basic.h File Reference
Functions to deal with sets of energy parameters. More...
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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 data structure 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... | |
Detailed Description
Functions to deal with sets of energy parameters.
