RNAlib-2.2.7
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This module contains all functions and variables related to energy evaluation of sequence/structure pairs. More...
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) |
int | vrna_eval_ext_hp_loop (vrna_fold_compound_t *vc, int i, int j) |
Evaluate free energy of an exterior hairpin loop. | |
int | vrna_eval_hp_loop (vrna_fold_compound_t *vc, int i, int j) |
Evaluate free energy of a hairpin loop. More... | |
Variables | |
int | cut_point |
set to first pos of second seq for cofolding | |
int | eos_debug |
verbose info from energy_of_struct | |
This module contains all functions and variables related to energy evaluation of sequence/structure pairs.
float vrna_eval_structure | ( | vrna_fold_compound_t * | vc, |
const char * | structure | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
This function allows for energy evaluation of a given pair of structure and sequence (alignment). Model details, energy parameters, and possibly soft constraints are used as provided via the parameter 'vc'. The vrna_fold_compound_t does not need to contain any DP matrices, but requires all most basic init values as one would get from a call like this:
vc | A vrna_fold_compound_t containing the energy parameters and model details |
structure | Secondary structure in dot-bracket notation |
float vrna_eval_covar_structure | ( | vrna_fold_compound_t * | vc, |
const char * | structure | ||
) |
#include <ViennaRNA/eval.h>
Calculate the pseudo energy derived by the covariance scores of a set of aligned sequences.
Consensus structure prediction is driven by covariance scores of base pairs in rows of the provided alignment. This function allows to retrieve the total amount of this covariance pseudo energy scores. The vrna_fold_compound_t does not need to contain any DP matrices, but requires all most basic init values as one would get from a call like this:
vc | A vrna_fold_compound_t containing the energy parameters and model details |
structure | Secondary (consensus) structure in dot-bracket notation |
float vrna_eval_structure_simple | ( | const char * | string, |
const char * | structure | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
This function allows for energy evaluation of a given sequence/structure pair. In contrast to vrna_eval_structure() this function assumes default model details and default energy parameters in order to evaluate the free energy of the secondary structure. Therefore, it serves as a simple interface function for energy evaluation for situations where no changes on the energy model are required.
string | RNA sequence in uppercase letters |
structure | Secondary structure in dot-bracket notation |
float vrna_eval_structure_verbose | ( | vrna_fold_compound_t * | vc, |
const char * | structure, | ||
FILE * | file | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA and print contributions on a per-loop base.
This function allows for detailed energy evaluation of a given sequence/structure pair. In contrast to vrna_eval_structure() this function prints detailed energy contributions based on individual loops to a file handle. If NULL is passed as file handle, this function defaults to print to stdout. Model details, energy parameters, and possibly soft constraints are used as provided via the parameter 'vc'. The fold_compound does not need to contain any DP matrices, but all the most basic init values as one would get from a call like this:
vc | A vrna_fold_compound_t containing the energy parameters and model details |
structure | Secondary structure in dot-bracket notation |
file | A file handle where this function should print to (may be NULL). |
float vrna_eval_structure_simple_verbose | ( | const char * | string, |
const char * | structure, | ||
FILE * | file | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA and print contributions per loop.
This function allows for detailed energy evaluation of a given sequence/structure pair. In contrast to vrna_eval_structure() this function prints detailed energy contributions based on individual loops to a file handle. If NULL is passed as file handle, this function defaults to print to stdout. In contrast to vrna_eval_structure_verbose() this function assumes default model details and default energy parameters in order to evaluate the free energy of the secondary structure. Threefore, it serves as a simple interface function for energy evaluation for situations where no changes on the energy model are required.
string | RNA sequence in uppercase letters |
structure | Secondary structure in dot-bracket notation |
file | A file handle where this function should print to (may be NULL). |
int vrna_eval_structure_pt | ( | vrna_fold_compound_t * | vc, |
const short * | pt | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
This function allows for energy evaluation of a given sequence/structure pair where the structure is provided in pair_table format as obtained from vrna_ptable(). Model details, energy parameters, and possibly soft constraints are used as provided via the parameter 'vc'. The fold_compound does not need to contain any DP matrices, but all the most basic init values as one would get from a call like this:
vc | A vrna_fold_compound_t containing the energy parameters and model details |
pt | Secondary structure as pair_table |
int vrna_eval_structure_pt_simple | ( | const char * | string, |
const short * | pt | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
In contrast to vrna_eval_structure_pt() this function assumes default model details and default energy parameters in order to evaluate the free energy of the secondary structure. Threefore, it serves as a simple interface function for energy evaluation for situations where no changes on the energy model are required.
string | RNA sequence in uppercase letters |
pt | Secondary structure as pair_table |
int vrna_eval_structure_pt_verbose | ( | vrna_fold_compound_t * | vc, |
const short * | pt, | ||
FILE * | file | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
This function allows for energy evaluation of a given sequence/structure pair where the structure is provided in pair_table format as obtained from vrna_ptable(). Model details, energy parameters, and possibly soft constraints are used as provided via the parameter 'vc'. The fold_compound does not need to contain any DP matrices, but all the most basic init values as one would get from a call like this:
In contrast to vrna_eval_structure_pt() this function prints detailed energy contributions based on individual loops to a file handle. If NULL is passed as file handle, this function defaults to print to stdout.
vc | A vrna_fold_compound_t containing the energy parameters and model details |
pt | Secondary structure as pair_table |
file | A file handle where this function should print to (may be NULL). |
int vrna_eval_structure_pt_simple_verbose | ( | const char * | string, |
const short * | pt, | ||
FILE * | file | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
This function allows for energy evaluation of a given sequence/structure pair where the structure is provided in pair_table format as obtained from vrna_ptable(). Model details, energy parameters, and possibly soft constraints are used as provided via the parameter 'vc'. The fold_compound does not need to contain any DP matrices, but all the most basic init values as one would get from a call like this:
In contrast to vrna_eval_structure_pt_verbose() this function assumes default model details and default energy parameters in order to evaluate the free energy of the secondary structure. Threefore, it serves as a simple interface function for energy evaluation for situations where no changes on the energy model are required.
string | RNA sequence in uppercase letters |
pt | Secondary structure as pair_table |
file | A file handle where this function should print to (may be NULL). |
int vrna_eval_loop_pt | ( | vrna_fold_compound_t * | vc, |
int | i, | ||
const short * | pt | ||
) |
#include <ViennaRNA/eval.h>
Calculate energy of a loop.
vc | A vrna_fold_compound_t containing the energy parameters and model details |
i | position of covering base pair |
pt | the pair table of the secondary structure |
float vrna_eval_move | ( | vrna_fold_compound_t * | vc, |
const char * | structure, | ||
int | m1, | ||
int | m2 | ||
) |
#include <ViennaRNA/eval.h>
Calculate energy of a move (closing or opening of a base pair)
If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).
vc | A vrna_fold_compound_t containing the energy parameters and model details |
structure | secondary structure in dot-bracket notation |
m1 | first coordinate of base pair |
m2 | second coordinate of base pair |
int vrna_eval_move_pt | ( | vrna_fold_compound_t * | vc, |
short * | pt, | ||
int | m1, | ||
int | m2 | ||
) |
#include <ViennaRNA/eval.h>
Calculate energy of a move (closing or opening of a base pair)
If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).
vc | A vrna_fold_compound_t containing the energy parameters and model details |
pt | the pair table of the secondary structure |
m1 | first coordinate of base pair |
m2 | second coordinate of base pair |
float energy_of_structure | ( | const char * | string, |
const char * | structure, | ||
int | verbosity_level | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA using global model detail settings.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
string | RNA sequence |
structure | secondary structure in dot-bracket notation |
verbosity_level | a flag to turn verbose output on/off |
float energy_of_struct_par | ( | const char * | string, |
const char * | structure, | ||
vrna_param_t * | parameters, | ||
int | verbosity_level | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
string | RNA sequence in uppercase letters |
structure | Secondary structure in dot-bracket notation |
parameters | A data structure containing the prescaled energy contributions and the model details. |
verbosity_level | A flag to turn verbose output on/off |
float energy_of_circ_structure | ( | const char * | string, |
const char * | structure, | ||
int | verbosity_level | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded circular RNA.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
string | RNA sequence |
structure | Secondary structure in dot-bracket notation |
verbosity_level | A flag to turn verbose output on/off |
float energy_of_circ_struct_par | ( | const char * | string, |
const char * | structure, | ||
vrna_param_t * | parameters, | ||
int | verbosity_level | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded circular RNA.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
string | RNA sequence |
structure | Secondary structure in dot-bracket notation |
parameters | A data structure containing the prescaled energy contributions and the model details. |
verbosity_level | A flag to turn verbose output on/off |
int energy_of_structure_pt | ( | const char * | string, |
short * | ptable, | ||
short * | s, | ||
short * | s1, | ||
int | verbosity_level | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
string | RNA sequence |
ptable | the pair table of the secondary structure |
s | encoded RNA sequence |
s1 | encoded RNA sequence |
verbosity_level | a flag to turn verbose output on/off |
int energy_of_struct_pt_par | ( | const char * | string, |
short * | ptable, | ||
short * | s, | ||
short * | s1, | ||
vrna_param_t * | parameters, | ||
int | verbosity_level | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
string | RNA sequence in uppercase letters |
ptable | The pair table of the secondary structure |
s | Encoded RNA sequence |
s1 | Encoded RNA sequence |
parameters | A data structure containing the prescaled energy contributions and the model details. |
verbosity_level | A flag to turn verbose output on/off |
float energy_of_move | ( | const char * | string, |
const char * | structure, | ||
int | m1, | ||
int | m2 | ||
) |
#include <ViennaRNA/eval.h>
Calculate energy of a move (closing or opening of a base pair)
If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).
string | RNA sequence |
structure | secondary structure in dot-bracket notation |
m1 | first coordinate of base pair |
m2 | second coordinate of base pair |
int energy_of_move_pt | ( | short * | pt, |
short * | s, | ||
short * | s1, | ||
int | m1, | ||
int | m2 | ||
) |
#include <ViennaRNA/eval.h>
Calculate energy of a move (closing or opening of a base pair)
If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).
pt | the pair table of the secondary structure |
s | encoded RNA sequence |
s1 | encoded RNA sequence |
m1 | first coordinate of base pair |
m2 | second coordinate of base pair |
int loop_energy | ( | short * | ptable, |
short * | s, | ||
short * | s1, | ||
int | i | ||
) |
#include <ViennaRNA/eval.h>
Calculate energy of a loop.
ptable | the pair table of the secondary structure |
s | encoded RNA sequence |
s1 | encoded RNA sequence |
i | position of covering base pair |
float energy_of_struct | ( | const char * | string, |
const char * | structure | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA
string | RNA sequence |
structure | secondary structure in dot-bracket notation |
int energy_of_struct_pt | ( | const char * | string, |
short * | ptable, | ||
short * | s, | ||
short * | s1 | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA
string | RNA sequence |
ptable | the pair table of the secondary structure |
s | encoded RNA sequence |
s1 | encoded RNA sequence |
float energy_of_circ_struct | ( | const char * | string, |
const char * | structure | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded circular RNA
string | RNA sequence |
structure | secondary structure in dot-bracket notation |
int vrna_eval_hp_loop | ( | vrna_fold_compound_t * | vc, |
int | i, | ||
int | j | ||
) |
#include <ViennaRNA/hairpin_loops.h>
Evaluate free energy of a hairpin loop.
vc | The vrna_fold_compound_t for the particular energy evaluation |
i | 5'-position of the base pair |
j | 3'-position of the base pair |