params.h File Reference
Energy Parameter Sets and Boltzmann Factors
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## Data Structures

struct | vrna_param_s
| The datastructure that contains temperature scaled energy parameters. More...
struct | vrna_exp_param_s
| The datastructure that contains temperature scaled Boltzmann weights of the energy parameters. More...

## Typedefs

typedef struct vrna_param_s | vrna_param_t
| Typename for the free energy parameter data structure vrna_params.
typedef struct vrna_exp_param_s | vrna_exp_param_t
| Typename for the Boltzmann factor data structure vrna_exp_params.
typedef struct vrna_param_s | paramT
| Old typename of vrna_param_s. More...
typedef struct vrna_exp_param_s | pf_paramT
| Old typename of vrna_exp_param_s. More...

## Functions

vrna_param_t * | vrna_params (vrna_md_t *md)
| Get a data structure containing prescaled free energy parameters. More...
vrna_param_t * | vrna_params_copy (vrna_param_t *par)
| Get a copy of the provided free energy parameters. More...
vrna_exp_param_t * | vrna_exp_params (vrna_md_t *md)
| Get a data structure containing prescaled free energy parameters already transformed to Boltzmann factors. More...
vrna_exp_param_t * | vrna_exp_params_comparative (unsigned int n_seq, vrna_md_t *md)
| Get a data structure containing prescaled free energy parameters already transformed to Boltzmann factors (alifold version) More...
vrna_exp_param_t * | vrna_exp_params_copy (vrna_exp_param_t *par)
| Get a copy of the provided free energy parameters (provided as Boltzmann factors) More...
void | vrna_params_subst (vrna_fold_compound_t *vc, vrna_param_t *par)
| Update/Reset energy parameters data structure within a vrna_fold_compound_t. More...
void | vrna_exp_params_subst (vrna_fold_compound_t *vc, vrna_exp_param_t *params)
| Update the energy parameters for subsequent partition function computations. More...
void | vrna_exp_params_rescale (vrna_fold_compound_t *vc, double *mfe)
| Rescale Boltzmann factors for partition function computations. More...
void | vrna_params_reset (vrna_fold_compound_t *vc, vrna_md_t *md_p)
| Reset free energy parameters within a vrna_fold_compound_t according to provided, or default model details. More...
void | vrna_exp_params_reset (vrna_fold_compound_t *vc, vrna_md_t *md_p)
| Reset Boltzmann factors for partition function computations within a vrna_fold_compound_t according to provided, or default model details. More...
vrna_exp_param_t * | get_scaled_pf_parameters (void)
vrna_exp_param_t * | get_boltzmann_factors (double temperature, double betaScale, vrna_md_t md, double pf_scale)
| Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent thermodynamic temperature. More...
vrna_exp_param_t * | get_boltzmann_factor_copy (vrna_exp_param_t *parameters)
| Get a copy of already precomputed Boltzmann factors. More...
vrna_exp_param_t * | get_scaled_alipf_parameters (unsigned int n_seq)
| Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) More...
vrna_exp_param_t * | get_boltzmann_factors_ali (unsigned int n_seq, double temperature, double betaScale, vrna_md_t md, double pf_scale)
| Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) with independent thermodynamic temperature. More...
vrna_param_t * | scale_parameters (void)
| Get precomputed energy contributions for all the known loop types. More...
vrna_param_t * | get_scaled_parameters (double temperature, vrna_md_t md)
| Get precomputed energy contributions for all the known loop types. More...