method parseReaction.

private ReactionParticipant[] parseReaction(ReactionStep reactionStep, BioModel bioModel, RelationshipObject relationshipObject) throws ExpressionException, PropertyVetoException {
    if (reactionStep == null || bioModel == null || bioModel.getRelationshipModel() == null) {
        return null;
    }
    // create the reaction equation string
    String leftHand = getParticipantsString(((Conversion) relationshipObject.getBioPaxObject()).getLeft());
    String rightHand = getParticipantsString(((Conversion) relationshipObject.getBioPaxObject()).getRight());
    StringTokenizer st = new StringTokenizer(leftHand, "+");
    HashMap<String, SpeciesContext> speciesContextMap = new HashMap<String, SpeciesContext>();
    ArrayList<ReactionParticipant> rplist = new ArrayList<ReactionParticipant>();
    // create and add reaction participants to list for left-hand side of equation
    Model model = bioModel.getModel();
    Structure structure = reactionStep.getStructure();
    while (st.hasMoreElements()) {
        String nextToken = st.nextToken().trim();
        if (nextToken.length() == 0) {
            continue;
        }
        int stoichiIndex = 0;
        while (true) {
            if (Character.isDigit(nextToken.charAt(stoichiIndex))) {
                stoichiIndex++;
            } else {
                break;
            }
        }
        int stoichi = 1;
        String tmp = nextToken.substring(0, stoichiIndex);
        if (tmp.length() > 0) {
            stoichi = Integer.parseInt(tmp);
        }
        String var = nextToken.substring(stoichiIndex).trim();
        // get speciesContext object based on its name
        // if the speciesContext is not existed, create a new one
        SpeciesContext sc = model.getSpeciesContext(var);
        if (sc == null) {
            sc = speciesContextMap.get(var);
            if (sc == null) {
                // get species object based on its name
                // if the species is not existed, create a new one
                Species species = model.getSpecies(var);
                if (species == null) {
                    species = new Species(var, null);
                }
                sc = new SpeciesContext(species, structure);
                sc.setName(var);
                speciesContextMap.put(var, sc);
            }
        }
        // add the existed speciesContext objects or new speciesContext objects to reaction participant list
        if (reactionStep instanceof SimpleReaction || reactionStep instanceof FluxReaction) {
            rplist.add(new Reactant(null, (SimpleReaction) reactionStep, sc, stoichi));
        }
    }
    // create and add reaction participants to list for right-hand side of equation
    st = new StringTokenizer(rightHand, "+");
    while (st.hasMoreElements()) {
        String nextToken = st.nextToken().trim();
        if (nextToken.length() == 0) {
            continue;
        }
        int stoichiIndex = 0;
        while (true) {
            if (Character.isDigit(nextToken.charAt(stoichiIndex))) {
                stoichiIndex++;
            } else {
                break;
            }
        }
        int stoichi = 1;
        String tmp = nextToken.substring(0, stoichiIndex);
        if (tmp.length() > 0) {
            stoichi = Integer.parseInt(tmp);
        }
        String var = nextToken.substring(stoichiIndex);
        SpeciesContext sc = model.getSpeciesContext(var);
        if (sc == null) {
            sc = speciesContextMap.get(var);
            if (sc == null) {
                Species species = model.getSpecies(var);
                if (species == null) {
                    species = new Species(var, null);
                }
                sc = new SpeciesContext(species, structure);
                sc.setName(var);
                speciesContextMap.put(var, sc);
            }
        }
        if (reactionStep instanceof SimpleReaction || reactionStep instanceof FluxReaction) {
            rplist.add(new Product(null, (SimpleReaction) reactionStep, sc, stoichi));
        }
    }
    return rplist.toArray(new ReactionParticipant[0]);
}

Example 29 with Product

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

the class PathwayMapping method createReactionStep.

/*
	 * for reaction:
	 * 1. annotate the selected vcell object using linked pathway conversion
	 * 2. add non-existing speciesContexts from linked pathway conversion
	 * 3. add links between relative vcell objects and pathway objects
	 * Questions:
	 * - how to deal with the case that the reaction is existing in the model?
	 * 		+ add it in no matter what? 
	 * 				(this is the version we have now: 
	 * 					add the duplicated reactions in without name changing, 
	 * 				 	all duplicated reactions share the same participant objects)
	 *      + just modify the existing one?
	 */
private void createReactionStep(BioModel bioModel, Process process, ReactionStep reactionStep, RelationshipObject relationshipObject, ArrayList<ConversionTableRow> participants, boolean addSubunits) throws Exception {
    if (reactionStep == null || bioModel == null || bioModel.getRelationshipModel() == null || participants.size() < 1) {
        return;
    }
    ArrayList<ReactionParticipant> rplist = new ArrayList<ReactionParticipant>();
    // create and add reaction participants to list
    for (ConversionTableRow ctr : participants) {
        if (ctr.getBioPaxObject() instanceof Conversion)
            continue;
        int stoich = ctr.stoich().intValue();
        String safeId = getSafetyName(ctr.id());
        // get speciesContext object based on its name
        // if the speciesContext is not existed, create a new one
        createSpeciesContextFromTableRow(bioModel, (PhysicalEntity) ctr.getBioPaxObject(), ctr.stoich(), ctr.id(), ctr.location(), addSubunits);
        // add the existed speciesContext objects or new speciesContext objects to reaction participant list
        if (ctr.participantType().equals("Reactant")) {
            if (reactionStep instanceof SimpleReaction || reactionStep instanceof FluxReaction) {
                rplist.add(new Reactant(null, reactionStep, bioModel.getModel().getSpeciesContext(safeId), stoich));
            }
        } else if (ctr.participantType().equals("Product")) {
            if (reactionStep instanceof SimpleReaction || reactionStep instanceof FluxReaction) {
                rplist.add(new Product(null, reactionStep, bioModel.getModel().getSpeciesContext(safeId), stoich));
            }
        }
    // we do not add catalysts
    }
    ReactionParticipant[] rpArray = rplist.toArray(new ReactionParticipant[0]);
    reactionStep.setReactionParticipants(rpArray);
    // add Controls to the reaction
    Set<PhysicalEntity> controllers = process.getControllers();
    for (ConversionTableRow ctr : participants) {
        if (controllers.contains(ctr.getBioPaxObject())) {
            if (ctr.participantType().equals("Catalyst")) {
                String safeId = getSafetyName(ctr.id());
                /* 
					 * using addCatalyst() to create catalyst in reaction: 
					 * this function cannot allow an object to be catalyst and (reactant/product) in the same reaction
					 */
                // reactionStep.addCatalyst(bioModel.getModel().getSpeciesContext(safeId));
                /* However, in pathway interaction object, an physicalEntity can be catalyst and (reactant/product) in the same reaction
					 * So we just call create catalyst for the reaction no matter what rolls the object is playing in the reaction
					 * Switch back to the addCatalyst() function when it is necessary, but exceptions make be reported for some reactions
					 */
                reactionStep.addReactionParticipant(new Catalyst(null, reactionStep, bioModel.getModel().getSpeciesContext(safeId)));
            } else if (ctr.participantType().equals("Control")) {
                String safeId = getSafetyName(ctr.id());
                // reactionStep.addCatalyst(bioModel.getModel().getSpeciesContext(safeId));
                reactionStep.addReactionParticipant(new Catalyst(null, reactionStep, bioModel.getModel().getSpeciesContext(safeId)));
            }
        }
    }
}

Example 30 with Product

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

the class SBMLImporter method addReactionParticipants.

/**
 * addReactionParticipant : Adds reactants and products and modifiers to a
 * reaction. Input args are the sbml reaction, vc reaction This method was
 * created mainly to handle reactions where there are reactants and/or
 * products that appear multiple times in a reaction. Virtual Cell now
 * allows the import of such reactions.
 */
private void addReactionParticipants(org.sbml.jsbml.Reaction sbmlRxn, ReactionStep vcRxn) throws Exception {
    Model vcModel = vcBioModel.getSimulationContext(0).getModel();
    // if (!(vcRxn instanceof FluxReaction)) {
    if (true) {
        // reactants in sbmlRxn
        HashMap<String, Integer> sbmlReactantsHash = new HashMap<String, Integer>();
        for (int j = 0; j < (int) sbmlRxn.getNumReactants(); j++) {
            SpeciesReference spRef = sbmlRxn.getReactant(j);
            String sbmlReactantSpId = spRef.getSpecies();
            if (sbmlModel.getSpecies(sbmlReactantSpId) != null) {
                // check
                // if
                // spRef
                // is in
                // sbml
                // model
                // If stoichiometry of speciesRef is not an integer, it is
                // not handled in the VCell at this time; no point going
                // further
                double stoichiometry = 0.0;
                if (level < 3) {
                    // for SBML models < L3, default
                    // stoichiometry is 1, if field is not
                    // set.
                    // default value of stoichiometry,
                    stoichiometry = 1.0;
                    // if not set.
                    if (spRef.isSetStoichiometry()) {
                        stoichiometry = spRef.getStoichiometry();
                        if (((int) stoichiometry != stoichiometry) || spRef.isSetStoichiometryMath()) {
                            throw new SBMLImportException("Non-integer stoichiometry ('" + stoichiometry + "' for reactant '" + sbmlReactantSpId + "' in reaction '" + sbmlRxn.getId() + "') or stoichiometryMath not handled in VCell at this time.", Category.NON_INTEGER_STOICH);
                        // logger.sendMessage(VCLogger.Priority.HighPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.");
                        }
                    }
                } else {
                    if (spRef.isSetStoichiometry()) {
                        stoichiometry = spRef.getStoichiometry();
                        if (((int) stoichiometry != stoichiometry) || spRef.isSetStoichiometryMath()) {
                            throw new SBMLImportException("Non-integer stoichiometry ('" + stoichiometry + "' for reactant '" + sbmlReactantSpId + "' in reaction '" + sbmlRxn.getId() + "') or stoichiometryMath not handled in VCell at this time.", Category.NON_INTEGER_STOICH);
                        // logger.sendMessage(VCLogger.Priority.HighPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.");
                        // logger.sendMessage(VCLogger.Priority.HighPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.");
                        }
                    } else {
                        throw new SBMLImportException("This is a SBML level 3 model, stoichiometry is not set for the reactant '" + sbmlReactantSpId + "' and no default value can be assumed.");
                    // logger.sendMessage(VCLogger.Priority.HighPriority,
                    // VCLogger.ErrorType.ReactionError,
                    // "This is a SBML level 3 model, stoichiometry is not set for the reactant '"
                    // + spRef.getSpecies() +
                    // "' and no default value can be assumed.");
                    }
                }
                if (sbmlReactantsHash.get(sbmlReactantSpId) == null) {
                    // if sbmlReactantSpId is NOT in sbmlReactantsHash, add
                    // it with its stoichiometry
                    sbmlReactantsHash.put(sbmlReactantSpId, Integer.valueOf((int) stoichiometry));
                } else {
                    // if sbmlReactantSpId IS in sbmlReactantsHash, update
                    // its stoichiometry value to (existing-from-hash +
                    // stoichiometry) and put it back in hash
                    int intStoich = sbmlReactantsHash.get(sbmlReactantSpId).intValue();
                    intStoich += (int) stoichiometry;
                    sbmlReactantsHash.put(sbmlReactantSpId, Integer.valueOf(intStoich));
                }
            } else {
                // spRef is not in model, throw exception
                throw new SBMLImportException("Reactant '" + sbmlReactantSpId + "' in reaction '" + sbmlRxn.getId() + "' not found as species in SBML model.");
            }
        // end - if (spRef is species in model)
        }
        // sbmlReactionParticipantsHash as reactants to vcRxn
        for (Entry<String, Integer> es : sbmlReactantsHash.entrySet()) {
            SpeciesContext speciesContext = vcModel.getSpeciesContext(es.getKey());
            int stoich = es.getValue();
            vcRxn.addReactant(speciesContext, stoich);
        }
        /*
			Iterator<String> sbmlReactantsIter = sbmlReactantsHash.keySet()
					.iterator();
			while (sbmlReactantsIter.hasNext()) {
				String sbmlReactantStr = sbmlReactantsIter.next();
				SpeciesContext speciesContext = vcModel
						.getSpeciesContext(sbmlReactantStr);
				int stoich = sbmlReactantsHash.get(sbmlReactantStr).intValue();
				((SimpleReaction) vcRxn).addReactant(speciesContext, stoich);
			}
			*/
        // products in sbmlRxn
        HashMap<String, Integer> sbmlProductsHash = new HashMap<String, Integer>();
        for (int j = 0; j < (int) sbmlRxn.getNumProducts(); j++) {
            SpeciesReference spRef = sbmlRxn.getProduct(j);
            String sbmlProductSpId = spRef.getSpecies();
            if (sbmlModel.getSpecies(sbmlProductSpId) != null) {
                /* check if spRef is in sbml model
					If stoichiometry of speciesRef is not an integer, it is
					not handled in the VCell at this time; no point going
					further */
                double stoichiometry = 0.0;
                if (level < 3) {
                    // for sBML models < L3, default
                    // stoichiometry is 1, if field is not
                    // set.
                    // default value of stoichiometry,
                    stoichiometry = 1.0;
                    // if not set.
                    if (spRef.isSetStoichiometry()) {
                        stoichiometry = spRef.getStoichiometry();
                        if (((int) stoichiometry != stoichiometry) || spRef.isSetStoichiometryMath()) {
                            throw new SBMLImportException("Non-integer stoichiometry ('" + stoichiometry + "' for product '" + sbmlProductSpId + "' in reaction '" + sbmlRxn.getId() + "') or stoichiometryMath not handled in VCell at this time.", Category.NON_INTEGER_STOICH);
                        // logger.sendMessage(VCLogger.Priority.HighPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.");
                        }
                    }
                } else {
                    if (spRef.isSetStoichiometry()) {
                        stoichiometry = spRef.getStoichiometry();
                        if (((int) stoichiometry != stoichiometry) || spRef.isSetStoichiometryMath()) {
                            throw new SBMLImportException("Non-integer stoichiometry ('" + stoichiometry + "' for product '" + sbmlProductSpId + "' in reaction '" + sbmlRxn.getId() + "') or stoichiometryMath not handled in VCell at this time.", Category.NON_INTEGER_STOICH);
                        // logger.sendMessage(VCLogger.Priority.HighPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.");
                        }
                    } else {
                        throw new SBMLImportException("This is a SBML level 3 model, stoichiometry is not set for the product '" + sbmlProductSpId + "' and no default value can be assumed.");
                    // logger.sendMessage(VCLogger.Priority.HighPriority,
                    // VCLogger.ErrorType.ReactionError,
                    // "This is a SBML level 3 model, stoichiometry is not set for the product '"
                    // + spRef.getSpecies() +
                    // "' and no default value can be assumed.");
                    }
                }
                if (sbmlProductsHash.get(sbmlProductSpId) == null) {
                    // if sbmlProductSpId is NOT in sbmlProductsHash, add it
                    // with its stoichiometry
                    sbmlProductsHash.put(sbmlProductSpId, Integer.valueOf((int) stoichiometry));
                } else {
                    // if sbmlProductSpId IS in sbmlProductsHash, update its
                    // stoichiometry value to (existing-value-from-hash +
                    // stoichiometry) and put it back in hash
                    int intStoich = sbmlProductsHash.get(sbmlProductSpId).intValue();
                    intStoich += (int) stoichiometry;
                    sbmlProductsHash.put(sbmlProductSpId, Integer.valueOf(intStoich));
                }
            } else {
                // spRef is not in model, throw exception
                throw new SBMLImportException("Product '" + sbmlProductSpId + "' in reaction '" + sbmlRxn.getId() + "' not found as species in SBML model.");
            }
        // end - if (spRef is species in model)
        }
        // as products to vcRxn
        for (Entry<String, Integer> es : sbmlProductsHash.entrySet()) {
            SpeciesContext speciesContext = vcModel.getSpeciesContext(es.getKey());
            int stoich = es.getValue();
            vcRxn.addProduct(speciesContext, stoich);
        }
    /*
			Iterator<String> sbmlProductsIter = sbmlProductsHash.keySet()
					.iterator();
			while (sbmlProductsIter.hasNext()) {
				String sbmlProductStr = sbmlProductsIter.next();
				SpeciesContext speciesContext = vcModel
						.getSpeciesContext(sbmlProductStr);
				int stoich = sbmlProductsHash.get(sbmlProductStr).intValue();
				((SimpleReaction) vcRxn).addProduct(speciesContext, stoich);
			}
			*/
    // proxy.addProducts(sbmlProductsHash);
    }
    // modifiers
    for (int j = 0; j < (int) sbmlRxn.getNumModifiers(); j++) {
        ModifierSpeciesReference spRef = sbmlRxn.getModifier(j);
        String sbmlSpId = spRef.getSpecies();
        if (sbmlModel.getSpecies(sbmlSpId) != null) {
            // check if this modifier species is preesent in vcRxn (could
            // have been added as reactamt/product/catalyst).
            // If alreay a catalyst in vcRxn, do nothing
            ArrayList<ReactionParticipant> vcRxnParticipants = getVCReactionParticipantsFromSymbol(vcRxn, sbmlSpId);
            SpeciesContext speciesContext = vcModel.getSpeciesContext(sbmlSpId);
            if (vcRxnParticipants == null || vcRxnParticipants.size() == 0) {
                // If not in reactionParticipantList of vcRxn, add as
                // catalyst.
                vcRxn.addCatalyst(speciesContext);
            } else {
                for (ReactionParticipant rp : vcRxnParticipants) {
                    if (rp instanceof Reactant || rp instanceof Product) {
                        // If already a reactant or product in vcRxn, add
                        // warning to localIssuesList, don't do anything
                        localIssueList.add(new Issue(speciesContext, issueContext, IssueCategory.SBMLImport_Reaction, "Species " + speciesContext.getName() + " was already added as a reactant and/or product to " + vcRxn.getName() + "; Cannot add it as a catalyst also.", Issue.SEVERITY_INFO));
                        break;
                    }
                }
            }
        } else {
            // spRef is not in model, throw exception
            throw new SBMLImportException("Modifier '" + sbmlSpId + "' in reaction '" + sbmlRxn.getId() + "' not found as species in SBML model.");
        }
    // end - if (spRef is species in model)
    }
// end - for modifiers
}