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))));
}
public DMatrix vectorNorm() {
DMatrix m = DMath.createMatrix(this.rows(), this.columns(), this.toArray());
DMatrix Denom = this.mul(this).sumColumns();
Denom.sqrti();
return m.divRows(Denom);
}
public DMatrix sumColumns() {
DMatrix sum = DMath.createMatrix(this.rows, 1);
DMatrix multiplier = DMath.createOnesMatrix(this.columns, 1);
SimpleCuBlas.gemm(false, false, this, multiplier, sum, 1.0, 0.0);
return sum;
}
public DMatrix sumRows(int startRow, int howMany) {
DMatrix sum = DMath.createMatrix(1, this.columns());
DMatrix multiplier = DMath.createOnesMatrix(1, howMany);
SimpleCuBlas.cust_gemv(false, this, multiplier, sum, 1.0, 0.0, startRow, howMany);
return sum;
}
public DMatrix sumRows() {
DMatrix sum = DMath.createZerosMatrix(1, this.columns());
DMatrix multiplier = DMath.createOnesMatrix(1, this.rows);
SimpleCuBlas.gemv(false, this, multiplier, sum, 1.0, 0.0);
return sum;
}
public DMatrix sub(double v) {
DMatrix m = DMath.createMatrix(this.rows(), this.columns(), this.toArray());
for (int i = 0; i < this.length(); i++) m.put(i, m.get(i) - v);
return m;
}
public DMatrix inv() {
DMatrix m = DMath.createMatrix(this.rows(), this.columns(), this.toArray());
SimpleCuBlas.inverseElements(m);
return m;
}