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

Example 6 with SimpleReaction

use of cbit.vcell.model.SimpleReaction 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 SimpleReaction

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

the class KineticsTypeTemplatePanel method initKineticChoices.

private void initKineticChoices() {
    KineticsDescription[] kineticTypes = reactionStep == null || reactionStep instanceof SimpleReaction ? Simple_Reaction_Kinetic_Types : Flux_Reaction_KineticTypes;
    javax.swing.DefaultComboBoxModel model = new DefaultComboBoxModel();
    for (int i = 0; i < kineticTypes.length; i++) {
        model.addElement(kineticTypes[i]);
    }
    getKineticsTypeComboBox().setModel(model);
    return;
}

Example 8 with SimpleReaction

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

the class SimpleReactionPanel method setTornOffSimpleReaction.

/**
 * Set the TornOffSimpleReaction to a new value.
 * @param newValue cbit.vcell.model.SimpleReaction
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void setTornOffSimpleReaction(SimpleReaction newValue) {
    if (ivjTornOffSimpleReaction != newValue) {
        try {
            SimpleReaction oldValue = getTornOffSimpleReaction();
            /* Stop listening for events from the current object */
            if (ivjTornOffSimpleReaction != null) {
                ivjTornOffSimpleReaction.removePropertyChangeListener(ivjEventHandler);
            }
            ivjTornOffSimpleReaction = newValue;
            /* Listen for events from the new object */
            if (ivjTornOffSimpleReaction != null) {
                ivjTornOffSimpleReaction.addPropertyChangeListener(ivjEventHandler);
            }
            connPtoP1SetSource();
            getReactionCanvas().setReactionStep(ivjTornOffSimpleReaction);
            if (ivjTornOffSimpleReaction != null) {
                getSimpleReactionNameTextField().setText(getTornOffSimpleReaction().getName());
            }
            getReactionElectricalPropertiesPanel1().setKinetics(ivjTornOffSimpleReaction.getKinetics());
            boolean electricalPropertiesVisible = ivjTornOffSimpleReaction != null && ivjTornOffSimpleReaction.getStructure() instanceof Membrane;
            getReactionElectricalPropertiesPanel1().setVisible(electricalPropertiesVisible);
            getKineticsTypeTemplatePanel().setReactionStep(getSimpleReaction());
            firePropertyChange("simpleReaction", oldValue, newValue);
        // user code begin {1}
        // user code end
        } catch (java.lang.Throwable ivjExc) {
            // user code begin {2}
            // user code end
            handleException(ivjExc);
        }
    }
    ;
// user code begin {3}
// user code end
}

Example 9 with SimpleReaction

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

the class TransformMassActionTableModel method saveTransformedReactions.

public void saveTransformedReactions() throws Exception {
    // isTransformable and TransformedREactions are stored according to the indexes in model reaction steps.
    boolean[] isTransformable = getTransformMassActions().getIsTransformable();
    TransformMassActions.TransformedReaction[] trs = getTransformMassActions().getTransformedReactionSteps();
    ReactionStep[] origReactions = getModel().getReactionSteps();
    // names of those who can be transformed and will be transformed
    String okTransReacNames = "";
    // names of those who can be transformed and will not be transformed
    String noTransReacNames = "";
    // names of those who can not be transformed
    String errReacNames = "";
    for (int i = 0; i < isTransformable.length; i++) {
        if (trs[i].getTransformType() == TransformMassActions.TransformedReaction.TRANSFORMABLE && getIsSelected(i)) {
            okTransReacNames = okTransReacNames + origReactions[i].getName() + ",";
        } else if (trs[i].getTransformType() == TransformMassActions.TransformedReaction.TRANSFORMABLE && !getIsSelected(i)) {
            noTransReacNames = noTransReacNames + origReactions[i].getName() + ",";
        } else if (!isTransformable[i]) {
            errReacNames = errReacNames + origReactions[i].getName() + ",";
        }
    }
    // set transformed Mass Action kinetics to model reactions
    for (int i = 0; i < origReactions.length; i++) {
        if (getIsSelected(i)) {
            // for simple reaction, we replace the original kinetics with MassActionKinetics if it wasn't MassActionKinetics
            if (origReactions[i] instanceof SimpleReaction) {
                if (!(origReactions[i].getKinetics() instanceof MassActionKinetics)) {
                    // ***Below we will physically change the simple reaction***
                    // put all kinetic parameters together into array newKps
                    Vector<Kinetics.KineticsParameter> newKps = new Vector<Kinetics.KineticsParameter>();
                    // get original kinetic parameters which are not current density and reaction rate.
                    // those parameters are basically the symbols in rate expression.
                    Vector<Kinetics.KineticsParameter> origKps = new Vector<Kinetics.KineticsParameter>();
                    Kinetics.KineticsParameter[] Kps = origReactions[i].getKinetics().getKineticsParameters();
                    for (int j = 0; j < Kps.length; j++) {
                        if (!(Kps[j].getRole() == Kinetics.ROLE_CurrentDensity || Kps[j].getRole() == Kinetics.ROLE_ReactionRate)) {
                            origKps.add(Kps[j]);
                        }
                    }
                    // create mass action kinetics for the original reaction step
                    MassActionKinetics maKinetics = new MassActionKinetics(origReactions[i]);
                    maKinetics.getKineticsParameterFromRole(Kinetics.ROLE_KForward).setExpression(trs[i].getMassActionFunction().getForwardRate());
                    maKinetics.getKineticsParameterFromRole(Kinetics.ROLE_KReverse).setExpression(trs[i].getMassActionFunction().getReverseRate());
                    // Kinetics)
                    for (int j = 0; j < maKinetics.getKineticsParameters().length; j++) {
                        newKps.add(maKinetics.getKineticsParameters(j));
                    }
                    // copy other kinetic parameters from original kinetics
                    for (int j = 0; j < origKps.size(); j++) {
                        newKps.add(origKps.elementAt(j));
                    }
                    // add parameters to mass action kinetics
                    KineticsParameter[] newParameters = new KineticsParameter[newKps.size()];
                    newParameters = (KineticsParameter[]) newKps.toArray(newParameters);
                    maKinetics.addKineticsParameters(newParameters);
                    // after adding all the parameters, we bind the forward/reverse rate expression with symbol table (the reaction step itself)
                    origReactions[i].getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_KForward).getExpression().bindExpression(origReactions[i]);
                    origReactions[i].getKinetics().getKineticsParameterFromRole(Kinetics.ROLE_KReverse).getExpression().bindExpression(origReactions[i]);
                }
            }
        // for flux, we set the flux reaction back, coz we will parse it to mass action form in stochastic math mapping.
        // However, we don't physically change it.
        }
    }
    String msg = "";
    if (!okTransReacNames.equals("")) {
        msg = msg + okTransReacNames + " have been transformed.\n";
    }
    // message to be displayed in popupdialog of DocumentWindow
    if (!msg.equals("")) {
        throw new Exception(msg);
    }
}

Example 10 with SimpleReaction

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

the class ReactionCartoonFull method applyDefaults.

public void applyDefaults(Diagram diagram) {
    List<NodeReference> nodeList = diagram.getNodeFullList();
    List<NodeReference> orphansList = new ArrayList<NodeReference>();
    for (int i = 0; i < nodeList.size(); i++) {
        NodeReference node = nodeList.get(i);
        Object obj = null;
        Structure struct = diagram.getStructure();
        boolean found = false;
        switch(node.nodeType) {
            case NodeReference.SIMPLE_REACTION_NODE:
                obj = getModel().getReactionStep(node.name);
                if (!(obj instanceof SimpleReaction)) {
                    System.out.println("ReactionCartoon.applyDefaults(), diagram reaction " + node.name + " type mismatch in model, using location anyway");
                }
                break;
            case NodeReference.FLUX_REACTION_NODE:
                obj = getModel().getReactionStep(node.name);
                if (!(obj instanceof FluxReaction)) {
                    System.out.println("ReactionCartoon.applyDefaults(), diagram flux " + node.name + " type mismatch in model, using location anyway");
                }
                break;
            case NodeReference.SPECIES_CONTEXT_NODE:
                obj = getModel().getSpeciesContext(node.name);
                break;
            case NodeReference.REACTION_RULE_NODE:
                obj = getModel().getRbmModelContainer().getReactionRule(node.name);
                break;
            case // obj is a RuleParticipantSignature
            NodeReference.RULE_PARTICIPANT_SIGNATURE_FULL_NODE:
                for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                    if (signature instanceof RuleParticipantLongSignature && signature.getStructure() == struct && signature.compareByCriteria(node.getName(), GroupingCriteria.full)) {
                        obj = signature;
                        found = true;
                        break;
                    }
                }
                if (!found) {
                    orphansList.add(node);
                }
                break;
            case NodeReference.RULE_PARTICIPANT_SIGNATURE_SHORT_NODE:
                System.out.println("ReactionCartoonFull, RULE_PARTICIPANT_SIGNATURE_SHORT_NODE detected");
                for (RuleParticipantSignature signature : ruleParticipantSignatures) {
                    if (signature instanceof RuleParticipantShortSignature && signature.getStructure() == struct && signature.compareByCriteria(node.getName(), GroupingCriteria.full)) {
                        obj = signature;
                        found = true;
                        break;
                    }
                }
                if (!found) {
                    orphansList.add(node);
                }
                break;
        }
        // -- switch
        Shape shape = getShapeFromModelObject(obj);
        if (shape != null) {
            Point relPosOld = shape.getRelPos();
            Point relPosNew = node.location;
            // In old models, the same node can appear in multiple diagrams.
            // Now, we have only one diagram, so if a node has multiple positions,
            // some would overwrite others.
            // This attempts to prevent overwriting a position with a worse one.
            // if(relPosOld.x + relPosOld.y < relPosNew.x + relPosNew.y) {
            shape.setRelPos(relPosNew);
        // }
        }
    }
    if (!orphansList.isEmpty()) {
        diagram.removeNodeReferences(NodeReference.Mode.full, orphansList);
    }
}