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 )
int cut_point
int eos_debug
float vrna_eval_structure ( vrna_fold_compound_t* vc, const char* structure )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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 )
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
See also:
int vrna_eval_move_pt ( vrna_fold_compound_t* vc, short* pt, int m1, int m2 )
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:
float energy_of_structure ( const char* string, const char* structure, int verbosity_level )
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.
See also:
float energy_of_struct_par ( const char* string, const char* structure, vrna_param_t* parameters, int verbosity_level )
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
See also:
float energy_of_circ_structure ( const char* string, const char* structure, int verbosity_level )
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.
See also:
float energy_of_circ_struct_par ( const char* string, const char* structure, vrna_param_t* parameters, int verbosity_level )
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
See also:
int energy_of_structure_pt ( const char* string, short* ptable, short* s, short* s1, int verbosity_level )
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.
See also:
int energy_of_struct_pt_par ( const char* string, short* ptable, short* s, short* s1, vrna_param_t* parameters, int verbosity_level )
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
See also:
float energy_of_move ( const char* string, const char* structure, int m1, int m2 )
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:
int energy_of_move_pt ( short* pt, short* s, short* s1, int m1, int m2 )
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
See also:
int loop_energy ( short* ptable, short* s, short* s1, int i )
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
See also:
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…
See also:
energy_of_structure , energy_of_circ_struct() , energy_of_struct_pt()
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…
See also:
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…