PRIVATE void update_dfold_params(void){
vrna_md_t md;
if(P)
free(P);
set_model_details(&md);
P = vrna_params(&md);
make_pair_matrix();
}
PRIVATE void
add_params( vrna_fold_compound_t *vc,
vrna_md_t *md_p,
unsigned int options){
/* ALWAYS add regular energy parameters */
vc->params = vrna_params(md_p);
if(options & VRNA_OPTION_PF){
vc->exp_params = (vc->type == VRNA_VC_TYPE_SINGLE) ? \
vrna_exp_params(md_p) : \
vrna_exp_params_comparative(vc->n_seq, md_p);
}
}
InteractionEnergyVrna::InteractionEnergyVrna(
const Accessibility & accS1
, const ReverseAccessibility & accS2
, VrnaHandler &vrnaHandler
, const size_t maxInternalLoopSize1
, const size_t maxInternalLoopSize2
, const bool initES
)
:
InteractionEnergy(accS1, accS2, maxInternalLoopSize1, maxInternalLoopSize2)
// get final VRNA folding parameters
, foldModel( vrnaHandler.getModel() )
, foldParams( vrna_params( &foldModel ) )
, RT(vrnaHandler.getRT())
, bpCG( BP_pair[RnaSequence::getCodeForChar('C')][RnaSequence::getCodeForChar('G')] )
, bpGC( BP_pair[RnaSequence::getCodeForChar('G')][RnaSequence::getCodeForChar('C')] )
, esValues1(NULL)
, esValues2(NULL)
{
vrna_md_defaults_reset( &foldModel );
// init ES values if needed
if (initES) {
// 23.11.2017 : should not be relevant anymore
//#if INTARNA_MULITHREADING
// #pragma omp critical(intarna_omp_callingVRNA)
//#endif
// {
// create ES container to be filled
esValues1 = new EsMatrix();
esValues2 = new EsMatrix();
// fill ES container
computeES( accS1, *esValues1 );
computeES( accS2, *esValues2 );
// } // omp critical(intarna_omp_callingVRNA)
}
}
