RNAlib-2.4.4
Free energy evaluation

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

Detailed Description

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

+ Collaboration diagram for Free energy evaluation:

Modules

 Process and evaluate individual loops
 

Files

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

Variables

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

Basic Energy Evaluation Interface with Dot-Bracket Structure String

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_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_v (vrna_fold_compound_t *vc, const char *structure, int verbosity_level, FILE *file)
 Calculate the free energy of an already folded RNA and print contributions on a per-loop base. More...
 

Basic Energy Evaluation Interface with Structure Pair Table

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_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_v (vrna_fold_compound_t *vc, const short *pt, int verbosity_level, FILE *file)
 Calculate the free energy of an already folded RNA. More...
 

Simplified Energy Evaluation with Sequence and Dot-Bracket Strings

float vrna_eval_structure_simple (const char *string, const char *structure)
 Calculate the free energy of an already folded RNA. More...
 
float vrna_eval_circ_structure (const char *string, const char *structure)
 Evaluate the free energy of a sequence/structure pair where the sequence is circular. More...
 
float vrna_eval_gquad_structure (const char *string, const char *structure)
 Evaluate the free energy of a sequence/structure pair where the structure may contain G-Quadruplexes. More...
 
float vrna_eval_circ_gquad_structure (const char *string, const char *structure)
 Evaluate the free energy of a sequence/structure pair where the sequence is circular and the structure may contain G-Quadruplexes. 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...
 
float vrna_eval_structure_simple_v (const char *string, const char *structure, int verbosity_level, FILE *file)
 Calculate the free energy of an already folded RNA and print contributions per loop. More...
 
float vrna_eval_circ_structure_v (const char *string, const char *structure, int verbosity_level, FILE *file)
 Evaluate free energy of a sequence/structure pair, assume sequence to be circular and print contributions per loop. More...
 
float vrna_eval_gquad_structure_v (const char *string, const char *structure, int verbosity_level, FILE *file)
 Evaluate free energy of a sequence/structure pair, allow for G-Quadruplexes in the structure and print contributions per loop. More...
 
float vrna_eval_circ_gquad_structure_v (const char *string, const char *structure, int verbosity_level, FILE *file)
 Evaluate free energy of a sequence/structure pair, assume sequence to be circular, allow for G-Quadruplexes in the structure, and print contributions per loop. More...
 

Simplified Energy Evaluation with Sequence Alignments and Consensus Structure Dot-Bracket String

float vrna_eval_consensus_structure_simple (const char **alignment, const char *structure)
 Calculate the free energy of an already folded RNA sequence alignment. More...
 
float vrna_eval_circ_consensus_structure (const char **alignment, const char *structure)
 Evaluate the free energy of a multiple sequence alignment/consensus structure pair where the sequences are circular. More...
 
float vrna_eval_gquad_consensus_structure (const char **alignment, const char *structure)
 Evaluate the free energy of a multiple sequence alignment/consensus structure pair where the structure may contain G-Quadruplexes. More...
 
float vrna_eval_circ_gquad_consensus_structure (const char **alignment, const char *structure)
 Evaluate the free energy of a multiple sequence alignment/consensus structure pair where the sequence is circular and the structure may contain G-Quadruplexes. More...
 
float vrna_eval_consensus_structure_simple_verbose (const char **alignment, const char *structure, FILE *file)
 Evaluate the free energy of a consensus structure for an RNA sequence alignment and print contributions per loop. More...
 
float vrna_eval_consensus_structure_simple_v (const char **alignment, const char *structure, int verbosity_level, FILE *file)
 Evaluate the free energy of a consensus structure for an RNA sequence alignment and print contributions per loop. More...
 
float vrna_eval_circ_consensus_structure_v (const char **alignment, const char *structure, int verbosity_level, FILE *file)
 Evaluate the free energy of a consensus structure for an alignment of circular RNA sequences and print contributions per loop. More...
 
float vrna_eval_gquad_consensus_structure_v (const char **alignment, const char *structure, int verbosity_level, FILE *file)
 Evaluate the free energy of a consensus structure for an RNA sequence alignment, allow for annotated G-Quadruplexes in the structure and print contributions per loop. More...
 
float vrna_eval_circ_gquad_consensus_structure_v (const char **alignment, const char *structure, int verbosity_level, FILE *file)
 Evaluate the free energy of a consensus structure for an alignment of circular RNA sequences, allow for annotated G-Quadruplexes in the structure and print contributions per loop. More...
 

Simplified Energy Evaluation with Sequence String and Structure Pair Table

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_simple_verbose (const char *string, const short *pt, FILE *file)
 Calculate the free energy of an already folded RNA. More...
 
int vrna_eval_structure_pt_simple_v (const char *string, const short *pt, int verbosity_level, FILE *file)
 Calculate the free energy of an already folded RNA. More...
 

Simplified Energy Evaluation with Sequence Alignment and Consensus Structure Pair Table

int vrna_eval_consensus_structure_pt_simple (const char **alignment, const short *pt)
 Evaluate the Free Energy of a Consensus Secondary Structure given a Sequence Alignment. More...
 
int vrna_eval_consensus_structure_pt_simple_verbose (const char **alignment, const short *pt, FILE *file)
 
int vrna_eval_consensus_structure_pt_simple_v (const char **alignment, const short *pt, int verbosity_level, FILE *file)
 

Basic Loop Energy Evaluation with Structure Pair Table

int vrna_eval_loop_pt (vrna_fold_compound_t *vc, int i, const short *pt)
 Calculate energy of a loop. More...
 
int vrna_eval_loop_pt_v (vrna_fold_compound_t *vc, int i, const short *pt, int verbosity_level)
 Calculate energy of a loop. More...
 

Basic Energy Evaluation for atomic moves

Here, atomic moves are considered opening or closing a single base pair, as well as shifting one pairing partner of an existing pair to a different location

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...
 
int vrna_eval_move_pt_simple (const char *string, short *pt, int m1, int m2)
 
int vrna_eval_move_shift_pt (vrna_fold_compound_t *vc, vrna_move_t *m, short *structure)
 

Deprecated Energy Evaluation functions

Using the functions below is discouraged as they have been marked deprecated and will be removed from the library in the (near) future!

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...
 
float energy_of_gquad_structure (const char *string, const char *structure, int verbosity_level)
 
float energy_of_gquad_struct_par (const char *string, const char *structure, vrna_param_t *parameters, int verbosity_level)
 
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)
 

Function Documentation

◆ vrna_eval_structure()

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_FC_TYPE_SINGLE and VRNA_FC_TYPE_COMPARATIVE
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
SWIG Wrapper Notes:
This function is attached as method eval_structure() to objects of type fold_compound

◆ vrna_eval_covar_structure()

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 one 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_FC_TYPE_COMPARATIVE 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
SWIG Wrapper Notes:
This function is attached as method eval_covar_structure() to objects of type fold_compound

◆ vrna_eval_structure_verbose()

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 is a simplyfied version of vrna_eval_structure_v() that uses the default verbosity level. (

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
SWIG Wrapper Notes:
This function is attached as method eval_structure_verbose() to objects of type fold_compound

◆ vrna_eval_structure_v()

float vrna_eval_structure_v ( vrna_fold_compound_t vc,
const char *  structure,
int  verbosity_level,
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. Any positive verbosity_level activates potential warning message of the energy evaluting functions, while values $ \ge 1 $ allow for detailed control of what data is printed. A negative parameter verbosity_level turns off printing all together.

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
verbosity_levelThe level of verbosity of this function
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

◆ vrna_eval_structure_pt()

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
SWIG Wrapper Notes:
This function is attached as method eval_structure_pt() to objects of type fold_compound

◆ vrna_eval_structure_pt_verbose()

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 is a simplyfied version of vrna_eval_structure_simple_v() that uses the default verbosity level.

See also
vrna_eval_structure_pt_v(), 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
SWIG Wrapper Notes:
This function is attached as method eval_structure_pt_verbose() to objects of type fold_compound

◆ vrna_eval_structure_pt_v()

int vrna_eval_structure_pt_v ( vrna_fold_compound_t vc,
const short *  pt,
int  verbosity_level,
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. Any positive verbosity_level activates potential warning message of the energy evaluting functions, while values $ \ge 1 $ allow for detailed control of what data is printed. A negative parameter verbosity_level turns off printing all together.

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
verbosity_levelThe level of verbosity of this function
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

◆ vrna_eval_structure_simple()

int vrna_eval_structure_simple ( const char *  sequence,
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
SWIG Wrapper Notes:
In the target scripting language, this function serves as a wrapper for vrna_eval_structure_simple_v() and, thus, allows for two additional, optional arguments, the verbosity level and a file handle which default to #VRNA_VERBOSITY_QUIET and NULL, respectively.

◆ vrna_eval_circ_structure()

int vrna_eval_circ_structure ( const char *  sequence,
const char *  structure 
)

#include <ViennaRNA/eval.h>

Evaluate the free energy of a sequence/structure pair where the sequence is circular.

See also
vrna_eval_structure_simple(), vrna_eval_gquad_structure(), vrna_eval_circ_consensus_structure(), vrna_eval_circ_structure_v(), vrna_eval_structure()
Parameters
stringRNA sequence in uppercase letters
structureSecondary structure in dot-bracket notation
Returns
The free energy of the structure given the circular input sequence in kcal/mol
SWIG Wrapper Notes:
In the target scripting language, this function serves as a wrapper for vrna_eval_circ_structure_v() and, thus, allows for two additional, optional arguments, the verbosity level and a file handle which default to #VRNA_VERBOSITY_QUIET and NULL, respectively.

◆ vrna_eval_gquad_structure()

int vrna_eval_gquad_structure ( const char *  sequence,
const char *  structure 
)

#include <ViennaRNA/eval.h>

Evaluate the free energy of a sequence/structure pair where the structure may contain G-Quadruplexes.

G-Quadruplexes are annotated as plus signs ('+') for each G involved in the motif. Linker sequences must be denoted by dots ('.') as they are considered unpaired. Below is an example of a 2-layer G-quadruplex:

GGAAGGAAAGGAGG
++..++...++.++
See also
vrna_eval_structure_simple(), vrna_eval_circ_structure(), vrna_eval_gquad_consensus_structure(), vrna_eval_gquad_structure_v(), vrna_eval_structure()
Parameters
stringRNA sequence in uppercase letters
structureSecondary structure in dot-bracket notation
Returns
The free energy of the structure including contributions of G-quadruplexes in kcal/mol
SWIG Wrapper Notes:
In the target scripting language, this function serves as a wrapper for vrna_eval_gquad_structure_v() and, thus, allows for two additional, optional arguments, the verbosity level and a file handle which default to #VRNA_VERBOSITY_QUIET and NULL, respectively.

◆ vrna_eval_circ_gquad_structure()

int vrna_eval_circ_gquad_structure ( const char *  sequence,
const char *  structure 
)

#include <ViennaRNA/eval.h>

Evaluate the free energy of a sequence/structure pair where the sequence is circular and the structure may contain G-Quadruplexes.

G-Quadruplexes are annotated as plus signs ('+') for each G involved in the motif. Linker sequences must be denoted by dots ('.') as they are considered unpaired. Below is an example of a 2-layer G-quadruplex:

GGAAGGAAAGGAGG
++..++...++.++
See also
vrna_eval_structure_simple(), vrna_eval_circ_gquad_consensus_structure(), vrna_eval_circ_gquad_structure_v(), vrna_eval_structure()
Parameters
stringRNA sequence in uppercase letters
structureSecondary structure in dot-bracket notation
Returns
The free energy of the structure including contributions of G-quadruplexes in kcal/mol
SWIG Wrapper Notes:
In the target scripting language, this function serves as a wrapper for vrna_eval_circ_gquad_structure_v() and, thus, allows for two additional, optional arguments, the verbosity level and a file handle which default to #VRNA_VERBOSITY_QUIET and NULL, respectively.

◆ vrna_eval_structure_simple_verbose()

int vrna_eval_structure_simple_verbose ( const char *  sequence,
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 is a simplyfied version of vrna_eval_structure_simple_v() that uses the default verbosity level.

See also
vrna_eval_structure_simple_v(), 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
SWIG Wrapper Notes:
This function is not available. Use vrna_eval_structure_simple_v() instead!

◆ vrna_eval_structure_simple_v()

int vrna_eval_structure_simple_v ( const char *  sequence,
const char *  structure,
int  verbosity_level,
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. Any positive verbosity_level activates potential warning message of the energy evaluting functions, while values $ \ge 1 $ allow for detailed control of what data is printed. A negative parameter verbosity_level turns off printing all together.

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_pt_verbose(),
Parameters
stringRNA sequence in uppercase letters
structureSecondary structure in dot-bracket notation
verbosity_levelThe level of verbosity of this function
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
SWIG Wrapper Notes:
This function is available through an overloaded version of vrna_eval_structure_simple(). The last two arguments for this function are optional and default to #VRNA_VERBOSITY_QUIET and NULL, respectively.

◆ vrna_eval_circ_structure_v()

int vrna_eval_circ_structure_v ( const char *  sequence,
const char *  structure,
int  verbosity_level,
FILE *  file 
)

#include <ViennaRNA/eval.h>

Evaluate free energy of a sequence/structure pair, assume sequence to be circular and print contributions per loop.

This function is the same as vrna_eval_structure_simple_v() but assumes the input sequence to be circularized.

See also
vrna_eval_structure_simple_v(), vrna_eval_circ_structure(), vrna_eval_structure_verbose()
Parameters
stringRNA sequence in uppercase letters
structureSecondary structure in dot-bracket notation
verbosity_levelThe level of verbosity of this function
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
SWIG Wrapper Notes:
This function is available through an overloaded version of vrna_eval_circ_structure(). The last two arguments for this function are optional and default to #VRNA_VERBOSITY_QUIET and NULL, respectively.

◆ vrna_eval_gquad_structure_v()

int vrna_eval_gquad_structure_v ( const char *  sequence,
const char *  structure,
int  verbosity_level,
FILE *  file 
)

#include <ViennaRNA/eval.h>

Evaluate free energy of a sequence/structure pair, allow for G-Quadruplexes in the structure and print contributions per loop.

This function is the same as vrna_eval_structure_simple_v() but allows for annotated G-Quadruplexes in the dot-bracket structure input.

G-Quadruplexes are annotated as plus signs ('+') for each G involved in the motif. Linker sequences must be denoted by dots ('.') as they are considered unpaired. Below is an example of a 2-layer G-quadruplex:

GGAAGGAAAGGAGG
++..++...++.++
See also
vrna_eval_structure_simple_v(), vrna_eval_gquad_structure(), vrna_eval_structure_verbose()
Parameters
stringRNA sequence in uppercase letters
structureSecondary structure in dot-bracket notation
verbosity_levelThe level of verbosity of this function
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
SWIG Wrapper Notes:
This function is available through an overloaded version of vrna_eval_gquad_structure(). The last two arguments for this function are optional and default to #VRNA_VERBOSITY_QUIET and NULL, respectively.

◆ vrna_eval_circ_gquad_structure_v()

int vrna_eval_circ_gquad_structure_v ( const char *  sequence,
const char *  structure,
int  verbosity_level,
FILE *  file 
)

#include <ViennaRNA/eval.h>

Evaluate free energy of a sequence/structure pair, assume sequence to be circular, allow for G-Quadruplexes in the structure, and print contributions per loop.

This function is the same as vrna_eval_structure_simple_v() but assumes the input sequence to be circular and allows for annotated G-Quadruplexes in the dot-bracket structure input.

G-Quadruplexes are annotated as plus signs ('+') for each G involved in the motif. Linker sequences must be denoted by dots ('.') as they are considered unpaired. Below is an example of a 2-layer G-quadruplex:

GGAAGGAAAGGAGG
++..++...++.++
Parameters
stringRNA sequence in uppercase letters
structureSecondary structure in dot-bracket notation
verbosity_levelThe level of verbosity of this function
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
SWIG Wrapper Notes:
This function is available through an overloaded version of vrna_eval_circ_gquad_structure(). The last two arguments for this function are optional and default to #VRNA_VERBOSITY_QUIET and NULL, respectively.

◆ vrna_eval_consensus_structure_simple()

int vrna_eval_consensus_structure_simple ( const char **  alignment,
const char *  structure 
)

#include <ViennaRNA/eval.h>

Calculate the free energy of an already folded RNA sequence alignment.

This function allows for energy evaluation for a given multiple sequence alignment and consensus 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.

Note
The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.
See also
vrna_eval_covar_structure(), vrna_eval_structure(), vrna_eval_structure_pt(), vrna_eval_structure_verbose(), vrna_eval_structure_pt_verbose()
Parameters
alignmentRNA sequence alignment in uppercase letters and hyphen ('-') to denote gaps
structureConsensus Secondary structure in dot-bracket notation
Returns
The free energy of the consensus structure given the input alignment in kcal/mol
SWIG Wrapper Notes:
This function is available through an overloadeded version of vrna_eval_structure_simple(). Simply pass a sequence alignment as list of strings (including gaps) as first, and the consensus structure as second argument

◆ vrna_eval_circ_consensus_structure()

int vrna_eval_circ_consensus_structure ( const char **  alignment,
const char *  structure 
)

#include <ViennaRNA/eval.h>

Evaluate the free energy of a multiple sequence alignment/consensus structure pair where the sequences are circular.

Note
The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.
See also
vrna_eval_covar_structure(), vrna_eval_consensus_structure_simple(), vrna_eval_gquad_consensus_structure(), vrna_eval_circ_structure(), vrna_eval_circ_consensus_structure_v(), vrna_eval_structure()
Parameters
alignmentRNA sequence alignment in uppercase letters
structureConsensus secondary structure in dot-bracket notation
Returns
The free energy of the consensus structure given the circular input sequence in kcal/mol
SWIG Wrapper Notes:
This function is available through an overloadeded version of vrna_eval_circ_structure(). Simply pass a sequence alignment as list of strings (including gaps) as first, and the consensus structure as second argument

◆ vrna_eval_gquad_consensus_structure()

int vrna_eval_gquad_consensus_structure ( const char **  alignment,
const char *  structure 
)

#include <ViennaRNA/eval.h>

Evaluate the free energy of a multiple sequence alignment/consensus structure pair where the structure may contain G-Quadruplexes.

G-Quadruplexes are annotated as plus signs ('+') for each G involved in the motif. Linker sequences must be denoted by dots ('.') as they are considered unpaired. Below is an example of a 2-layer G-quadruplex:

GGAAGGAAAGGAGG
++..++...++.++
Note
The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.
See also
vrna_eval_covar_structure(), vrna_eval_consensus_structure_simple(), vrna_eval_circ_consensus_structure(), vrna_eval_gquad_structure(), vrna_eval_gquad_consensus_structure_v(), vrna_eval_structure()
Parameters
alignmentRNA sequence alignment in uppercase letters
structureConsensus secondary structure in dot-bracket notation
Returns
The free energy of the consensus structure including contributions of G-quadruplexes in kcal/mol
SWIG Wrapper Notes:
This function is available through an overloadeded version of vrna_eval_gquad_structure(). Simply pass a sequence alignment as list of strings (including gaps) as first, and the consensus structure as second argument

◆ vrna_eval_circ_gquad_consensus_structure()

int vrna_eval_circ_gquad_consensus_structure ( const char **  alignment,
const char *  structure 
)

#include <ViennaRNA/eval.h>

Evaluate the free energy of a multiple sequence alignment/consensus structure pair where the sequence is circular and the structure may contain G-Quadruplexes.

G-Quadruplexes are annotated as plus signs ('+') for each G involved in the motif. Linker sequences must be denoted by dots ('.') as they are considered unpaired. Below is an example of a 2-layer G-quadruplex:

GGAAGGAAAGGAGG
++..++...++.++
Note
The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.
See also
vrna_eval_covar_structure(), vrna_eval_consensus_structure_simple(), vrna_eval_circ_consensus_structure(), vrna_eval_gquad_structure(), vrna_eval_circ_gquad_consensus_structure_v(), vrna_eval_structure()
Parameters
alignmentRNA sequence alignment in uppercase letters
structureConsensus secondary structure in dot-bracket notation
Returns
The free energy of the consensus structure including contributions of G-quadruplexes in kcal/mol
SWIG Wrapper Notes:
This function is available through an overloadeded version of vrna_eval_circ_gquad_structure(). Simply pass a sequence alignment as list of strings (including gaps) as first, and the consensus structure as second argument

◆ vrna_eval_consensus_structure_simple_verbose()

int vrna_eval_consensus_structure_simple_verbose ( const char **  alignment,
const char *  structure,
FILE *  file 
)

#include <ViennaRNA/eval.h>

Evaluate the free energy of a consensus structure for an RNA sequence alignment and print contributions per loop.

This function is a simplyfied version of vrna_eval_consensus_structure_simple_v() that uses the default verbosity level.

Note
The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.
See also
vrna_eval_consensus_structure_simple_v(), vrna_eval_structure_verbose(), vrna_eval_structure_pt(), vrna_eval_structure_pt_verbose()
Parameters
alignmentRNA sequence alignment in uppercase letters. Gaps are denoted by hyphens ('-')
structureConsensus secondary structure in dot-bracket notation
fileA file handle where this function should print to (may be NULL).
Returns
The free energy of the conensus structure given the aligned input sequences in kcal/mol
SWIG Wrapper Notes:
This function is not available. Use vrna_eval_consensus_structure_simple_v() instead!

◆ vrna_eval_consensus_structure_simple_v()

int vrna_eval_consensus_structure_simple_v ( const char **  alignment,
const char *  structure,
int  verbosity_level,
FILE *  file 
)

#include <ViennaRNA/eval.h>

Evaluate the free energy of a consensus structure for an RNA sequence alignment and print contributions per loop.

This function allows for detailed energy evaluation of a given sequence alignment/consensus structure pair. In contrast to vrna_eval_consensus_structure_simple() 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. Any positive verbosity_level activates potential warning message of the energy evaluting functions, while values $ \ge 1 $ allow for detailed control of what data is printed. A negative parameter verbosity_level turns off printing all together.

Note
The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.
See also
vrna_eval_consensus_structure(), vrna_eval_structure()
Parameters
alignmentRNA sequence alignment in uppercase letters. Gaps are denoted by hyphens ('-')
structureConsensus secondary structure in dot-bracket notation
verbosity_levelThe level of verbosity of this function
fileA file handle where this function should print to (may be NULL).
Returns
The free energy of the consensus structure given the sequence alignment in kcal/mol
SWIG Wrapper Notes:
This function is available through an overloaded version of vrna_eval_structure_simple(). Simply pass a sequence alignment as list of strings (including gaps) as first, and the consensus structure as second argument. The last two arguments are optional and default to #VRNA_VERBOSITY_QUIET and NULL, respectively.

◆ vrna_eval_circ_consensus_structure_v()

int vrna_eval_circ_consensus_structure_v ( const char **  alignment,
const char *  structure,
int  verbosity_level,
FILE *  file 
)

#include <ViennaRNA/eval.h>

Evaluate the free energy of a consensus structure for an alignment of circular RNA sequences and print contributions per loop.

This function is identical with vrna_eval_consensus_structure_simple_v() but assumed the aligned sequences to be circular.

Note
The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.
See also
vrna_eval_consensus_structure_simple_v(), vrna_eval_circ_consensus_structure(), vrna_eval_structure()
Parameters
alignmentRNA sequence alignment in uppercase letters. Gaps are denoted by hyphens ('-')
structureConsensus secondary structure in dot-bracket notation
verbosity_levelThe level of verbosity of this function
fileA file handle where this function should print to (may be NULL).
Returns
The free energy of the consensus structure given the sequence alignment in kcal/mol
SWIG Wrapper Notes:
This function is available through an overloaded version of vrna_eval_circ_structure(). Simply pass a sequence alignment as list of strings (including gaps) as first, and the consensus structure as second argument. The last two arguments are optional and default to #VRNA_VERBOSITY_QUIET and NULL, respectively.

◆ vrna_eval_gquad_consensus_structure_v()

int vrna_eval_gquad_consensus_structure_v ( const char **  alignment,
const char *  structure,
int  verbosity_level,
FILE *  file 
)

#include <ViennaRNA/eval.h>

Evaluate the free energy of a consensus structure for an RNA sequence alignment, allow for annotated G-Quadruplexes in the structure and print contributions per loop.

This function is identical with vrna_eval_consensus_structure_simple_v() but allows for annotated G-Quadruplexes in the consensus structure.

G-Quadruplexes are annotated as plus signs ('+') for each G involved in the motif. Linker sequences must be denoted by dots ('.') as they are considered unpaired. Below is an example of a 2-layer G-quadruplex:

GGAAGGAAAGGAGG
++..++...++.++
Note
The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.
See also
vrna_eval_consensus_structure_simple_v(), vrna_eval_gquad_consensus_structure(), vrna_eval_structure()
Parameters
alignmentRNA sequence alignment in uppercase letters. Gaps are denoted by hyphens ('-')
structureConsensus secondary structure in dot-bracket notation
verbosity_levelThe level of verbosity of this function
fileA file handle where this function should print to (may be NULL).
Returns
The free energy of the consensus structure given the sequence alignment in kcal/mol
SWIG Wrapper Notes:
This function is available through an overloaded version of vrna_eval_gquad_structure(). Simply pass a sequence alignment as list of strings (including gaps) as first, and the consensus structure as second argument. The last two arguments are optional and default to #VRNA_VERBOSITY_QUIET and NULL, respectively.

◆ vrna_eval_circ_gquad_consensus_structure_v()

int vrna_eval_circ_gquad_consensus_structure_v ( const char **  alignment,
const char *  structure,
int  verbosity_level,
FILE *  file 
)

#include <ViennaRNA/eval.h>

Evaluate the free energy of a consensus structure for an alignment of circular RNA sequences, allow for annotated G-Quadruplexes in the structure and print contributions per loop.

This function is identical with vrna_eval_consensus_structure_simple_v() but assumes the sequences in the alignment to be circular and allows for annotated G-Quadruplexes in the consensus structure.

G-Quadruplexes are annotated as plus signs ('+') for each G involved in the motif. Linker sequences must be denoted by dots ('.') as they are considered unpaired. Below is an example of a 2-layer G-quadruplex:

GGAAGGAAAGGAGG
++..++...++.++
Note
The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.
See also
vrna_eval_consensus_structure_simple_v(), vrna_eval_circ_gquad_consensus_structure(), vrna_eval_structure()
Parameters
alignmentRNA sequence alignment in uppercase letters. Gaps are denoted by hyphens ('-')
structureConsensus secondary structure in dot-bracket notation
verbosity_levelThe level of verbosity of this function
fileA file handle where this function should print to (may be NULL).
Returns
The free energy of the consensus structure given the sequence alignment in kcal/mol
SWIG Wrapper Notes:
This function is available through an overloaded version of vrna_eval_circ_gquad_structure(). Simply pass a sequence alignment as list of strings (including gaps) as first, and the consensus structure as second argument. The last two arguments are optional and default to #VRNA_VERBOSITY_QUIET and NULL, respectively.

◆ vrna_eval_structure_pt_simple()

int vrna_eval_structure_pt_simple ( const char *  sequence,
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
SWIG Wrapper Notes:
In the target scripting language, this function serves as a wrapper for vrna_eval_structure_pt_v() and, thus, allows for two additional, optional arguments, the verbosity level and a file handle which default to #VRNA_VERBOSITY_QUIET and NULL, respectively.

◆ vrna_eval_structure_pt_simple_verbose()

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 is a simplyfied version of vrna_eval_structure_pt_simple_v() that uses the default verbosity level.

See also
vrna_eval_structure_pt_simple_v(), 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

◆ vrna_eval_structure_pt_simple_v()

int vrna_eval_structure_pt_simple_v ( const char *  string,
const short *  pt,
int  verbosity_level,
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_v(), vrna_eval_structure_simple()
Parameters
stringRNA sequence in uppercase letters
ptSecondary structure as pair_table
verbosity_levelThe level of verbosity of this function
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

◆ vrna_eval_consensus_structure_pt_simple()

int vrna_eval_consensus_structure_pt_simple ( const char **  alignment,
const short *  pt 
)

#include <ViennaRNA/eval.h>

Evaluate the Free Energy of a Consensus Secondary Structure given a Sequence Alignment.

Note
The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.
See also
vrna_eval_consensus_structure_simple(), vrna_eval_structure_pt(), vrna_eval_structure(), vrna_eval_covar_structure()
Parameters
alignmentRNA sequence alignment in uppercase letters. Gaps are denoted by hyphens ('-')
ptSecondary structure in pair table format
Returns
Free energy of the consensus structure in 10cal/mol
SWIG Wrapper Notes:
This function is available through an overloadeded version of vrna_eval_structure_pt_simple(). Simply pass a sequence alignment as list of strings (including gaps) as first, and the consensus structure as second argument

◆ vrna_eval_loop_pt()

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
SWIG Wrapper Notes:
This function is attached as method eval_loop_pt() to objects of type fold_compound

◆ vrna_eval_loop_pt_v()

int vrna_eval_loop_pt_v ( vrna_fold_compound_t vc,
int  i,
const short *  pt,
int  verbosity_level 
)

#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
verbosity_levelThe level of verbosity of this function
Returns
free energy of the loop in 10cal/mol

◆ vrna_eval_move()

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
SWIG Wrapper Notes:
This function is attached as method eval_move() to objects of type fold_compound

◆ vrna_eval_move_pt()

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
SWIG Wrapper Notes:
This function is attached as method eval_move_pt() to objects of type fold_compound

◆ energy_of_structure()

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

◆ energy_of_struct_par()

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

◆ energy_of_circ_structure()

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

◆ energy_of_circ_struct_par()

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

◆ energy_of_structure_pt()

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

◆ energy_of_struct_pt_par()

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

◆ energy_of_move()

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

◆ energy_of_move_pt()

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

◆ loop_energy()

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

◆ energy_of_struct()

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

◆ energy_of_struct_pt()

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

◆ energy_of_circ_struct()

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