RNAlib-2.2.7
Free Energy Evaluation for given Sequence / Structure Pairs

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
 

Detailed Description

This module contains all functions and variables related to energy evaluation of sequence/structure pairs.

Function Documentation

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:

Note
Accepts vrna_fold_compound_t of type VRNA_VC_TYPE_SINGLE and VRNA_VC_TYPE_ALIGNMENT
See also
vrna_eval_structure_pt(), vrna_eval_structure_verbose(), vrna_eval_structure_pt_verbose(), vrna_fold_compound(), vrna_fold_compound_comparative(), vrna_eval_covar_structure()
Parameters
vcA vrna_fold_compound_t containing the energy parameters and model details
structureSecondary structure in dot-bracket notation
Returns
The free energy of the input structure given the input sequence in kcal/mol
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:

Note
Accepts vrna_fold_compound_t of type VRNA_VC_TYPE_ALIGNMENT only!
See also
vrna_fold_compound_comparative(), vrna_eval_structure()
Parameters
vcA vrna_fold_compound_t containing the energy parameters and model details
structureSecondary (consensus) structure in dot-bracket notation
Returns
The covariance pseudo energy score of the input structure given the input sequence alignment in kcal/mol
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.

See also
vrna_eval_structure(), vrna_eval_structure_pt(), vrna_eval_structure_verbose(), vrna_eval_structure_pt_verbose(),
Parameters
stringRNA sequence in uppercase letters
structureSecondary structure in dot-bracket notation
Returns
The free energy of the input structure given the input sequence in kcal/mol
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:

See also
vrna_eval_structure_pt(), vrna_eval_structure_verbose(), vrna_eval_structure_pt_verbose(),
Parameters
vcA vrna_fold_compound_t containing the energy parameters and model details
structureSecondary structure in dot-bracket notation
fileA file handle where this function should print to (may be NULL).
Returns
The free energy of the input structure given the input sequence in kcal/mol
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.

See also
vrna_eval_structure_verbose(), vrna_eval_structure_pt(), vrna_eval_structure_verbose(), vrna_eval_structure_pt_verbose(),
Parameters
stringRNA sequence in uppercase letters
structureSecondary structure in dot-bracket notation
fileA file handle where this function should print to (may be NULL).
Returns
The free energy of the input structure given the input sequence in kcal/mol
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:

See also
vrna_ptable(), vrna_eval_structure(), vrna_eval_structure_pt_verbose()
Parameters
vcA vrna_fold_compound_t containing the energy parameters and model details
ptSecondary structure as pair_table
Returns
The free energy of the input structure given the input sequence in 10cal/mol
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.

See also
vrna_ptable(), vrna_eval_structure_simple(), vrna_eval_structure_pt()
Parameters
stringRNA sequence in uppercase letters
ptSecondary structure as pair_table
Returns
The free energy of the input structure given the input sequence in 10cal/mol
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.

See also
vrna_ptable(), vrna_eval_structure_pt(), vrna_eval_structure_verbose()
Parameters
vcA vrna_fold_compound_t containing the energy parameters and model details
ptSecondary structure as pair_table
fileA file handle where this function should print to (may be NULL).
Returns
The free energy of the input structure given the input sequence in 10cal/mol
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.

See also
vrna_ptable(), vrna_eval_structure_pt_verbose(), vrna_eval_structure_simple()
Parameters
stringRNA sequence in uppercase letters
ptSecondary structure as pair_table
fileA file handle where this function should print to (may be NULL).
Returns
The free energy of the input structure given the input sequence in 10cal/mol
int vrna_eval_loop_pt ( vrna_fold_compound_t vc,
int  i,
const short *  pt 
)

#include <ViennaRNA/eval.h>

Calculate energy of a loop.

Parameters
vcA vrna_fold_compound_t containing the energy parameters and model details
iposition of covering base pair
ptthe pair table of the secondary structure
Returns
free energy of the loop in 10cal/mol
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).

See also
vrna_eval_move_pt()
Parameters
vcA vrna_fold_compound_t containing the energy parameters and model details
structuresecondary structure in dot-bracket notation
m1first coordinate of base pair
m2second coordinate of base pair
Returns
energy change of the move in kcal/mol
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).

See also
vrna_eval_move()
Parameters
vcA vrna_fold_compound_t containing the energy parameters and model details
ptthe pair table of the secondary structure
m1first coordinate of base pair
m2second coordinate of base pair
Returns
energy change of the move in 10cal/mol
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

Note
OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See energy_of_struct_par() for a completely threadsafe implementation.
Deprecated:
Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!
See also
vrna_eval_structure()
Parameters
stringRNA sequence
structuresecondary structure in dot-bracket notation
verbosity_levela flag to turn verbose output on/off
Returns
the free energy of the input structure given the input sequence in kcal/mol
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

Deprecated:
Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!
See also
vrna_eval_structure()
Parameters
stringRNA sequence in uppercase letters
structureSecondary structure in dot-bracket notation
parametersA data structure containing the prescaled energy contributions and the model details.
verbosity_levelA flag to turn verbose output on/off
Returns
The free energy of the input structure given the input sequence in kcal/mol
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.

Note
OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See energy_of_circ_struct_par() for a completely threadsafe implementation.

If verbosity level is set to a value >0, energies of structure elements are printed to stdout

Deprecated:
Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!
See also
vrna_eval_structure()
Parameters
stringRNA sequence
structureSecondary structure in dot-bracket notation
verbosity_levelA flag to turn verbose output on/off
Returns
The free energy of the input structure given the input sequence in kcal/mol
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

Deprecated:
Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!
See also
vrna_eval_structure()
Parameters
stringRNA sequence
structureSecondary structure in dot-bracket notation
parametersA data structure containing the prescaled energy contributions and the model details.
verbosity_levelA flag to turn verbose output on/off
Returns
The free energy of the input structure given the input sequence in kcal/mol
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

Note
OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See energy_of_struct_pt_par() for a completely threadsafe implementation.
Deprecated:
Use vrna_eval_structure_pt() or vrna_eval_structure_pt_verbose() instead!
See also
vrna_eval_structure_pt()
Parameters
stringRNA sequence
ptablethe pair table of the secondary structure
sencoded RNA sequence
s1encoded RNA sequence
verbosity_levela flag to turn verbose output on/off
Returns
the free energy of the input structure given the input sequence in 10kcal/mol
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

Deprecated:
Use vrna_eval_structure_pt() or vrna_eval_structure_pt_verbose() instead!
See also
vrna_eval_structure_pt()
Parameters
stringRNA sequence in uppercase letters
ptableThe pair table of the secondary structure
sEncoded RNA sequence
s1Encoded RNA sequence
parametersA data structure containing the prescaled energy contributions and the model details.
verbosity_levelA flag to turn verbose output on/off
Returns
The free energy of the input structure given the input sequence in 10kcal/mol
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).

Deprecated:
Use vrna_eval_move() instead!
See also
vrna_eval_move()
Parameters
stringRNA sequence
structuresecondary structure in dot-bracket notation
m1first coordinate of base pair
m2second coordinate of base pair
Returns
energy change of the move in kcal/mol
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).

Deprecated:
Use vrna_eval_move_pt() instead!
See also
vrna_eval_move_pt()
Parameters
ptthe pair table of the secondary structure
sencoded RNA sequence
s1encoded RNA sequence
m1first coordinate of base pair
m2second coordinate of base pair
Returns
energy change of the move in 10cal/mol
int loop_energy ( short *  ptable,
short *  s,
short *  s1,
int  i 
)

#include <ViennaRNA/eval.h>

Calculate energy of a loop.

Deprecated:
Use vrna_eval_loop_pt() instead!
See also
vrna_eval_loop_pt()
Parameters
ptablethe pair table of the secondary structure
sencoded RNA sequence
s1encoded RNA sequence
iposition of covering base pair
Returns
free energy of the loop in 10cal/mol
float energy_of_struct ( const char *  string,
const char *  structure 
)

#include <ViennaRNA/eval.h>

Calculate the free energy of an already folded RNA

Note
This function is not entirely threadsafe! Depending on the state of the global variable eos_debug it prints energy information to stdout or not...
Deprecated:
This function is deprecated and should not be used in future programs! Use energy_of_structure() instead!
See also
energy_of_structure, energy_of_circ_struct(), energy_of_struct_pt()
Parameters
stringRNA sequence
structuresecondary structure in dot-bracket notation
Returns
the free energy of the input structure given the input sequence in kcal/mol
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

Note
This function is not entirely threadsafe! Depending on the state of the global variable eos_debug it prints energy information to stdout or not...
Deprecated:
This function is deprecated and should not be used in future programs! Use energy_of_structure_pt() instead!
See also
make_pair_table(), energy_of_structure()
Parameters
stringRNA sequence
ptablethe pair table of the secondary structure
sencoded RNA sequence
s1encoded RNA sequence
Returns
the free energy of the input structure given the input sequence in 10kcal/mol
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

Note
This function is not entirely threadsafe! Depending on the state of the global variable eos_debug it prints energy information to stdout or not...
Deprecated:
This function is deprecated and should not be used in future programs Use energy_of_circ_structure() instead!
See also
energy_of_circ_structure(), energy_of_struct(), energy_of_struct_pt()
Parameters
stringRNA sequence
structuresecondary structure in dot-bracket notation
Returns
the free energy of the input structure given the input sequence in kcal/mol
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.

Note
This function is polymorphic! The provided vrna_fold_compound_t may be of type VRNA_VC_TYPE_SINGLE or VRNA_VC_TYPE_ALIGNMENT
Parameters
vcThe vrna_fold_compound_t for the particular energy evaluation
i5'-position of the base pair
j3'-position of the base pair
Returns
Free energy of the hairpin loop closed by $ (i,j) $ in deka-kal/mol