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

Example 16 with Catalyst

use of cbit.vcell.model.Catalyst 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 17 with Catalyst

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

the class SBPAXHMMRevLawBuilder method addKinetics.

public void addKinetics(KineticContext context) {
    try {
        ReactionStep reaction = context.getReaction();
        HMM_REVKinetics kinetics = new HMM_REVKinetics((SimpleReaction) reaction);
        NameScope modelScope = reaction.getModel().getNameScope();
        ModelParameter kMichaelisFwd = context.getParameter(SBOList.MICHAELIS_CONST_FORW);
        if (kMichaelisFwd != null) {
            KineticsParameter kmfParameter = kinetics.getKmFwdParameter();
            kmfParameter.setExpression(new Expression(kMichaelisFwd, modelScope));
            kmfParameter.setUnitDefinition(kMichaelisFwd.getUnitDefinition());
        }
        ModelParameter kcatf = context.getParameter(SBOList.CATALYTIC_RATE_CONST_FORW);
        if (kcatf != null && context.getCatalysts().size() == 1) {
            KineticsParameter vmaxfParameter = kinetics.getVmaxFwdParameter();
            Catalyst catalyst = context.getCatalysts().iterator().next();
            vmaxfParameter.setExpression(Expression.mult(new Expression(kcatf, modelScope), new Expression(catalyst.getSpeciesContext(), modelScope)));
        // vmaxParameter.setUnitDefinition(vMax.getUnitDefinition());
        } else {
            ModelParameter vMaxf = context.getParameter(SBOList.MAXIMAL_VELOCITY_FORW);
            if (vMaxf != null) {
                KineticsParameter vmaxfParameter = kinetics.getVmaxFwdParameter();
                vmaxfParameter.setExpression(new Expression(vMaxf, modelScope));
                vmaxfParameter.setUnitDefinition(vMaxf.getUnitDefinition());
            }
        }
        ModelParameter kMichaelisRev = context.getParameter(SBOList.MICHAELIS_CONST_REV);
        if (kMichaelisRev != null) {
            KineticsParameter kmrParameter = kinetics.getKmRevParameter();
            kmrParameter.setExpression(new Expression(kMichaelisRev, modelScope));
            kmrParameter.setUnitDefinition(kMichaelisRev.getUnitDefinition());
        }
        ModelParameter kcatr = context.getParameter(SBOList.CATALYTIC_RATE_CONST_FORW);
        if (kcatr != null && context.getCatalysts().size() == 1) {
            KineticsParameter vmaxrParameter = kinetics.getVmaxRevParameter();
            Catalyst catalyst = context.getCatalysts().iterator().next();
            vmaxrParameter.setExpression(Expression.mult(new Expression(kcatr, modelScope), new Expression(catalyst.getSpeciesContext(), modelScope)));
        // vmaxParameter.setUnitDefinition(vMax.getUnitDefinition());
        } else {
            ModelParameter vMaxr = context.getParameter(SBOList.MAXIMAL_VELOCITY_REV);
            if (vMaxr != null) {
                KineticsParameter vmaxrParameter = kinetics.getVmaxRevParameter();
                vmaxrParameter.setExpression(new Expression(vMaxr, modelScope));
                vmaxrParameter.setUnitDefinition(vMaxr.getUnitDefinition());
            }
        }
    } catch (ExpressionException e) {
        e.printStackTrace();
    }
}

Example 18 with Catalyst

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

the class SBPAXKineticsExtractor method setVMForwardParamAsExpression.

private static void setVMForwardParamAsExpression(ReactionStep reaction, SBOParam kCat, Kinetics kinetics) throws ExpressionException, PropertyVetoException {
    if (kCat != null) {
        KineticsParameter Vmax = ((HMM_IRRKinetics) kinetics).getVmaxParameter();
        String unitF = SBOParam.formatUnit(kCat.getUnit());
        VCUnitDefinition kCatUnit = reaction.getModel().getUnitSystem().getInstance(unitF);
        Double numberKCat = 0.0;
        if (kCat.hasNumber()) {
            numberKCat = kCat.getNumber();
        }
        Expression KCatExpression = new Expression(numberKCat);
        KineticsParameter Kcat = kinetics.addUserDefinedKineticsParameter("Kcat", KCatExpression, kCatUnit);
        String enzymeName = "";
        ReactionParticipant[] participants = reaction.getReactionParticipants();
        for (int i = 0; i < participants.length; i++) {
            ReactionParticipant rp = participants[i];
            if (rp instanceof Catalyst) {
                enzymeName = rp.getName();
            }
        }
        SpeciesContext enzyme = reaction.getModel().getSpeciesContext(enzymeName);
        Vmax.setExpression(Expression.mult(new Expression(Kcat, reaction.getNameScope()), new Expression(enzyme, reaction.getNameScope())));
    }
}

Example 19 with Catalyst

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

the class ReactPartTable method getReactionParticipant.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.ReactionParticipant
 * @param rset java.sql.ResultSet
 */
public ReactionParticipant getReactionParticipant(KeyValue rpKey, java.sql.ResultSet rset) throws java.sql.SQLException, DataAccessException {
    ReactionParticipant rp = null;
    KeyValue key = rpKey;
    String role = rset.getString(ReactPartTable.table.role.toString());
    int stoichiometry = rset.getInt(ReactPartTable.table.stoich.toString());
    if (role.equals(ROLE_CATALYST)) {
        rp = new Catalyst(key, null, null);
    } else if (role.equals(ROLE_PRODUCT)) {
        rp = new Product(key, null, null, stoichiometry);
    } else if (role.equals(ROLE_REACTANT)) {
        rp = new Reactant(key, null, null, stoichiometry);
    } else if (role.equals(ROLE_FLUX)) {
        rp = new FluxReaction.Flux(key, null, null);
    } else {
        throw new DataAccessException("unexpected value of " + ReactPartTable.table.role.toString() + "'" + role + "'");
    }
    rp.setStoichiometry(stoichiometry);
    return rp;
}