struct vrna_unstructured_domain_s

#include <ViennaRNA/unstructured_domains.h>

Detailed Documentation

Data structure to store all functionality for ligand binding.

Fields

int uniq_motif_count
The unique number of motifs of different lengths.
unsigned int* uniq_motif_size
An array storing a unique list of motif lengths.
int motif_count
Total number of distinguished motifs.
char** motif
Motif sequences.
unsigned int* motif_size
Motif lengths.
double* motif_en
Ligand binding free energy contribution.
unsigned int* motif_type
Type of motif, i.e. loop type the ligand binds to.
vrna_callback_ud_production* prod_cb
Callback to ligand binding production rule, i.e. create/fill DP free energy matrices.
This callback will be executed right before the actual secondary structure decompositions, and, therefore, any implementation must not interleave with the regular DP matrices.
vrna_callback_ud_exp_production* exp_prod_cb
Callback to ligand binding production rule, i.e. create/fill DP partition function matrices.
vrna_callback_ud_energy* energy_cb
Callback to evaluate free energy of ligand binding to a particular unpaired stretch.
vrna_callback_ud_exp_energy* exp_energy_cb
Callback to evaluate Boltzmann factor of ligand binding to a particular unpaired stretch.
void* data
Auxiliary data structure passed to energy evaluation callbacks.
vrna_callback_free_auxdata* free_data
Callback to free auxiliary data structure.
vrna_callback_ud_probs_add* probs_add
Callback to store/add outside partition function.
vrna_callback_ud_probs_get* probs_get
Callback to retrieve outside partition function.