equilibrium_probs.h

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#ifndef VIENNA_RNA_PACKAGE_EQUILIBRIUM_PROBS_H
#define VIENNA_RNA_PACKAGE_EQUILIBRIUM_PROBS_H

#include <ViennaRNA/datastructures/basic.h>
#include <ViennaRNA/fold_compound.h>
#include <ViennaRNA/utils/structures.h>
#include <ViennaRNA/params/basic.h>

/*
 #################################################
 # BASE PAIR PROBABILITY RELATED FUNCTIONS       #
 #################################################
 */

int
vrna_pairing_probs(vrna_fold_compound_t *vc,
                   char                 *structure);


double
vrna_mean_bp_distance_pr(int        length,
                         FLT_OR_DBL *pr);


double
vrna_mean_bp_distance(vrna_fold_compound_t *vc);


double
vrna_ensemble_defect(vrna_fold_compound_t *fc,
                     const char           *structure);


double *
vrna_positional_entropy(vrna_fold_compound_t *fc);


vrna_ep_t *
vrna_stack_prob(vrna_fold_compound_t  *vc,
                double                cutoff);


/* End base pair related functions */
void
vrna_pf_dimer_probs(double                  FAB,
                    double                  FA,
                    double                  FB,
                    vrna_ep_t               *prAB,
                    const vrna_ep_t         *prA,
                    const vrna_ep_t         *prB,
                    int                     Alength,
                    const vrna_exp_param_t  *exp_params);


double
vrna_pr_structure(vrna_fold_compound_t  *fc,
                  const char            *structure);


double
vrna_pr_energy(vrna_fold_compound_t *vc,
               double               e);


#endif