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

Example 6 with HMM_IRRKinetics

use of cbit.vcell.model.HMM_IRRKinetics 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 7 with HMM_IRRKinetics

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

the class SBPAXKineticsExtractor method setMichaelisForwardParam.

private static void setMichaelisForwardParam(ReactionStep reaction, SBOParam kMichaelis, Kinetics kinetics) throws ExpressionException, PropertyVetoException {
    if (kMichaelis != null) {
        KineticsParameter fwdParam = ((HMM_IRRKinetics) kinetics).getKmParameter();
        kinetics.setParameterValue(fwdParam, new Expression(kMichaelis.getNumber()));
        String unitF = SBOParam.formatUnit(kMichaelis.getUnit());
        VCUnitDefinition fwdUnit = reaction.getModel().getUnitSystem().getInstance(unitF);
        fwdParam.setUnitDefinition(fwdUnit);
    }
}