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.

Several different functions to evaluate the free energy of a particular secondary structure under a particular set of parameters and the Nearest Neighbor Energy model are available. For most of them, two different forms of representations for the secondary structure may be used:

• The Dot-Bracket string
• A pair table representation

Furthermore, the evaluation functions are divided into basic and simplified variants, where basic functions require the use of a vrna_fold_compound_t data structure holding the sequence string, and model configuration (settings and parameters). The simplified functions, on the other hand, provide often used default model settings that may be called directly with only sequence and structure data.

Finally, verbose options exist for some functions that allow one to print the (individual) free energy contributions to some FILE stream.

Collaboration diagram for Free Energy Evaluation:

Modules
	Energy Evaluation for Individual Loops
	Functions to evaluate the free energy of particular types of loops.
	Energy Evaluation for Atomic Moves
	Functions to evaluate the free energy change of a structure after application of (a set of) atomic moves.
	Deprecated Interface for Free Energy Evaluation
	Deprecated Energy Evaluation functions.

Files
file	eval.h
	Functions and variables related to energy evaluation of sequence/structure pairs.
file	all.h
	Energy evaluation for MFE and partition function calculations.
file	external.h
	Energy evaluation of exterior loops for MFE and partition function calculations.
file	hairpin.h
	Energy evaluation of hairpin loops for MFE and partition function calculations.
file	internal.h
	Energy evaluation of interior loops for MFE and partition function calculations.
file	multibranch.h
	Energy evaluation of multibranch loops for MFE and partition function calculations.

Macros
#define	VRNA_VERBOSITY_QUIET   -1
	Quiet level verbosity setting.
#define	VRNA_VERBOSITY_DEFAULT   1
	Default level verbosity setting.

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...
float	vrna_eval_structure_cstr (vrna_fold_compound_t *vc, const char *structure, int verbosity_level, vrna_cstr_t output_stream)

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)

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:

vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_EVAL_ONLY);

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

vc	A vrna_fold_compound_t containing the energy parameters and model details
structure	Secondary 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

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:

vc = vrna_fold_compound_comparative(alignment, NULL, VRNA_OPTION_EVAL_ONLY);

Note

Accepts vrna_fold_compound_t of type VRNA_FC_TYPE_COMPARATIVE only!

See also

vrna_fold_compound_comparative(), vrna_eval_structure()

Parameters

vc	A vrna_fold_compound_t containing the energy parameters and model details
structure	Secondary (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

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

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).

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

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 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:

vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_EVAL_ONLY);

See also

vrna_eval_structure_pt(), vrna_eval_structure_verbose(), vrna_eval_structure_pt_verbose(),

Parameters

vc	A vrna_fold_compound_t containing the energy parameters and model details
structure	Secondary structure in dot-bracket notation
verbosity_level	The level of verbosity of this function
file	A 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:

vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_EVAL_ONLY);

See also

vrna_ptable(), vrna_eval_structure(), vrna_eval_structure_pt_verbose()

Parameters

vc	A vrna_fold_compound_t containing the energy parameters and model details
pt	Secondary 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

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

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).

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

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:

vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_EVAL_ONLY);

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 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

vc	A vrna_fold_compound_t containing the energy parameters and model details
pt	Secondary structure as pair_table
verbosity_level	The level of verbosity of this function
file	A 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_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

string	RNA sequence in uppercase letters
structure	Secondary 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.

int vrna_eval_circ_structure	(	const char *	string,
		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

string	RNA sequence in uppercase letters
structure	Secondary 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.

int vrna_eval_gquad_structure	(	const char *	string,
		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

string	RNA sequence in uppercase letters
structure	Secondary 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.

int vrna_eval_circ_gquad_structure	(	const char *	string,
		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

string	RNA sequence in uppercase letters
structure	Secondary 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.

int 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 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

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).

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!

int vrna_eval_structure_simple_v	(	const char *	string,
		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 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

string	RNA sequence in uppercase letters
structure	Secondary structure in dot-bracket notation
verbosity_level	The level of verbosity of this function
file	A 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.

int vrna_eval_circ_structure_v	(	const char *	string,
		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

string	RNA sequence in uppercase letters
structure	Secondary structure in dot-bracket notation
verbosity_level	The level of verbosity of this function
file	A 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.

int vrna_eval_gquad_structure_v	(	const char *	string,
		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

string	RNA sequence in uppercase letters
structure	Secondary structure in dot-bracket notation
verbosity_level	The level of verbosity of this function
file	A 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.

int vrna_eval_circ_gquad_structure_v	(	const char *	string,
		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

string	RNA sequence in uppercase letters
structure	Secondary structure in dot-bracket notation
verbosity_level	The level of verbosity of this function
file	A 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.

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

alignment	RNA sequence alignment in uppercase letters and hyphen ('-') to denote gaps
structure	Consensus 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

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

alignment	RNA sequence alignment in uppercase letters
structure	Consensus 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

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

alignment	RNA sequence alignment in uppercase letters
structure	Consensus 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

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

alignment	RNA sequence alignment in uppercase letters
structure	Consensus 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

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

alignment	RNA sequence alignment in uppercase letters. Gaps are denoted by hyphens ('-')
structure	Consensus secondary structure in dot-bracket notation
file	A 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!

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 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

alignment	RNA sequence alignment in uppercase letters. Gaps are denoted by hyphens ('-')
structure	Consensus secondary structure in dot-bracket notation
verbosity_level	The level of verbosity of this function
file	A 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.

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

alignment	RNA sequence alignment in uppercase letters. Gaps are denoted by hyphens ('-')
structure	Consensus secondary structure in dot-bracket notation
verbosity_level	The level of verbosity of this function
file	A 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.

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

alignment	RNA sequence alignment in uppercase letters. Gaps are denoted by hyphens ('-')
structure	Consensus secondary structure in dot-bracket notation
verbosity_level	The level of verbosity of this function
file	A 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.

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

alignment	RNA sequence alignment in uppercase letters. Gaps are denoted by hyphens ('-')
structure	Consensus secondary structure in dot-bracket notation
verbosity_level	The level of verbosity of this function
file	A 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.

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

string	RNA sequence in uppercase letters
pt	Secondary 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.

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

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).

Returns

The free energy of the input structure given the input sequence in 10cal/mol

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:

vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_EVAL_ONLY);

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

string	RNA sequence in uppercase letters
pt	Secondary structure as pair_table
verbosity_level	The level of verbosity of this function
file	A 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_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

alignment	RNA sequence alignment in uppercase letters. Gaps are denoted by hyphens ('-')
pt	Secondary 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