struct vrna_sc_s

#include <ViennaRNA/constraints_soft.h>

Detailed Documentation

The soft constraints data structure.

Fields

int** energy_up
Energy contribution for stretches of unpaired nucleotides.
FLT_OR_DBL** exp_energy_up
Boltzmann Factors of the energy contributions for unpaired sequence stretches.
int* up_storage
Storage container for energy contributions per unpaired nucleotide.
vrna_sc_bp_storage_t** bp_storage
Storage container for energy contributions per base pair.
int* energy_bp
Energy contribution for base pairs.
FLT_OR_DBL* exp_energy_bp
Boltzmann Factors of the energy contribution for base pairs.
int** energy_bp_local
Energy contribution for base pairs (sliding window approach)
FLT_OR_DBL** exp_energy_bp_local
Boltzmann Factors of the energy contribution for base pairs (sliding window approach)
int* energy_stack
Pseudo Energy contribution per base pair involved in a stack.
FLT_OR_DBL* exp_energy_stack
Boltzmann weighted pseudo energy contribution per nucleotide involved in a stack.
vrna_callback_sc_energy* f
A function pointer used for pseudo energy contribution in MFE calculations.

See also:

vrna_sc_add_f()

vrna_callback_sc_backtrack* bt
A function pointer used to obtain backtraced base pairs in loop regions that were altered by soft constrained pseudo energy contributions.

See also:

vrna_sc_add_bt()

vrna_callback_sc_exp_energy* exp_f
A function pointer used for pseudo energy contribution boltzmann factors in PF calculations.
void* data
A pointer to the data object provided for for pseudo energy contribution functions of the generic soft constraints feature.