Examples with Expression cbit.vcell.parser.Expression used on opensource projects

Example 66 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class SBPAXParameterExtractor method extractParameter.

public static Map<SBOTerm, ModelParameter> extractParameter(ReactionStep reaction, SBMeasurable measurable) throws PropertyVetoException {
    Map<SBOTerm, ModelParameter> sboToParameters = new HashMap<SBOTerm, ModelParameter>();
    Set<SBOTerm> sboTerms = SBPAXSBOExtractor.extractSBOTerms(measurable);
    String symbol = null;
    VCUnitDefinition targetUnit = null;
    Model model = reaction.getModel();
    ModelUnitSystem modelUnitSystem = model.getUnitSystem();
    Set<SBOTerm> termsWithUnituM = SetUtil.newSet(SBOList.sbo0000027MichaelisConstant, SBOList.sbo0000322MichaelisConstantForSubstrate);
    for (SBOTerm sboTerm : sboTerms) {
        if (termsWithUnituM.contains(sboTerm)) {
            targetUnit = modelUnitSystem.getVolumeConcentrationUnit();
        // targetUnit = VCUnitDefinition.UNIT_uM;
        }
        if (StringUtil.notEmpty(sboTerm.getSymbol())) {
            symbol = sboTerm.getSymbol();
        }
        for (int i = 0; i < symbol.length(); ++i) {
            char charAt = symbol.charAt(i);
            if (!Character.isJavaIdentifierPart(charAt)) {
                symbol = symbol.replace(charAt, '_');
            }
        }
    }
    VCUnitDefinition unit = UOMEUnitExtractor.extractVCUnitDefinition(measurable, modelUnitSystem);
    double conversionFactor = 1.0;
    if (targetUnit != null && unit != null && unit != modelUnitSystem.getInstance_TBD() && !targetUnit.equals(unit)) {
        // if(unit.equals(VCUnitDefinition.UNIT_M) && targetUnit.equals(VCUnitDefinition.UNIT_uM)) {
        if (unit.isCompatible(targetUnit)) {
            conversionFactor = unit.convertTo(conversionFactor, targetUnit);
            unit = targetUnit;
        }
    }
    ArrayList<Double> numbers = measurable.getNumber();
    if (StringUtil.isEmpty(symbol)) {
        symbol = "p" + (++nParameter);
    }
    for (Double number : numbers) {
        String parameterName = symbol + "_" + reaction.getName();
        if (model.getModelParameter(parameterName) != null) {
            int count = 0;
            while (model.getModelParameter(parameterName + "_" + count) != null) {
                ++count;
            }
            parameterName = parameterName + "_" + count;
        }
        ModelParameter parameter = model.new ModelParameter(parameterName, new Expression(conversionFactor * number.doubleValue()), Model.ROLE_UserDefined, unit);
        model.addModelParameter(parameter);
        for (SBOTerm sboTerm : sboTerms) {
            sboToParameters.put(sboTerm, parameter);
        }
    }
    return sboToParameters;
}

Example 67 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class RefinementLevel method setRoiExpression.

public void setRoiExpression(String roiExp) throws ExpressionException {
    Expression exp = null;
    if (roiExp != null) {
        roiExp = roiExp.trim();
        if (roiExp.length() > 0) {
            exp = new Expression(roiExp);
            exp.bindExpression(new SimpleSymbolTable(new String[] { "x", "y", "z" }));
        }
    }
    this.roiExpression = exp;
}

Example 68 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class SimulationContext method createRateRule.

public RateRule createRateRule(SymbolTableEntry varSTE) throws PropertyVetoException {
    String rateRuleName = getFreeRateRuleName();
    RateRule rateRule = new RateRule(rateRuleName, varSTE, new Expression(0.0), this);
    return addRateRule(rateRule);
}

Example 69 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class SimulationContext method createSimulationContextParameter.

public SimulationContextParameter createSimulationContextParameter() {
    String name = "appParm0";
    while (getSimulationContextParameter(name) != null) {
        name = TokenMangler.getNextEnumeratedToken(name);
    }
    Expression expression = new Expression(1.0);
    int role = SimulationContext.ROLE_UserDefined;
    VCUnitDefinition unit = getModel().getUnitSystem().getInstance_DIMENSIONLESS();
    SimulationContextParameter parameter = new SimulationContextParameter(name, expression, role, unit);
    try {
        addSimulationContextParameter(parameter);
        return parameter;
    } catch (PropertyVetoException e) {
        e.printStackTrace();
        throw new RuntimeException("error creating new application parameter: " + e.getMessage(), e);
    }
}

Example 70 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class SpeciesContextSpec method convertParticlesToConcentration.

public Expression convertParticlesToConcentration(Expression iniParticles) throws ExpressionException, MappingException {
    Expression iniConcentrationExpr = null;
    Structure structure = getSpeciesContext().getStructure();
    double structSize = computeStructureSize();
    if (structure instanceof Membrane) {
        // iniConcentration(molecules/um2) = particles/size(um2)
        try {
            iniConcentrationExpr = new Expression((iniParticles.evaluateConstant() * 1.0) / structSize);
        } catch (ExpressionException e) {
            iniConcentrationExpr = Expression.div(iniParticles, new Expression(structSize)).flatten();
        }
    } else {
        // convert concentration(particles/volume) to number of particles
        // particles = [iniParticles(uM)/size(um3)]*KMOLE
        // @Note : 'kMole' variable here is used only as a var name, it does not represent the previously known ReservedSymbol KMOLE.
        ModelUnitSystem modelUnitSystem = getSimulationContext().getModel().getUnitSystem();
        VCUnitDefinition stochasticToVolSubstance = modelUnitSystem.getVolumeSubstanceUnit().divideBy(modelUnitSystem.getStochasticSubstanceUnit());
        double stochasticToVolSubstanceScale = stochasticToVolSubstance.getDimensionlessScale().doubleValue();
        try {
            iniConcentrationExpr = new Expression((iniParticles.evaluateConstant() * stochasticToVolSubstanceScale / structSize));
        } catch (ExpressionException e) {
            Expression numeratorExpr = Expression.mult(iniParticles, new Expression(stochasticToVolSubstanceScale));
            Expression denominatorExpr = new Expression(structSize);
            iniConcentrationExpr = Expression.div(numeratorExpr, denominatorExpr).flatten();
        }
    }
    return iniConcentrationExpr;
}