Examples with ConstraintContainerImpl cbit.vcell.constraints.ConstraintContainerImpl used on opensource projects

Example 1 with ConstraintContainerImpl

use of cbit.vcell.constraints.ConstraintContainerImpl in project vcell by virtualcell.

the class ConstraintsGraphModel method setConstraintContainerImpl.

public void setConstraintContainerImpl(ConstraintContainerImpl constraintContainerImpl) {
    ConstraintContainerImpl oldValue = fieldConstraintContainerImpl;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(this);
        GeneralConstraint[] oldConstraints = oldValue.getGeneralConstraints();
        for (int i = 0; i < oldConstraints.length; i++) {
            oldConstraints[i].removePropertyChangeListener(this);
        }
        SimpleBounds[] oldSimpleBounds = oldValue.getSimpleBounds();
        for (int i = 0; i < oldSimpleBounds.length; i++) {
            oldSimpleBounds[i].removePropertyChangeListener(this);
        }
    }
    fieldConstraintContainerImpl = constraintContainerImpl;
    if (fieldConstraintContainerImpl != null) {
        fieldConstraintContainerImpl.addPropertyChangeListener(this);
        GeneralConstraint[] newConstraints = fieldConstraintContainerImpl.getGeneralConstraints();
        for (int i = 0; i < newConstraints.length; i++) {
            newConstraints[i].addPropertyChangeListener(this);
        }
        SimpleBounds[] newSimpleBounds = fieldConstraintContainerImpl.getSimpleBounds();
        for (int i = 0; i < newSimpleBounds.length; i++) {
            newSimpleBounds[i].addPropertyChangeListener(this);
        }
    }
    firePropertyChange("constraintContainerImpl", oldValue, constraintContainerImpl);
    refreshAll();
}

Example 2 with ConstraintContainerImpl

use of cbit.vcell.constraints.ConstraintContainerImpl in project vcell by virtualcell.

the class SimpleBoundsTableModel method setConstraintContainerImpl.

/**
 * Sets the constraintContainerImpl property (cbit.vcell.constraints.ConstraintContainerImpl) value.
 * @param constraintContainerImpl The new value for the property.
 * @see #getConstraintContainerImpl
 */
public void setConstraintContainerImpl(ConstraintContainerImpl constraintContainerImpl) {
    ConstraintContainerImpl oldValue = fieldConstraintContainerImpl;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(this);
        SimpleBounds[] oldBounds = oldValue.getSimpleBounds();
        for (int i = 0; i < oldBounds.length; i++) {
            oldBounds[i].removePropertyChangeListener(this);
        }
    }
    fieldConstraintContainerImpl = constraintContainerImpl;
    firePropertyChange("constraintContainerImpl", oldValue, constraintContainerImpl);
    if (constraintContainerImpl != null) {
        constraintContainerImpl.addPropertyChangeListener(this);
        SimpleBounds[] newBounds = constraintContainerImpl.getSimpleBounds();
        for (int i = 0; i < newBounds.length; i++) {
            newBounds[i].addPropertyChangeListener(this);
        }
    }
}

Example 3 with ConstraintContainerImpl

use of cbit.vcell.constraints.ConstraintContainerImpl in project vcell by virtualcell.

the class ApplicationConstraintsGenerator method steadyStateFromApplication.

/**
 * Insert the method's description here.
 * Creation date: (6/26/01 8:25:55 AM)
 * @return cbit.vcell.constraints.ConstraintContainerImpl
 */
public static ConstraintContainerImpl steadyStateFromApplication(SimulationContext simContext, double tolerance) {
    try {
        ConstraintContainerImpl ccImpl = new ConstraintContainerImpl();
        // ====================
        // add physical limits
        // ====================
        // 
        // no negative concentrations
        // 
        cbit.vcell.model.Model model = simContext.getModel();
        cbit.vcell.model.SpeciesContext[] speciesContexts = model.getSpeciesContexts();
        for (int i = 0; i < speciesContexts.length; i++) {
            ccImpl.addSimpleBound(new SimpleBounds(speciesContexts[i].getName(), new RealInterval(0, Double.POSITIVE_INFINITY), AbstractConstraint.PHYSICAL_LIMIT, "non-negative concentration"));
        }
        for (int i = 0; i < speciesContexts.length; i++) {
            SpeciesContextSpecParameter initParam = (simContext.getReactionContext().getSpeciesContextSpec(speciesContexts[i])).getInitialConditionParameter();
            if (initParam != null) {
                double initialValue = initParam.getExpression().evaluateConstant();
                double lowInitialValue = Math.min(initialValue / tolerance, initialValue * tolerance);
                double highInitialValue = Math.max(initialValue / tolerance, initialValue * tolerance);
                ccImpl.addSimpleBound(new SimpleBounds(speciesContexts[i].getName(), new RealInterval(lowInitialValue, highInitialValue), AbstractConstraint.MODELING_ASSUMPTION, "close to specified \"initialCondition\""));
            }
        }
        // =========================
        // add modeling assumptions
        // =========================
        // 
        // mass action forward and reverse rates should be non-negative
        // 
        cbit.vcell.model.ReactionStep[] reactionSteps = model.getReactionSteps();
        for (int i = 0; i < reactionSteps.length; i++) {
            Kinetics kinetics = reactionSteps[i].getKinetics();
            if (kinetics instanceof MassActionKinetics) {
                Expression forwardRateConstraintExp = new Expression(((MassActionKinetics) kinetics).getForwardRateParameter().getExpression().infix() + ">=0");
                forwardRateConstraintExp = getSteadyStateExpression(forwardRateConstraintExp);
                if (!forwardRateConstraintExp.compareEqual(new Expression(1.0))) {
                    ccImpl.addGeneralConstraint(new GeneralConstraint(forwardRateConstraintExp, AbstractConstraint.MODELING_ASSUMPTION, "non-negative forward rate"));
                }
                Expression reverseRateConstraintExp = new Expression(((MassActionKinetics) kinetics).getReverseRateParameter().getExpression().infix() + ">=0");
                reverseRateConstraintExp = getSteadyStateExpression(reverseRateConstraintExp);
                if (!reverseRateConstraintExp.compareEqual(new Expression(1.0))) {
                    ccImpl.addGeneralConstraint(new GeneralConstraint(reverseRateConstraintExp, AbstractConstraint.MODELING_ASSUMPTION, "non-negative reverse rate"));
                }
            }
            KineticsParameter authoritativeParameter = kinetics.getAuthoritativeParameter();
            Expression kineticRateConstraintExp = new Expression(authoritativeParameter.getName() + "==" + authoritativeParameter.getExpression().infix());
            kineticRateConstraintExp = getSteadyStateExpression(kineticRateConstraintExp);
            if (!kineticRateConstraintExp.compareEqual(new Expression(1.0))) {
                ccImpl.addGeneralConstraint(new GeneralConstraint(kineticRateConstraintExp, AbstractConstraint.MODELING_ASSUMPTION, "definition"));
            }
        }
        // 
        try {
            simContext.setMathDescription(simContext.createNewMathMapping().getMathDescription());
        } catch (Throwable e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("cannot create mathDescription");
        }
        MathDescription mathDesc = simContext.getMathDescription();
        if (mathDesc.getGeometry().getDimension() > 0) {
            throw new RuntimeException("spatial simulations not yet supported");
        }
        CompartmentSubDomain subDomain = (CompartmentSubDomain) mathDesc.getSubDomains().nextElement();
        java.util.Enumeration<Equation> enumEquations = subDomain.getEquations();
        while (enumEquations.hasMoreElements()) {
            Equation equation = (Equation) enumEquations.nextElement();
            Expression rateConstraintExp = new Expression(equation.getRateExpression().infix() + "==0");
            rateConstraintExp = getSteadyStateExpression(rateConstraintExp);
            if (!rateConstraintExp.compareEqual(new Expression(1.0))) {
                // not a trivial constraint (always true)
                ccImpl.addGeneralConstraint(new GeneralConstraint(rateConstraintExp, AbstractConstraint.PHYSICAL_LIMIT, "definition of steady state"));
            }
        }
        // 
        for (int i = 0; i < reactionSteps.length; i++) {
            Kinetics kinetics = reactionSteps[i].getKinetics();
            Kinetics.KineticsParameter[] parameters = kinetics.getKineticsParameters();
            for (int j = 0; j < parameters.length; j++) {
                Expression exp = parameters[j].getExpression();
                if (exp.getSymbols() == null || exp.getSymbols().length == 0) {
                    // 
                    try {
                        double constantValue = exp.evaluateConstant();
                        double lowValue = Math.min(constantValue / tolerance, constantValue * tolerance);
                        double highValue = Math.max(constantValue / tolerance, constantValue * tolerance);
                        RealInterval interval = new RealInterval(lowValue, highValue);
                        ccImpl.addSimpleBound(new SimpleBounds(parameters[j].getName(), interval, AbstractConstraint.MODELING_ASSUMPTION, "parameter close to model default"));
                    } catch (cbit.vcell.parser.ExpressionException e) {
                        System.out.println("error evaluating parameter " + parameters[j].getName() + " in reaction step " + reactionSteps[i].getName());
                    }
                } else {
                    Expression parameterDefinitionExp = new Expression(parameters[j].getName() + "==" + parameters[j].getExpression().infix());
                    ccImpl.addGeneralConstraint(new GeneralConstraint(getSteadyStateExpression(parameterDefinitionExp), AbstractConstraint.MODELING_ASSUMPTION, "parameter definition"));
                }
            }
        }
        ccImpl.addSimpleBound(new SimpleBounds(model.getFARADAY_CONSTANT().getName(), new RealInterval(model.getFARADAY_CONSTANT().getExpression().evaluateConstant()), AbstractConstraint.PHYSICAL_LIMIT, "Faraday's constant"));
        ccImpl.addSimpleBound(new SimpleBounds(model.getTEMPERATURE().getName(), new RealInterval(300), AbstractConstraint.PHYSICAL_LIMIT, "Absolute Temperature Kelvin"));
        ccImpl.addSimpleBound(new SimpleBounds(model.getGAS_CONSTANT().getName(), new RealInterval(model.getGAS_CONSTANT().getExpression().evaluateConstant()), AbstractConstraint.PHYSICAL_LIMIT, "ideal gas constant"));
        ccImpl.addSimpleBound(new SimpleBounds(model.getKMILLIVOLTS().getName(), new RealInterval(model.getKMILLIVOLTS().getExpression().evaluateConstant()), AbstractConstraint.PHYSICAL_LIMIT, "ideal gas constant"));
        // 
        // add K_fluxs
        // 
        java.util.Enumeration<Variable> enumVars = mathDesc.getVariables();
        while (enumVars.hasMoreElements()) {
            Variable var = (Variable) enumVars.nextElement();
            if (var.getName().startsWith("Kflux_") && var instanceof Function) {
                Expression kfluxExp = new Expression(((Function) var).getExpression());
                kfluxExp.bindExpression(mathDesc);
                kfluxExp = MathUtilities.substituteFunctions(kfluxExp, mathDesc);
                kfluxExp = kfluxExp.flatten();
                ccImpl.addSimpleBound(new SimpleBounds(var.getName(), new RealInterval(kfluxExp.evaluateConstant()), AbstractConstraint.MODELING_ASSUMPTION, "flux conversion factor"));
            }
        }
        return ccImpl;
    } catch (cbit.vcell.parser.ExpressionException e) {
        e.printStackTrace(System.out);
        return null;
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        return null;
    }
}

Example 4 with ConstraintContainerImpl

use of cbit.vcell.constraints.ConstraintContainerImpl in project vcell by virtualcell.

the class ApplicationConstraintsGenerator method fromApplication.

/**
 * Insert the method's description here.
 * Creation date: (6/26/01 8:25:55 AM)
 * @return cbit.vcell.constraints.ConstraintContainerImpl
 */
public static ConstraintContainerImpl fromApplication(SimulationContext simContext) {
    try {
        ConstraintContainerImpl ccImpl = new ConstraintContainerImpl();
        // ====================
        // add physical limits
        // ====================
        // 
        // no negative concentrations
        // 
        cbit.vcell.model.Model model = simContext.getModel();
        cbit.vcell.model.SpeciesContext[] speciesContexts = model.getSpeciesContexts();
        for (int i = 0; i < speciesContexts.length; i++) {
            ccImpl.addSimpleBound(new SimpleBounds(speciesContexts[i].getName(), new RealInterval(0, Double.POSITIVE_INFINITY), AbstractConstraint.PHYSICAL_LIMIT, "non-negative concentration"));
        }
        for (int i = 0; i < speciesContexts.length; i++) {
            SpeciesContextSpecParameter initParam = (simContext.getReactionContext().getSpeciesContextSpec(speciesContexts[i])).getInitialConditionParameter();
            if (initParam != null) {
                double initialValue = initParam.getExpression().evaluateConstant();
                ccImpl.addSimpleBound(new SimpleBounds(speciesContexts[i].getName(), new RealInterval(initialValue), AbstractConstraint.MODELING_ASSUMPTION, "specified \"initialCondition\""));
            }
        }
        // =========================
        // add modeling assumptions
        // =========================
        // 
        // mass action forward and reverse rates should be non-negative
        // 
        cbit.vcell.model.ReactionStep[] reactionSteps = model.getReactionSteps();
        for (int i = 0; i < reactionSteps.length; i++) {
            Kinetics kinetics = reactionSteps[i].getKinetics();
            if (kinetics instanceof MassActionKinetics) {
                Expression forwardRateConstraintExp = new Expression(((MassActionKinetics) kinetics).getForwardRateParameter().getExpression().infix() + ">=0");
                forwardRateConstraintExp = getSteadyStateExpression(forwardRateConstraintExp);
                if (!forwardRateConstraintExp.compareEqual(new Expression(1.0))) {
                    ccImpl.addGeneralConstraint(new GeneralConstraint(forwardRateConstraintExp, AbstractConstraint.MODELING_ASSUMPTION, "non-negative forward rate"));
                }
                Expression reverseRateConstraintExp = new Expression(((MassActionKinetics) kinetics).getReverseRateParameter().getExpression().infix() + ">=0");
                reverseRateConstraintExp = getSteadyStateExpression(reverseRateConstraintExp);
                if (!reverseRateConstraintExp.compareEqual(new Expression(1.0))) {
                    ccImpl.addGeneralConstraint(new GeneralConstraint(reverseRateConstraintExp, AbstractConstraint.MODELING_ASSUMPTION, "non-negative reverse rate"));
                }
            }
            KineticsParameter authoritativeParameter = kinetics.getAuthoritativeParameter();
            Expression kineticRateConstraintExp = new Expression(authoritativeParameter.getName() + "==" + authoritativeParameter.getExpression().infix());
            kineticRateConstraintExp = getSteadyStateExpression(kineticRateConstraintExp);
            if (!kineticRateConstraintExp.compareEqual(new Expression(1.0))) {
                ccImpl.addGeneralConstraint(new GeneralConstraint(kineticRateConstraintExp, AbstractConstraint.MODELING_ASSUMPTION, "definition"));
            }
        }
        // 
        for (int i = 0; i < reactionSteps.length; i++) {
            Kinetics kinetics = reactionSteps[i].getKinetics();
            Kinetics.KineticsParameter[] parameters = kinetics.getKineticsParameters();
            for (int j = 0; j < parameters.length; j++) {
                Expression exp = parameters[j].getExpression();
                if (exp.getSymbols() == null || exp.getSymbols().length == 0) {
                    // 
                    try {
                        double constantValue = exp.evaluateConstant();
                        RealInterval interval = new RealInterval(constantValue);
                        ccImpl.addSimpleBound(new SimpleBounds(parameters[j].getName(), interval, AbstractConstraint.MODELING_ASSUMPTION, "model value"));
                    } catch (cbit.vcell.parser.ExpressionException e) {
                        System.out.println("error evaluating parameter " + parameters[j].getName() + " in reaction step " + reactionSteps[i].getName());
                    }
                } else {
                    Expression parameterDefinitionExp = new Expression(parameters[j].getName() + "==" + parameters[j].getExpression().infix());
                    parameterDefinitionExp = getSteadyStateExpression(parameterDefinitionExp);
                    if (!parameterDefinitionExp.compareEqual(new Expression(1.0))) {
                        ccImpl.addGeneralConstraint(new GeneralConstraint(parameterDefinitionExp, AbstractConstraint.MODELING_ASSUMPTION, "parameter definition"));
                    }
                }
            }
        }
        ccImpl.addSimpleBound(new SimpleBounds(model.getFARADAY_CONSTANT().getName(), new RealInterval(model.getFARADAY_CONSTANT().getExpression().evaluateConstant()), AbstractConstraint.PHYSICAL_LIMIT, "Faraday's constant"));
        ccImpl.addSimpleBound(new SimpleBounds(model.getTEMPERATURE().getName(), new RealInterval(300), AbstractConstraint.PHYSICAL_LIMIT, "Absolute Temperature Kelvin"));
        ccImpl.addSimpleBound(new SimpleBounds(model.getGAS_CONSTANT().getName(), new RealInterval(model.getGAS_CONSTANT().getExpression().evaluateConstant()), AbstractConstraint.PHYSICAL_LIMIT, "ideal gas constant"));
        ccImpl.addSimpleBound(new SimpleBounds(model.getKMILLIVOLTS().getName(), new RealInterval(model.getKMILLIVOLTS().getExpression().evaluateConstant()), AbstractConstraint.PHYSICAL_LIMIT, "ideal gas constant"));
        return ccImpl;
    } catch (cbit.vcell.parser.ExpressionException e) {
        e.printStackTrace(System.out);
        return null;
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        return null;
    }
}

Example 5 with ConstraintContainerImpl

use of cbit.vcell.constraints.ConstraintContainerImpl in project vcell by virtualcell.

the class GeneralConstraintsTableModel method setConstraintContainerImpl.

/**
 * Sets the constraintContainerImpl property (cbit.vcell.constraints.ConstraintContainerImpl) value.
 * @param constraintContainerImpl The new value for the property.
 * @see #getConstraintContainerImpl
 */
public void setConstraintContainerImpl(ConstraintContainerImpl constraintContainerImpl) {
    ConstraintContainerImpl oldValue = fieldConstraintContainerImpl;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(this);
        GeneralConstraint[] oldConstraints = oldValue.getGeneralConstraints();
        for (int i = 0; i < oldConstraints.length; i++) {
            oldConstraints[i].removePropertyChangeListener(this);
        }
    }
    fieldConstraintContainerImpl = constraintContainerImpl;
    firePropertyChange("constraintContainerImpl", oldValue, constraintContainerImpl);
    if (constraintContainerImpl != null) {
        constraintContainerImpl.addPropertyChangeListener(this);
        GeneralConstraint[] newConstraints = constraintContainerImpl.getGeneralConstraints();
        for (int i = 0; i < newConstraints.length; i++) {
            newConstraints[i].addPropertyChangeListener(this);
        }
    }
}