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

Example 1 with Catalyst

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

the class PathwayMapping method createReactionStepFromPathway.

/*
	 * 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 createReactionStepFromPathway(BioModel bioModel, Process process, ReactionStep reactionStep, RelationshipObject relationshipObject, boolean addSubunits) throws Exception {
    // annotate the selected vcell object using linked pathway object
    // add non-existing speciesContexts from linked pathway conversion
    ReactionParticipant[] rpArray = parseReaction(reactionStep, bioModel, relationshipObject);
    // create a hashtable for interaction Participants
    Hashtable<String, BioPaxObject> participantTable = new Hashtable<String, BioPaxObject>();
    for (BioPaxObject bpObject : ((Conversion) relationshipObject.getBioPaxObject()).getLeft()) {
        if (((PhysicalEntity) bpObject).getName().size() == 0) {
            participantTable.put(getSafetyName(((PhysicalEntity) bpObject).getID()), bpObject);
        } else {
            participantTable.put(getSafetyName(((PhysicalEntity) bpObject).getName().get(0)), bpObject);
        }
    }
    for (BioPaxObject bpObject : ((Conversion) relationshipObject.getBioPaxObject()).getRight()) {
        if (((PhysicalEntity) bpObject).getName().size() == 0) {
            participantTable.put(getSafetyName(((PhysicalEntity) bpObject).getID()), bpObject);
        } else {
            participantTable.put(getSafetyName(((PhysicalEntity) bpObject).getName().get(0)), bpObject);
        }
    }
    for (ReactionParticipant rp : rpArray) {
        SpeciesContext speciesContext = rp.getSpeciesContext();
        if (bioModel.getModel().getSpeciesContext(speciesContext.getName()) == null) {
            // if the speciesContext is not existed, then add it to the bioModel and link it to the corresponding pathway object
            if (bioModel.getModel().getSpecies(speciesContext.getName()) == null) {
                bioModel.getModel().addSpecies(speciesContext.getSpecies());
            }
            bioModel.getModel().addSpeciesContext(speciesContext);
            RelationshipObject newSpeciesContext = new RelationshipObject(speciesContext, participantTable.get(speciesContext.getName()));
            bioModel.getRelationshipModel().addRelationshipObject(newSpeciesContext);
        } else {
            // if it is in the bioModel, then check whether it links to pathway object or not
            HashSet<RelationshipObject> linkedReObjects = bioModel.getRelationshipModel().getRelationshipObjects(bioModel.getModel().getSpeciesContext(speciesContext.getName()));
            if (linkedReObjects != null) {
                boolean isLinked = false;
                for (RelationshipObject reObject : linkedReObjects) {
                    if (reObject.getBioPaxObject() == participantTable.get(speciesContext.getName())) {
                        isLinked = true;
                        break;
                    }
                }
                if (!isLinked) {
                    RelationshipObject newSpeciesContext = new RelationshipObject(speciesContext, participantTable.get(speciesContext.getName()));
                    bioModel.getRelationshipModel().addRelationshipObject(newSpeciesContext);
                }
            } else {
                RelationshipObject newSpeciesContext = new RelationshipObject(speciesContext, participantTable.get(speciesContext.getName()));
                bioModel.getRelationshipModel().addRelationshipObject(newSpeciesContext);
            }
        }
    }
    (reactionStep).setReactionParticipants(rpArray);
    // add Control to the reaction
    if (process.getControl() != null) {
        for (InteractionParticipant pe : process.getControl().getParticipants()) {
            SpeciesContext newSpeciescontext = createSpeciesContextFromBioPaxObject(bioModel, pe.getPhysicalEntity(), addSubunits);
            (reactionStep).addReactionParticipant(new Catalyst(null, reactionStep, newSpeciescontext));
        }
    }
    addKinetics(reactionStep, process);
}

Example 2 with Catalyst

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

the class Xmlproducer method getXML.

/**
 * This method returns the XML represntation of a Simple reaction object.
 * Creation date: (2/27/2001 2:27:28 PM)
 * @return Element
 * @param param cbit.vcell.model.SimpleReaction
 */
private Element getXML(SimpleReaction param) throws XmlParseException {
    Element simplereaction = new Element(XMLTags.SimpleReactionTag);
    // Add attribute
    String nameStr = (param.getName() != null) ? (mangle(param.getName())) : "unnamed_SimpleReaction";
    simplereaction.setAttribute(XMLTags.StructureAttrTag, mangle(param.getStructure().getName()));
    simplereaction.setAttribute(XMLTags.NameAttrTag, nameStr);
    simplereaction.setAttribute(XMLTags.ReversibleAttrTag, mangle(Boolean.valueOf(param.isReversible()).toString()));
    if (param.getPhysicsOptions() == SimpleReaction.PHYSICS_ELECTRICAL_ONLY) {
        simplereaction.setAttribute(XMLTags.FluxOptionAttrTag, XMLTags.FluxOptionElectricalOnly);
    } else if (param.getPhysicsOptions() == SimpleReaction.PHYSICS_MOLECULAR_AND_ELECTRICAL) {
        simplereaction.setAttribute(XMLTags.FluxOptionAttrTag, XMLTags.FluxOptionMolecularAndElectrical);
    } else if (param.getPhysicsOptions() == SimpleReaction.PHYSICS_MOLECULAR_ONLY) {
        simplereaction.setAttribute(XMLTags.FluxOptionAttrTag, XMLTags.FluxOptionMolecularOnly);
    }
    // If keyFlag is on print the Keyvalue
    if (param.getKey() != null && this.printKeysFlag) {
        simplereaction.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)
                simplereaction.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++) simplereaction.addContent((Element) products.get(i));
    for (int i = 0; i < modifiers.size(); i++) simplereaction.addContent((Element) modifiers.get(i));
    // Add kinetics
    simplereaction.addContent(getXML(param.getKinetics()));
    return simplereaction;
}

Example 3 with Catalyst

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

the class XmlReader method getCatalyst.

/**
 * This method returns a Catalyst object from a XML representation.
 * Creation date: (5/4/2001 2:22:56 PM)
 * @return cbit.vcell.model.Product
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
private Catalyst getCatalyst(Element param, ReactionStep reaction, Model model) throws XmlParseException {
    // retrieve the key if there is one
    KeyValue key = null;
    String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag);
    if (keystring != null && keystring.length() > 0 && this.readKeysFlag) {
        key = new KeyValue(keystring);
    }
    String speccontref = unMangle(param.getAttributeValue(XMLTags.SpeciesContextRefAttrTag));
    SpeciesContext speccont = model.getSpeciesContext(speccontref);
    if (speccont == null) {
        throw new XmlParseException("The reference to the SpecieContext " + speccontref + " for a Catalyst could not be resolved!");
    }
    return new Catalyst(key, reaction, speccont);
}

Example 4 with Catalyst

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

the class SBPAXHMMIrrevLawBuilder method addKinetics.

public void addKinetics(KineticContext context) {
    try {
        ReactionStep reaction = context.getReaction();
        HMM_IRRKinetics kinetics = new HMM_IRRKinetics((SimpleReaction) reaction);
        NameScope modelScope = reaction.getModel().getNameScope();
        ModelParameter kMichaelis = context.getParameter(SBOList.MICHAELIS_CONST_FORW);
        if (kMichaelis != null) {
            KineticsParameter kmParameter = kinetics.getKmParameter();
            kmParameter.setExpression(new Expression(kMichaelis, modelScope));
            kmParameter.setUnitDefinition(kMichaelis.getUnitDefinition());
        }
        ModelParameter kcat = context.getParameter(SBOList.CATALYTIC_RATE_CONST_FORW);
        if (kcat != null && context.getCatalysts().size() == 1) {
            KineticsParameter vmaxParameter = kinetics.getVmaxParameter();
            Catalyst catalyst = context.getCatalysts().iterator().next();
            vmaxParameter.setExpression(Expression.mult(new Expression(kcat, modelScope), new Expression(catalyst.getSpeciesContext(), modelScope)));
        // vmaxParameter.setUnitDefinition(vMax.getUnitDefinition());
        } else {
            ModelParameter vMax = context.getParameter(SBOList.MAXIMAL_VELOCITY_FORW);
            if (vMax != null) {
                KineticsParameter vmaxParameter = kinetics.getVmaxParameter();
                vmaxParameter.setExpression(new Expression(vMax, modelScope));
                vmaxParameter.setUnitDefinition(vMax.getUnitDefinition());
            }
        }
    } catch (ExpressionException e) {
        e.printStackTrace();
    }
}

Example 5 with Catalyst

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

the class StructureAnalyzer method getCorrectedRateExpression.

public Expression getCorrectedRateExpression(ReactionStep reactionStep, ReactionParticipant reactionParticipant, RateType rateType) 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);
    }
    // 
    // make distributed rate with correct stoichiometry for this participant
    // 
    VCUnitDefinition correctedReactionRateUnit = null;
    Expression distribRate = null;
    if (reactionStep.getKinetics() instanceof DistributedKinetics) {
        DistributedKinetics distributedKinetics = (DistributedKinetics) reactionStep.getKinetics();
        KineticsParameter distribReactionRateParameter = distributedKinetics.getReactionRateParameter();
        distribRate = new Expression(distribReactionRateParameter, mathMapping.getNameScope());
        correctedReactionRateUnit = distribReactionRateParameter.getUnitDefinition();
    } else if (reactionStep.getKinetics() instanceof LumpedKinetics) {
        // 
        // need to put this into concentration/time with respect to structure for reaction.
        // 
        Structure.StructureSize structureSize = reactionStep.getStructure().getStructureSize();
        LumpedKinetics lumpedKinetics = (LumpedKinetics) reactionStep.getKinetics();
        KineticsParameter lumpedReactionRateParameter = lumpedKinetics.getLumpedReactionRateParameter();
        Expression lumpedReactionRateExp = new Expression(lumpedReactionRateParameter, mathMapping.getNameScope());
        distribRate = Expression.div(lumpedReactionRateExp, new Expression(structureSize, mathMapping.getNameScope()));
        ;
        correctedReactionRateUnit = lumpedReactionRateParameter.getUnitDefinition().divideBy(structureSize.getUnitDefinition());
    }
    // correct for stoichiometry
    Expression distribRateWithStoich = distribRate;
    if (stoich != 1) {
        distribRateWithStoich = Expression.mult(new Expression(stoich), distribRateWithStoich);
    }
    // flux correction if reaction and reactionParticipant are in different compartments. (not necessarily dimensionless, use KFlux parameter).
    Expression distribRateWithStoichFlux = distribRateWithStoich;
    if (reactionStep.getStructure() != reactionParticipant.getStructure()) {
        StructureMapping reactionSM = mathMapping.getSimulationContext().getGeometryContext().getStructureMapping(reactionStep.getStructure());
        StructureMapping speciesSM = mathMapping.getSimulationContext().getGeometryContext().getStructureMapping(reactionParticipant.getStructure());
        Parameter fluxCorrectionParameter = mathMapping.getFluxCorrectionParameter(reactionSM, speciesSM);
        Expression fluxCorrection = new Expression(fluxCorrectionParameter, mathMapping.getNameScope());
        distribRateWithStoichFlux = Expression.mult(fluxCorrection, distribRateWithStoichFlux);
        correctedReactionRateUnit = correctedReactionRateUnit.multiplyBy(fluxCorrectionParameter.getUnitDefinition());
    }
    // apply unit factor for difference substance
    ModelUnitSystem unitSystem = mathMapping.getSimulationContext().getModel().getUnitSystem();
    VCUnitDefinition timeUnit = unitSystem.getTimeUnit();
    VCUnitDefinition speciesConcUnit = reactionParticipant.getSpeciesContext().getUnitDefinition();
    VCUnitDefinition speciesConcRateUnit = speciesConcUnit.divideBy(timeUnit);
    Expression unitFactor = null;
    if (rateType == RateType.ConcentrationRate) {
        unitFactor = mathMapping.getUnitFactor(speciesConcRateUnit.divideBy(correctedReactionRateUnit));
    } else if (rateType == RateType.ResolvedFluxRate) {
        unitFactor = mathMapping.getUnitFactor(speciesConcRateUnit.multiplyBy(unitSystem.getLengthUnit()).divideBy(correctedReactionRateUnit));
    }
    return Expression.mult(unitFactor, distribRateWithStoichFlux).flatten();
}