Examples with VCUnitDefinition cbit.vcell.units.VCUnitDefinition used on opensource projects

Example 41 with VCUnitDefinition

use of cbit.vcell.units.VCUnitDefinition in project vcell by virtualcell.

the class BioEvent method setTriggerType.

public void setTriggerType(TriggerType triggerType) {
    if (triggerType == this.triggerType) {
        return;
    }
    this.triggerType = triggerType;
    ModelUnitSystem modelUnitSystem = getSimulationContext().getModel().getUnitSystem();
    VCUnitDefinition unit_TBD = modelUnitSystem.getInstance_TBD();
    VCUnitDefinition unit_Dimensionless = modelUnitSystem.getInstance_DIMENSIONLESS();
    VCUnitDefinition unit_modelTime = modelUnitSystem.getTimeUnit();
    LocalParameter delayParam = parameterContext.new LocalParameter(BioEventParameterType.TriggerDelay.getDefaultName(), new Expression(0.0), BioEventParameterType.TriggerDelay, unit_modelTime, BioEventParameterType.TriggerDelay.getDescription());
    LocalParameter generatedGeneralTriggerParam = parameterContext.new LocalParameter(BioEventParameterType.GeneralTriggerFunction.getDefaultName(), null, BioEventParameterType.GeneralTriggerFunction, unit_Dimensionless, BioEventParameterType.GeneralTriggerFunction.getDescription());
    switch(triggerType) {
        case GeneralTrigger:
            {
                try {
                    parameterContext.setLocalParameters(new LocalParameter[] { delayParam, parameterContext.new LocalParameter(BioEventParameterType.GeneralTriggerFunction.getDefaultName(), new Expression(0.0), BioEventParameterType.GeneralTriggerFunction, unit_Dimensionless, BioEventParameterType.GeneralTriggerFunction.getDescription()) });
                } catch (PropertyVetoException | ExpressionBindingException e) {
                    e.printStackTrace();
                    throw new RuntimeException(e.getMessage(), e);
                }
                break;
            }
        case ObservableAboveThreshold:
        case ObservableBelowThreshold:
            {
                try {
                    parameterContext.setLocalParameters(new LocalParameter[] { delayParam, generatedGeneralTriggerParam, parameterContext.new LocalParameter(BioEventParameterType.Observable.getDefaultName(), null, BioEventParameterType.Observable, unit_TBD, BioEventParameterType.Observable.getDescription()), parameterContext.new LocalParameter(BioEventParameterType.Threshold.getDefaultName(), new Expression(1.0), BioEventParameterType.Threshold, unit_TBD, BioEventParameterType.Threshold.getDescription()) });
                } catch (PropertyVetoException | ExpressionBindingException e) {
                    e.printStackTrace();
                    throw new RuntimeException(e.getMessage(), e);
                }
                break;
            }
        case SingleTriggerTime:
            {
                try {
                    parameterContext.setLocalParameters(new LocalParameter[] { delayParam, generatedGeneralTriggerParam, parameterContext.new LocalParameter(BioEventParameterType.SingleTriggerTime.getDefaultName(), new Expression(1.0), BioEventParameterType.SingleTriggerTime, unit_modelTime, BioEventParameterType.SingleTriggerTime.getDescription()) });
                } catch (PropertyVetoException | ExpressionBindingException e) {
                    e.printStackTrace();
                    throw new RuntimeException(e.getMessage(), e);
                }
                break;
            }
        case LinearRangeTimes:
        case LogRangeTimes:
            {
                try {
                    parameterContext.setLocalParameters(new LocalParameter[] { delayParam, generatedGeneralTriggerParam, parameterContext.new LocalParameter(BioEventParameterType.RangeMinTime.getDefaultName(), new Expression(1.0), BioEventParameterType.RangeMinTime, unit_modelTime, BioEventParameterType.RangeMinTime.getDescription()), parameterContext.new LocalParameter(BioEventParameterType.RangeMaxTime.getDefaultName(), new Expression(10.0), BioEventParameterType.RangeMaxTime, unit_modelTime, BioEventParameterType.RangeMaxTime.getDescription()), parameterContext.new LocalParameter(BioEventParameterType.RangeNumTimes.getDefaultName(), new Expression(9), BioEventParameterType.RangeNumTimes, unit_modelTime, BioEventParameterType.RangeNumTimes.getDescription()) });
                } catch (PropertyVetoException | ExpressionBindingException e) {
                    e.printStackTrace();
                    throw new RuntimeException(e.getMessage(), e);
                }
                break;
            }
        case ListOfTimes:
            {
                try {
                    parameterContext.setLocalParameters(new LocalParameter[] { delayParam, generatedGeneralTriggerParam, parameterContext.new LocalParameter(BioEventParameterType.TimeListItem.getDefaultName() + "0", new Expression(1.0), BioEventParameterType.TimeListItem, unit_modelTime, BioEventParameterType.TimeListItem.getDescription()), parameterContext.new LocalParameter(BioEventParameterType.TimeListItem.getDefaultName() + "1", new Expression(2.0), BioEventParameterType.TimeListItem, unit_modelTime, BioEventParameterType.TimeListItem.getDescription()), parameterContext.new LocalParameter(BioEventParameterType.TimeListItem.getDefaultName() + "2", new Expression(3.0), BioEventParameterType.TimeListItem, unit_modelTime, BioEventParameterType.TimeListItem.getDescription()) });
                } catch (PropertyVetoException | ExpressionBindingException e) {
                    e.printStackTrace();
                    throw new RuntimeException(e.getMessage(), e);
                }
                break;
            }
        default:
            {
                throw new RuntimeException("unsupported rule-based kinetic law " + triggerType);
            }
    }
}

Example 42 with VCUnitDefinition

use of cbit.vcell.units.VCUnitDefinition in project vcell by virtualcell.

the class DistributedKinetics method getInwardCurrentDensity.

private Expression getInwardCurrentDensity() throws ExpressionException, PropertyVetoException {
    // 
    // lumped kinetics always have same units (molecules/s) or (pA) whether used in a FluxReaction or a SimpleReaction
    // 
    // CurrentMagnitude = reactionRate * valence * F * unitFactor
    // 
    // for FluxReaction
    // 
    Model model = getReactionStep().getModel();
    Expression F = getSymbolExpression(model.getFARADAY_CONSTANT());
    Expression reactionRate = getSymbolExpression(getReactionRateParameter());
    Expression z = getSymbolExpression(getChargeValenceParameter());
    Expression tempInwardCurrentDensityExpression = Expression.mult(z, F, reactionRate);
    VCUnitDefinition tempRateUnit = getReactionRateParameter().getUnitDefinition().multiplyBy(model.getFARADAY_CONSTANT().getUnitDefinition()).multiplyBy(getChargeValenceParameter().getUnitDefinition());
    VCUnitDefinition desiredUnit = getCurrentDensityParameter().getUnitDefinition();
    Expression unitFactorExp = getElectricalUnitFactor(desiredUnit.divideBy(tempRateUnit));
    if (unitFactorExp != null) {
        tempInwardCurrentDensityExpression = Expression.mult(tempInwardCurrentDensityExpression, unitFactorExp);
    }
    if (hasOutwardFlux()) {
        tempInwardCurrentDensityExpression = Expression.negate(tempInwardCurrentDensityExpression);
    }
    return tempInwardCurrentDensityExpression;
}

Example 43 with VCUnitDefinition

use of cbit.vcell.units.VCUnitDefinition in project vcell by virtualcell.

the class DistributedKinetics method updateInwardCurrentDensityFromReactionRate.

protected void updateInwardCurrentDensityFromReactionRate() throws ExpressionException, PropertyVetoException {
    KineticsParameter rateParmInput = getReactionRateParameter();
    KineticsParameter currentParm = getCurrentDensityParameter();
    if (currentParm == null && rateParmInput == null) {
        return;
    }
    if (getReactionStep().getPhysicsOptions() == ReactionStep.PHYSICS_MOLECULAR_AND_ELECTRICAL) {
        Expression tempCurrentDensityExpression = getInwardCurrentDensity();
        if (currentParm == null) {
            Model model = getReactionStep().getModel();
            VCUnitDefinition currentUnit = model.getUnitSystem().getCurrentDensityUnit();
            addKineticsParameter(new KineticsParameter(getDefaultParameterName(ROLE_CurrentDensity), tempCurrentDensityExpression, ROLE_CurrentDensity, currentUnit));
        } else {
            currentParm.setExpression(tempCurrentDensityExpression);
        }
    } else {
        if (currentParm != null && !currentParm.getExpression().isZero()) {
            // removeKineticsParameter(rateParm);
            currentParm.setExpression(new Expression(0.0));
        }
        KineticsParameter unitParam = getKineticsParameterFromRole(ROLE_ElectricalUnitFactor);
        if (unitParam != null) {
            removeKineticsParameter(unitParam);
        }
    }
}

Example 44 with VCUnitDefinition

use of cbit.vcell.units.VCUnitDefinition in project vcell by virtualcell.

the class DistributedKinetics method updateReactionRatesFromInwardCurrentDensity.

protected void updateReactionRatesFromInwardCurrentDensity() throws ExpressionException, PropertyVetoException {
    KineticsParameter currentParm = getCurrentDensityParameter();
    KineticsParameter rateParm = getReactionRateParameter();
    if (currentParm == null && rateParm == null) {
        return;
    }
    if (getReactionStep().getPhysicsOptions() == ReactionStep.PHYSICS_MOLECULAR_AND_ELECTRICAL) {
        Expression tempRateExpression = getReactionRate();
        if (rateParm == null) {
            Model model = getReactionStep().getModel();
            VCUnitDefinition rateUnit = null;
            if (getReactionStep() instanceof SimpleReaction) {
                rateUnit = model.getUnitSystem().getMembraneReactionRateUnit();
            } else if (getReactionStep() instanceof FluxReaction) {
                rateUnit = model.getUnitSystem().getFluxReactionUnit();
            } else {
                rateUnit = model.getUnitSystem().getInstance_TBD();
            }
            addKineticsParameter(new KineticsParameter(getDefaultParameterName(ROLE_LumpedReactionRate), tempRateExpression, ROLE_LumpedReactionRate, rateUnit));
        } else {
            rateParm.setExpression(tempRateExpression);
        }
    } else {
        if (rateParm != null && !rateParm.getExpression().isZero()) {
            // removeKineticsParameter(rateParm);
            rateParm.setExpression(new Expression(0.0));
        }
        KineticsParameter unitParam = getKineticsParameterFromRole(ROLE_ElectricalUnitFactor);
        if (unitParam != null) {
            removeKineticsParameter(unitParam);
        }
    }
}

Example 45 with VCUnitDefinition

use of cbit.vcell.units.VCUnitDefinition in project vcell by virtualcell.

the class Kinetics method resolveUndefinedUnits.

/**
 * Insert the method's description here.
 * Creation date: (4/13/2004 3:09:21 PM)
 */
public void resolveUndefinedUnits() {
    // 
    if (!bResolvingUnits) {
        bResolvingUnits = true;
        try {
            if (getReactionStep().getModel() != null) {
                ModelUnitSystem modelUnitSystem = getReactionStep().getModel().getUnitSystem();
                boolean bAnyTBDUnits = false;
                for (int i = 0; i < fieldKineticsParameters.length; i++) {
                    if (fieldKineticsParameters[i].getUnitDefinition() == null) {
                        // not ready to resolve units yet
                        return;
                    } else if (fieldKineticsParameters[i].getUnitDefinition().isTBD()) {
                        bAnyTBDUnits = true;
                    }
                }
                // 
                if (bAnyTBDUnits) {
                    VCUnitEvaluator unitEvaluator = new VCUnitEvaluator(modelUnitSystem);
                    VCUnitDefinition[] vcUnitDefinitions = unitEvaluator.suggestUnitDefinitions(fieldKineticsParameters);
                    for (int i = 0; i < fieldKineticsParameters.length; i++) {
                        if (!fieldKineticsParameters[i].getUnitDefinition().isEquivalent(vcUnitDefinitions[i])) {
                            fieldKineticsParameters[i].setUnitDefinition(vcUnitDefinitions[i]);
                        }
                    }
                // System.out.println("successfully completed Kinetics.resolveUndefinedUnits() for ReactionStep '"+getReactionStep()+"'");
                }
            }
        } catch (Exception e) {
            if (lg.isEnabledFor(Level.WARN)) {
                lg.warn("Kinetics.resolveUndefinedUnits(): EXCEPTION: " + e.getMessage());
            }
        } finally {
            bResolvingUnits = false;
        }
    }
}