eval.h File Reference

Functions and variables related to energy evaluation of sequence/structure pairs. More...

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## Functions

float | vrna_eval_structure (vrna_fold_compound_t *vc, const char *structure)
| Calculate the free energy of an already folded RNA. More...
float | vrna_eval_covar_structure (vrna_fold_compound_t *vc, const char *structure)
| Calculate the pseudo energy derived by the covariance scores of a set of aligned sequences. More...
float | vrna_eval_structure_simple (const char *string, const char *structure)
| Calculate the free energy of an already folded RNA. More...
float | vrna_eval_structure_verbose (vrna_fold_compound_t *vc, const char *structure, FILE *file)
| Calculate the free energy of an already folded RNA and print contributions on a per-loop base. More...
float | vrna_eval_structure_simple_verbose (const char *string, const char *structure, FILE *file)
| Calculate the free energy of an already folded RNA and print contributions per loop. More...
int | vrna_eval_structure_pt (vrna_fold_compound_t *vc, const short *pt)
| Calculate the free energy of an already folded RNA. More...
int | vrna_eval_structure_pt_simple (const char *string, const short *pt)
| Calculate the free energy of an already folded RNA. More...
int | vrna_eval_structure_pt_verbose (vrna_fold_compound_t *vc, const short *pt, FILE *file)
| Calculate the free energy of an already folded RNA. More...
int | vrna_eval_structure_pt_simple_verbose (const char *string, const short *pt, FILE *file)
| Calculate the free energy of an already folded RNA. More...
int | vrna_eval_loop_pt (vrna_fold_compound_t *vc, int i, const short *pt)
| Calculate energy of a loop. More...
float | vrna_eval_move (vrna_fold_compound_t *vc, const char *structure, int m1, int m2)
| Calculate energy of a move (closing or opening of a base pair) More...
int | vrna_eval_move_pt (vrna_fold_compound_t *vc, short *pt, int m1, int m2)
| Calculate energy of a move (closing or opening of a base pair) More...
float | energy_of_structure (const char *string, const char *structure, int verbosity_level)
| Calculate the free energy of an already folded RNA using global model detail settings. More...
float | energy_of_struct_par (const char *string, const char *structure, vrna_param_t *parameters, int verbosity_level)
| Calculate the free energy of an already folded RNA. More...
float | energy_of_circ_structure (const char *string, const char *structure, int verbosity_level)
| Calculate the free energy of an already folded circular RNA. More...
float | energy_of_circ_struct_par (const char *string, const char *structure, vrna_param_t *parameters, int verbosity_level)
| Calculate the free energy of an already folded circular RNA. More...
int | energy_of_structure_pt (const char *string, short *ptable, short *s, short *s1, int verbosity_level)
| Calculate the free energy of an already folded RNA. More...
int | energy_of_struct_pt_par (const char *string, short *ptable, short *s, short *s1, vrna_param_t *parameters, int verbosity_level)
| Calculate the free energy of an already folded RNA. More...
float | energy_of_move (const char *string, const char *structure, int m1, int m2)
| Calculate energy of a move (closing or opening of a base pair) More...
int | energy_of_move_pt (short *pt, short *s, short *s1, int m1, int m2)
| Calculate energy of a move (closing or opening of a base pair) More...
int | loop_energy (short *ptable, short *s, short *s1, int i)
| Calculate energy of a loop. More...
float | energy_of_struct (const char *string, const char *structure)
int | energy_of_struct_pt (const char *string, short *ptable, short *s, short *s1)
float | energy_of_circ_struct (const char *string, const char *structure)

## Variables

int | cut_point
| set to first pos of second seq for cofolding
int | eos_debug
| verbose info from energy_of_struct

## Detailed Description

Functions and variables related to energy evaluation of sequence/structure pairs.