public void setup() {
clear();
Protein protein = gene.getProtein();
if (aminoAcid != null) addSubstance(aminoAcid, -1.0);
addSubstance(gene.getRibosome(), 0.0);
addSubstance(protein, 3.0 / (gene.getLength()));
rateExpression =
DMath.multiply(
gene.getRibosome().getElongationRate(),
DMath.min(
DMath.multiply(
gene.getRibosome(),
DMath.divide(
DMath.multiply(gene.getKTranslation(), gene.getRna()),
gene.getRibosome().getTotalTranslationActivity())),
//
// the maximum # of ribosomes that can be allocated to a
// gene
// is the gene length divided by the ribosome spacing
// requirement.
//
DMath.divide(
DMath.multiply(new Constant(gene.getLength() / 3.0), gene.getRna()),
gene.getRibosome().getSpacing())));
//
// hack: used to make sure that when aminoAcid is set, the rate should
// be zero
// when amino acids are all consumed.
//
// better implementation is by using the MichaelisMenten reaction
// scheme, but
// it needs an additional parameter.
//
if (aminoAcid != null)
rateExpression =
DMath.multiply(
rateExpression, DMath.divide(aminoAcid, DMath.sum(aminoAcid, new Constant(1e4))));
}