/**
* Virtual function to make the data structures from the
* object oriented specification of the signaling network.
*/
void GssaStoich::rebuildMatrix( Eref stoich, vector< Id >& ret )
{
Stoich::rebuildMatrix( stoich, ret );
// Stuff here to set up the dependencies.
unsigned int numRates = N_.nColumns();
assert ( numRates == rates_.size() );
// Here we fix the issue of having a single substrate at
// more than first order. Its rate must be computed differently
// for stoch calculations, since one molecule is consumed for
// each order.
for ( unsigned int i = 0; i < numRates; ++i ) {
vector< unsigned int > molIndex;
if ( rates_[i]->getReactants( molIndex, S_ ) > 1 ) {
if ( molIndex.size() == 2 && molIndex[0] == molIndex[1] ) {
RateTerm* oldRate = rates_[i];
rates_[ i ] = new StochSecondOrderSingleSubstrate(
oldRate->getR1(), &S_[ molIndex[ 0 ] ]
);
delete oldRate;
} else if ( molIndex.size() > 2 ) {
RateTerm* oldRate = rates_[ i ];
vector< const double* > v;
for ( vector< unsigned int >::iterator j =
molIndex.begin(); j != molIndex.end(); ++j )
v.push_back( &S_[ *j ] );
rates_[ i ] = new StochNOrder( oldRate->getR1(), v);
delete oldRate;
}
}
}
// Here we set up dependency stuff. First the basic reac deps.
transN_.setSize( numRates, N_.nRows() );
assert( N_.nRows() == nMols_ );
N_.transpose( transN_ );
transN_.truncateRow( nVarMols_ );
dependency_.resize( numRates );
for ( unsigned int i = 0; i < numRates; ++i ) {
transN_.getGillespieDependence( i, dependency_[ i ] );
}
// Fill in dependency list for MMEnzs: they depend on their enzymes.
fillMmEnzDep();
// Fill in dependency list for SumTots on reactions
fillMathDep();
makeReacDepsUnique();
}
void Gsolve::rebuildGssaSystem()
{
stoichPtr_->convertRatesToStochasticForm();
sys_.transposeN = stoichPtr_->getStoichiometryMatrix();
sys_.transposeN.transpose();
sys_.transposeN.truncateRow( stoichPtr_->getNumVarPools() );
vector< vector< unsigned int > > & dep = sys_.dependency;
dep.resize( stoichPtr_->getNumRates() );
for ( unsigned int i = 0; i < stoichPtr_->getNumRates(); ++i ) {
sys_.transposeN.getGillespieDependence( i, dep[i] );
}
fillMmEnzDep();
fillMathDep();
makeReacDepsUnique();
for ( vector< GssaVoxelPools >::iterator
i = pools_.begin(); i != pools_.end(); ++i ) {
i->setNumReac( stoichPtr_->getNumRates() );
}
sys_.isReady = true;
}