Free energy evaluation

Overview

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

// global variables

int cut_point
int eos_debug

// global functions

float vrna_eval_structure (
    vrna_fold_compound_t* vc,
    const char* structure
    )

float vrna_eval_covar_structure (
    vrna_fold_compound_t* vc,
    const char* structure
    )

float vrna_eval_structure_verbose (
    vrna_fold_compound_t* vc,
    const char* structure,
    FILE* file
    )

float vrna_eval_structure_v (
    vrna_fold_compound_t* vc,
    const char* structure,
    int verbosity_level,
    FILE* file
    )

int vrna_eval_structure_pt (
    vrna_fold_compound_t* vc,
    const short* pt
    )

int vrna_eval_structure_pt_verbose (
    vrna_fold_compound_t* vc,
    const short* pt,
    FILE* file
    )

int vrna_eval_structure_pt_v (
    vrna_fold_compound_t* vc,
    const short* pt,
    int verbosity_level,
    FILE* file
    )

float vrna_eval_structure_simple (
    const char* string,
    const char* structure
    )

float vrna_eval_circ_structure (
    const char* string,
    const char* structure
    )

float vrna_eval_gquad_structure (
    const char* string,
    const char* structure
    )

float vrna_eval_circ_gquad_structure (
    const char* string,
    const char* structure
    )

float vrna_eval_structure_simple_verbose (
    const char* string,
    const char* structure,
    FILE* file
    )

float vrna_eval_structure_simple_v (
    const char* string,
    const char* structure,
    int verbosity_level,
    FILE* file
    )

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

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

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

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

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

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

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

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

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

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

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

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

int vrna_eval_structure_pt_simple (
    const char* string,
    const short* pt
    )

int vrna_eval_structure_pt_simple_verbose (
    const char* string,
    const short* pt,
    FILE* file
    )

int vrna_eval_structure_pt_simple_v (
    const char* string,
    const short* pt,
    int verbosity_level,
    FILE* file
    )

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

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
    )

int vrna_eval_loop_pt (
    vrna_fold_compound_t* vc,
    int i,
    const short* pt
    )

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

float vrna_eval_move (
    vrna_fold_compound_t* vc,
    const char* structure,
    int m1,
    int m2
    )

int vrna_eval_move_pt (
    vrna_fold_compound_t* vc,
    short* pt,
    int m1,
    int m2
    )

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
    )

float energy_of_structure (
    const char* string,
    const char* structure,
    int verbosity_level
    )

float energy_of_struct_par (
    const char* string,
    const char* structure,
    vrna_param_t* parameters,
    int verbosity_level
    )

float energy_of_circ_structure (
    const char* string,
    const char* structure,
    int verbosity_level
    )

float energy_of_circ_struct_par (
    const char* string,
    const char* structure,
    vrna_param_t* parameters,
    int verbosity_level
    )

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
    )

int energy_of_struct_pt_par (
    const char* string,
    short* ptable,
    short* s,
    short* s1,
    vrna_param_t* parameters,
    int verbosity_level
    )

float energy_of_move (
    const char* string,
    const char* structure,
    int m1,
    int m2
    )

int energy_of_move_pt (
    short* pt,
    short* s,
    short* s1,
    int m1,
    int m2
    )

int loop_energy (
    short* ptable,
    short* s,
    short* s1,
    int i
    )

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
    )

Detailed Documentation

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

Global Variables

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

Global Functions

float vrna_eval_structure (
    vrna_fold_compound_t* vc,
    const char* structure
    )
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);

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

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

Note

Accepts vrna_fold_compound_t of type VRNA_FC_TYPE_SINGLE and VRNA_FC_TYPE_COMPARATIVE

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.

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);

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

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

Note

Accepts vrna_fold_compound_t of type VRNA_FC_TYPE_COMPARATIVE only!

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.

This function is a simplyfied version of vrna_eval_structure_v() that uses the default verbosity level. ( SWIG Wrapper Notes This function is attached as method eval_structure_verbose() to objects of type fold_compound

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

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.

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 :math:` 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:

vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_EVAL_ONLY);

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
    )
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);

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

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

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.

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

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

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

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.

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 :math:` ge 1 ` allow for detailed control of what data is printed. A negative parameter verbosity_level turns off printing all together.

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

float vrna_eval_structure_simple (
    const char* string,
    const char* structure
    )
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.

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.

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

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.

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.

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

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.

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
++..++...++.++

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.

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

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.

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
++..++...++.++

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.

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

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.

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

SWIG Wrapper Notes This function is not available. Use vrna_eval_structure_simple_v() instead!

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

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.

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 :math:` 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.

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.

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

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.

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

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.

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

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.

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
++..++...++.++

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.

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

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.

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
++..++...++.++

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.

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

float vrna_eval_consensus_structure_simple (
    const char** alignment,
    const char* structure
    )
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.

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

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

Note

The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.

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.

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

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

Note

The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.

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.

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
++..++...++.++

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

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

Note

The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.

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.

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
++..++...++.++

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

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

Note

The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.

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.

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

SWIG Wrapper Notes This function is not available. Use vrna_eval_consensus_structure_simple_v() instead!

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

Note

The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.

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.

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 :math:` ge 1 ` allow for detailed control of what data is printed. A negative parameter verbosity_level turns off printing all together.

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.

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

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()

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.

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

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.

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

Note

The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.

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.

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
++..++...++.++

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.

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

Note

The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.

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.

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
++..++...++.++

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.

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

Note

The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.

int vrna_eval_structure_pt_simple (
    const char* string,
    const short* pt
    )
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.

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.

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

int vrna_eval_structure_pt_simple_verbose (
    const char* string,
    const short* pt,
    FILE* file
    )
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.

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
    )
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.

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

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

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

Note

The free energy returned from this function already includes the covariation pseudo energies that is used fir comparative structure prediction within this library.

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

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

Parameters:

vc A vrna_fold_compound_t containing the energy parameters and model details
i position of covering base pair
pt the pair table of the secondary structure

Returns:

free energy of the loop in 10cal/mol

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

Parameters:

vc A vrna_fold_compound_t containing the energy parameters and model details
i position of covering base pair
pt the pair table of the secondary structure
verbosity_level The level of verbosity of this function

Returns:

free energy of the loop in 10cal/mol

float vrna_eval_move (
    vrna_fold_compound_t* vc,
    const char* structure,
    int m1,
    int m2
    )
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).

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

Parameters:

vc A vrna_fold_compound_t containing the energy parameters and model details
structure secondary structure in dot-bracket notation
m1 first coordinate of base pair
m2 second coordinate of base pair

Returns:

energy change of the move in kcal/mol

int vrna_eval_move_pt (
    vrna_fold_compound_t* vc,
    short* pt,
    int m1,
    int m2
    )
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).

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

Parameters:

vc A vrna_fold_compound_t containing the energy parameters and model details
pt the pair table of the secondary structure
m1 first coordinate of base pair
m2 second coordinate of base pair

Returns:

energy change of the move in 10cal/mol

See also:

vrna_eval_move()

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.

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!

Parameters:

string RNA sequence
structure secondary structure in dot-bracket notation
verbosity_level a flag to turn verbose output on/off

Returns:

the free energy of the input structure given the input sequence in kcal/mol

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.

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.

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!

Parameters:

string RNA sequence in uppercase letters
structure Secondary structure in dot-bracket notation
parameters A data structure containing the prescaled energy contributions and the model details.
verbosity_level A flag to turn verbose output on/off

Returns:

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

float energy_of_circ_structure (
    const char* string,
    const char* structure,
    int verbosity_level
    )
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!

Parameters:

string RNA sequence
structure Secondary structure in dot-bracket notation
verbosity_level A flag to turn verbose output on/off

Returns:

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

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.

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.

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!

Parameters:

string RNA sequence
structure Secondary structure in dot-bracket notation
parameters A data structure containing the prescaled energy contributions and the model details.
verbosity_level A flag to turn verbose output on/off

Returns:

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

int energy_of_structure_pt (
    const char* string,
    short* ptable,
    short* s,
    short* s1,
    int verbosity_level
    )
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!

Parameters:

string RNA sequence
ptable the pair table of the secondary structure
s encoded RNA sequence
s1 encoded RNA sequence
verbosity_level a flag to turn verbose output on/off

Returns:

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

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.

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.

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!

Parameters:

string RNA sequence in uppercase letters
ptable The pair table of the secondary structure
s Encoded RNA sequence
s1 Encoded RNA sequence
parameters A data structure containing the prescaled energy contributions and the model details.
verbosity_level A flag to turn verbose output on/off

Returns:

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

float energy_of_move (
    const char* string,
    const char* structure,
    int m1,
    int m2
    )
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!

Parameters:

string RNA sequence
structure secondary structure in dot-bracket notation
m1 first coordinate of base pair
m2 second coordinate of base pair

Returns:

energy change of the move in kcal/mol

See also:

vrna_eval_move()

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)

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!

Parameters:

pt the pair table of the secondary structure
s encoded RNA sequence
s1 encoded RNA sequence
m1 first coordinate of base pair
m2 second coordinate of base pair

Returns:

energy change of the move in 10cal/mol

int loop_energy (
    short* ptable,
    short* s,
    short* s1,
    int i
    )
Calculate energy of a loop.

Deprecated Use vrna_eval_loop_pt() instead!

Parameters:

ptable the pair table of the secondary structure
s encoded RNA sequence
s1 encoded RNA sequence
i position of covering base pair

Returns:

free energy of the loop in 10cal/mol

float energy_of_struct (
    const char* string,
    const char* structure
    )

Calculate the free energy of an already folded RNA

Deprecated This function is deprecated and should not be used in future programs! Use energy_of_structure() instead!

Parameters:

string RNA sequence
structure secondary structure in dot-bracket notation

Returns:

the free energy of the input structure given the input sequence in kcal/mol

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…

int energy_of_struct_pt (
    const char* string,
    short* ptable,
    short* s,
    short* s1
    )

Calculate the free energy of an already folded RNA

Deprecated This function is deprecated and should not be used in future programs! Use energy_of_structure_pt() instead!

Parameters:

string RNA sequence
ptable the pair table of the secondary structure
s encoded RNA sequence
s1 encoded RNA sequence

Returns:

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

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…

float energy_of_circ_struct (
    const char* string,
    const char* structure
    )

Calculate the free energy of an already folded circular RNA

Deprecated This function is deprecated and should not be used in future programs Use energy_of_circ_structure() instead!

Parameters:

string RNA sequence
structure secondary structure in dot-bracket notation

Returns:

the free energy of the input structure given the input sequence in kcal/mol

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…