RNAlib-2.4.4
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Functions and variables related to free energy evaluation of sequence/structure pairs. More...
Functions and variables related to free energy evaluation of sequence/structure pairs.
Modules | |
Process and evaluate individual loops | |
Files | |
file | eval.h |
Functions and variables related to energy evaluation of sequence/structure pairs. | |
Variables | |
int | cut_point |
set to first pos of second seq for cofolding | |
int | eos_debug |
verbose info from energy_of_struct | |
Basic Energy Evaluation Interface with Dot-Bracket Structure String | |
float | vrna_eval_structure (vrna_fold_compound_t *vc, const char *structure) |
Calculate the free energy of an already folded RNA. More... | |
float | vrna_eval_covar_structure (vrna_fold_compound_t *vc, const char *structure) |
Calculate the pseudo energy derived by the covariance scores of a set of aligned sequences. More... | |
float | vrna_eval_structure_verbose (vrna_fold_compound_t *vc, const char *structure, FILE *file) |
Calculate the free energy of an already folded RNA and print contributions on a per-loop base. More... | |
float | vrna_eval_structure_v (vrna_fold_compound_t *vc, const char *structure, int verbosity_level, FILE *file) |
Calculate the free energy of an already folded RNA and print contributions on a per-loop base. More... | |
Basic Energy Evaluation Interface with Structure Pair Table | |
int | vrna_eval_structure_pt (vrna_fold_compound_t *vc, const short *pt) |
Calculate the free energy of an already folded RNA. More... | |
int | vrna_eval_structure_pt_verbose (vrna_fold_compound_t *vc, const short *pt, FILE *file) |
Calculate the free energy of an already folded RNA. More... | |
int | vrna_eval_structure_pt_v (vrna_fold_compound_t *vc, const short *pt, int verbosity_level, FILE *file) |
Calculate the free energy of an already folded RNA. More... | |
Simplified Energy Evaluation with Sequence and Dot-Bracket Strings | |
float | vrna_eval_structure_simple (const char *string, const char *structure) |
Calculate the free energy of an already folded RNA. More... | |
float | vrna_eval_circ_structure (const char *string, const char *structure) |
Evaluate the free energy of a sequence/structure pair where the sequence is circular. More... | |
float | vrna_eval_gquad_structure (const char *string, const char *structure) |
Evaluate the free energy of a sequence/structure pair where the structure may contain G-Quadruplexes. More... | |
float | vrna_eval_circ_gquad_structure (const char *string, const char *structure) |
Evaluate the free energy of a sequence/structure pair where the sequence is circular and the structure may contain G-Quadruplexes. More... | |
float | vrna_eval_structure_simple_verbose (const char *string, const char *structure, FILE *file) |
Calculate the free energy of an already folded RNA and print contributions per loop. More... | |
float | vrna_eval_structure_simple_v (const char *string, const char *structure, int verbosity_level, FILE *file) |
Calculate the free energy of an already folded RNA and print contributions per loop. More... | |
float | vrna_eval_circ_structure_v (const char *string, const char *structure, int verbosity_level, FILE *file) |
Evaluate free energy of a sequence/structure pair, assume sequence to be circular and print contributions per loop. More... | |
float | vrna_eval_gquad_structure_v (const char *string, const char *structure, int verbosity_level, FILE *file) |
Evaluate free energy of a sequence/structure pair, allow for G-Quadruplexes in the structure and print contributions per loop. More... | |
float | vrna_eval_circ_gquad_structure_v (const char *string, const char *structure, int verbosity_level, FILE *file) |
Evaluate free energy of a sequence/structure pair, assume sequence to be circular, allow for G-Quadruplexes in the structure, and print contributions per loop. More... | |
Simplified Energy Evaluation with Sequence Alignments and Consensus Structure Dot-Bracket String | |
float | vrna_eval_consensus_structure_simple (const char **alignment, const char *structure) |
Calculate the free energy of an already folded RNA sequence alignment. More... | |
float | vrna_eval_circ_consensus_structure (const char **alignment, const char *structure) |
Evaluate the free energy of a multiple sequence alignment/consensus structure pair where the sequences are circular. More... | |
float | vrna_eval_gquad_consensus_structure (const char **alignment, const char *structure) |
Evaluate the free energy of a multiple sequence alignment/consensus structure pair where the structure may contain G-Quadruplexes. More... | |
float | vrna_eval_circ_gquad_consensus_structure (const char **alignment, const char *structure) |
Evaluate the free energy of a multiple sequence alignment/consensus structure pair where the sequence is circular and the structure may contain G-Quadruplexes. More... | |
float | vrna_eval_consensus_structure_simple_verbose (const char **alignment, const char *structure, FILE *file) |
Evaluate the free energy of a consensus structure for an RNA sequence alignment and print contributions per loop. More... | |
float | vrna_eval_consensus_structure_simple_v (const char **alignment, const char *structure, int verbosity_level, FILE *file) |
Evaluate the free energy of a consensus structure for an RNA sequence alignment and print contributions per loop. More... | |
float | vrna_eval_circ_consensus_structure_v (const char **alignment, const char *structure, int verbosity_level, FILE *file) |
Evaluate the free energy of a consensus structure for an alignment of circular RNA sequences and print contributions per loop. More... | |
float | vrna_eval_gquad_consensus_structure_v (const char **alignment, const char *structure, int verbosity_level, FILE *file) |
Evaluate the free energy of a consensus structure for an RNA sequence alignment, allow for annotated G-Quadruplexes in the structure and print contributions per loop. More... | |
float | vrna_eval_circ_gquad_consensus_structure_v (const char **alignment, const char *structure, int verbosity_level, FILE *file) |
Evaluate the free energy of a consensus structure for an alignment of circular RNA sequences, allow for annotated G-Quadruplexes in the structure and print contributions per loop. More... | |
Simplified Energy Evaluation with Sequence String and Structure Pair Table | |
int | vrna_eval_structure_pt_simple (const char *string, const short *pt) |
Calculate the free energy of an already folded RNA. More... | |
int | vrna_eval_structure_pt_simple_verbose (const char *string, const short *pt, FILE *file) |
Calculate the free energy of an already folded RNA. More... | |
int | vrna_eval_structure_pt_simple_v (const char *string, const short *pt, int verbosity_level, FILE *file) |
Calculate the free energy of an already folded RNA. More... | |
Simplified Energy Evaluation with Sequence Alignment and Consensus Structure Pair Table | |
int | vrna_eval_consensus_structure_pt_simple (const char **alignment, const short *pt) |
Evaluate the Free Energy of a Consensus Secondary Structure given a Sequence Alignment. More... | |
int | vrna_eval_consensus_structure_pt_simple_verbose (const char **alignment, const short *pt, FILE *file) |
int | vrna_eval_consensus_structure_pt_simple_v (const char **alignment, const short *pt, int verbosity_level, FILE *file) |
Basic Loop Energy Evaluation with Structure Pair Table | |
int | vrna_eval_loop_pt (vrna_fold_compound_t *vc, int i, const short *pt) |
Calculate energy of a loop. More... | |
int | vrna_eval_loop_pt_v (vrna_fold_compound_t *vc, int i, const short *pt, int verbosity_level) |
Calculate energy of a loop. More... | |
Basic Energy Evaluation for atomic moves | |
Here, atomic moves are considered opening or closing a single base pair, as well as shifting one pairing partner of an existing pair to a different location | |
float | vrna_eval_move (vrna_fold_compound_t *vc, const char *structure, int m1, int m2) |
Calculate energy of a move (closing or opening of a base pair) More... | |
int | vrna_eval_move_pt (vrna_fold_compound_t *vc, short *pt, int m1, int m2) |
Calculate energy of a move (closing or opening of a base pair) More... | |
int | vrna_eval_move_pt_simple (const char *string, short *pt, int m1, int m2) |
int | vrna_eval_move_shift_pt (vrna_fold_compound_t *vc, vrna_move_t *m, short *structure) |
Deprecated Energy Evaluation functions | |
Using the functions below is discouraged as they have been marked deprecated and will be removed from the library in the (near) future! | |
float | energy_of_structure (const char *string, const char *structure, int verbosity_level) |
Calculate the free energy of an already folded RNA using global model detail settings. More... | |
float | energy_of_struct_par (const char *string, const char *structure, vrna_param_t *parameters, int verbosity_level) |
Calculate the free energy of an already folded RNA. More... | |
float | energy_of_circ_structure (const char *string, const char *structure, int verbosity_level) |
Calculate the free energy of an already folded circular RNA. More... | |
float | energy_of_circ_struct_par (const char *string, const char *structure, vrna_param_t *parameters, int verbosity_level) |
Calculate the free energy of an already folded circular RNA. More... | |
float | energy_of_gquad_structure (const char *string, const char *structure, int verbosity_level) |
float | energy_of_gquad_struct_par (const char *string, const char *structure, vrna_param_t *parameters, int verbosity_level) |
int | energy_of_structure_pt (const char *string, short *ptable, short *s, short *s1, int verbosity_level) |
Calculate the free energy of an already folded RNA. More... | |
int | energy_of_struct_pt_par (const char *string, short *ptable, short *s, short *s1, vrna_param_t *parameters, int verbosity_level) |
Calculate the free energy of an already folded RNA. More... | |
float | energy_of_move (const char *string, const char *structure, int m1, int m2) |
Calculate energy of a move (closing or opening of a base pair) More... | |
int | energy_of_move_pt (short *pt, short *s, short *s1, int m1, int m2) |
Calculate energy of a move (closing or opening of a base pair) More... | |
int | loop_energy (short *ptable, short *s, short *s1, int i) |
Calculate energy of a loop. More... | |
float | energy_of_struct (const char *string, const char *structure) |
int | energy_of_struct_pt (const char *string, short *ptable, short *s, short *s1) |
float | energy_of_circ_struct (const char *string, const char *structure) |
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 | A vrna_fold_compound_t containing the energy parameters and model details |
structure | Secondary structure in dot-bracket notation |
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 | A vrna_fold_compound_t containing the energy parameters and model details |
structure | Secondary (consensus) structure in dot-bracket notation |
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. (
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). |
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 | 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). |
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 | A vrna_fold_compound_t containing the energy parameters and model details |
pt | Secondary structure as pair_table |
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.
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). |
int vrna_eval_structure_pt_v | ( | vrna_fold_compound_t * | vc, |
const short * | pt, | ||
int | verbosity_level, | ||
FILE * | file | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
This function allows for energy evaluation of a given sequence/structure pair where the structure is provided in pair_table format as obtained from vrna_ptable(). Model details, energy parameters, and possibly soft constraints are used as provided via the parameter 'vc'. The fold_compound does not need to contain any DP matrices, but all the most basic init values as one would get from a call like this:
In contrast to vrna_eval_structure_pt() this function prints detailed energy contributions based on individual loops to a file handle. If NULL is passed as file handle, this function defaults to print to stdout. Any positive verbosity_level
activates potential warning message of the energy evaluting functions, while values allow for detailed control of what data is printed. A negative parameter
verbosity_level
turns off printing all together.
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). |
int vrna_eval_structure_simple | ( | const char * | sequence, |
const char * | structure | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
This function allows for energy evaluation of a given sequence/structure pair. In contrast to vrna_eval_structure() this function assumes default model details and default energy parameters in order to evaluate the free energy of the secondary structure. Therefore, it serves as a simple interface function for energy evaluation for situations where no changes on the energy model are required.
string | RNA sequence in uppercase letters |
structure | Secondary structure in dot-bracket notation |
int vrna_eval_circ_structure | ( | const char * | sequence, |
const char * | structure | ||
) |
#include <ViennaRNA/eval.h>
Evaluate the free energy of a sequence/structure pair where the sequence is circular.
string | RNA sequence in uppercase letters |
structure | Secondary structure in dot-bracket notation |
int vrna_eval_gquad_structure | ( | const char * | sequence, |
const char * | structure | ||
) |
#include <ViennaRNA/eval.h>
Evaluate the free energy of a sequence/structure pair where the structure may contain G-Quadruplexes.
G-Quadruplexes are annotated as plus signs ('+') for each G involved in the motif. Linker sequences must be denoted by dots ('.') as they are considered unpaired. Below is an example of a 2-layer G-quadruplex:
string | RNA sequence in uppercase letters |
structure | Secondary structure in dot-bracket notation |
int vrna_eval_circ_gquad_structure | ( | const char * | sequence, |
const char * | structure | ||
) |
#include <ViennaRNA/eval.h>
Evaluate the free energy of a sequence/structure pair where the sequence is circular and the structure may contain G-Quadruplexes.
G-Quadruplexes are annotated as plus signs ('+') for each G involved in the motif. Linker sequences must be denoted by dots ('.') as they are considered unpaired. Below is an example of a 2-layer G-quadruplex:
string | RNA sequence in uppercase letters |
structure | Secondary structure in dot-bracket notation |
int vrna_eval_structure_simple_verbose | ( | const char * | sequence, |
const char * | structure, | ||
FILE * | file | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA and print contributions per loop.
This function is a simplyfied version of vrna_eval_structure_simple_v() that uses the default verbosity level.
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). |
int vrna_eval_structure_simple_v | ( | const char * | sequence, |
const char * | structure, | ||
int | verbosity_level, | ||
FILE * | file | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA and print contributions per loop.
This function allows for detailed energy evaluation of a given sequence/structure pair. In contrast to vrna_eval_structure() this function prints detailed energy contributions based on individual loops to a file handle. If NULL is passed as file handle, this function defaults to print to stdout. Any positive verbosity_level
activates potential warning message of the energy evaluting functions, while values 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.
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). |
int vrna_eval_circ_structure_v | ( | const char * | sequence, |
const char * | structure, | ||
int | verbosity_level, | ||
FILE * | file | ||
) |
#include <ViennaRNA/eval.h>
Evaluate free energy of a sequence/structure pair, assume sequence to be circular and print contributions per loop.
This function is the same as vrna_eval_structure_simple_v() but assumes the input sequence to be circularized.
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). |
int vrna_eval_gquad_structure_v | ( | const char * | sequence, |
const char * | structure, | ||
int | verbosity_level, | ||
FILE * | file | ||
) |
#include <ViennaRNA/eval.h>
Evaluate free energy of a sequence/structure pair, allow for G-Quadruplexes in the structure and print contributions per loop.
This function is the same as vrna_eval_structure_simple_v() but allows for annotated G-Quadruplexes in the dot-bracket structure input.
G-Quadruplexes are annotated as plus signs ('+') for each G involved in the motif. Linker sequences must be denoted by dots ('.') as they are considered unpaired. Below is an example of a 2-layer G-quadruplex:
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). |
int vrna_eval_circ_gquad_structure_v | ( | const char * | sequence, |
const char * | structure, | ||
int | verbosity_level, | ||
FILE * | file | ||
) |
#include <ViennaRNA/eval.h>
Evaluate free energy of a sequence/structure pair, assume sequence to be circular, allow for G-Quadruplexes in the structure, and print contributions per loop.
This function is the same as vrna_eval_structure_simple_v() but assumes the input sequence to be circular and allows for annotated G-Quadruplexes in the dot-bracket structure input.
G-Quadruplexes are annotated as plus signs ('+') for each G involved in the motif. Linker sequences must be denoted by dots ('.') as they are considered unpaired. Below is an example of a 2-layer G-quadruplex:
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). |
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.
alignment | RNA sequence alignment in uppercase letters and hyphen ('-') to denote gaps |
structure | Consensus Secondary structure in dot-bracket notation |
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.
alignment | RNA sequence alignment in uppercase letters |
structure | Consensus secondary structure in dot-bracket notation |
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:
alignment | RNA sequence alignment in uppercase letters |
structure | Consensus secondary structure in dot-bracket notation |
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:
alignment | RNA sequence alignment in uppercase letters |
structure | Consensus secondary structure in dot-bracket notation |
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.
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). |
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.
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). |
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.
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). |
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:
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). |
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:
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). |
int vrna_eval_structure_pt_simple | ( | const char * | sequence, |
const short * | pt | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
In contrast to vrna_eval_structure_pt() this function assumes default model details and default energy parameters in order to evaluate the free energy of the secondary structure. Threefore, it serves as a simple interface function for energy evaluation for situations where no changes on the energy model are required.
string | RNA sequence in uppercase letters |
pt | Secondary structure as pair_table |
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.
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). |
int vrna_eval_structure_pt_simple_v | ( | const char * | string, |
const short * | pt, | ||
int | verbosity_level, | ||
FILE * | file | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
This function allows for energy evaluation of a given sequence/structure pair where the structure is provided in pair_table format as obtained from vrna_ptable(). Model details, energy parameters, and possibly soft constraints are used as provided via the parameter 'vc'. The fold_compound does not need to contain any DP matrices, but all the most basic init values as one would get from a call like this:
In contrast to vrna_eval_structure_pt_verbose() this function assumes default model details and default energy parameters in order to evaluate the free energy of the secondary structure. Threefore, it serves as a simple interface function for energy evaluation for situations where no changes on the energy model are required.
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). |
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.
alignment | RNA sequence alignment in uppercase letters. Gaps are denoted by hyphens ('-') |
pt | Secondary structure in pair table format |
int vrna_eval_loop_pt | ( | vrna_fold_compound_t * | vc, |
int | i, | ||
const short * | pt | ||
) |
#include <ViennaRNA/eval.h>
Calculate energy of a loop.
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 |
int vrna_eval_loop_pt_v | ( | vrna_fold_compound_t * | vc, |
int | i, | ||
const short * | pt, | ||
int | verbosity_level | ||
) |
#include <ViennaRNA/eval.h>
Calculate energy of a loop.
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 |
float vrna_eval_move | ( | vrna_fold_compound_t * | vc, |
const char * | structure, | ||
int | m1, | ||
int | m2 | ||
) |
#include <ViennaRNA/eval.h>
Calculate energy of a move (closing or opening of a base pair)
If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).
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 |
int vrna_eval_move_pt | ( | vrna_fold_compound_t * | vc, |
short * | pt, | ||
int | m1, | ||
int | m2 | ||
) |
#include <ViennaRNA/eval.h>
Calculate energy of a move (closing or opening of a base pair)
If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).
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 |
float energy_of_structure | ( | const char * | string, |
const char * | structure, | ||
int | verbosity_level | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA using global model detail settings.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
string | RNA sequence |
structure | secondary structure in dot-bracket notation |
verbosity_level | a flag to turn verbose output on/off |
float energy_of_struct_par | ( | const char * | string, |
const char * | structure, | ||
vrna_param_t * | parameters, | ||
int | verbosity_level | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
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 |
float energy_of_circ_structure | ( | const char * | string, |
const char * | structure, | ||
int | verbosity_level | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded circular RNA.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
string | RNA sequence |
structure | Secondary structure in dot-bracket notation |
verbosity_level | A flag to turn verbose output on/off |
float energy_of_circ_struct_par | ( | const char * | string, |
const char * | structure, | ||
vrna_param_t * | parameters, | ||
int | verbosity_level | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded circular RNA.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
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 |
int energy_of_structure_pt | ( | const char * | string, |
short * | ptable, | ||
short * | s, | ||
short * | s1, | ||
int | verbosity_level | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
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 |
int energy_of_struct_pt_par | ( | const char * | string, |
short * | ptable, | ||
short * | s, | ||
short * | s1, | ||
vrna_param_t * | parameters, | ||
int | verbosity_level | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA.
If verbosity level is set to a value >0, energies of structure elements are printed to stdout
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 |
float energy_of_move | ( | const char * | string, |
const char * | structure, | ||
int | m1, | ||
int | m2 | ||
) |
#include <ViennaRNA/eval.h>
Calculate energy of a move (closing or opening of a base pair)
If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).
string | RNA sequence |
structure | secondary structure in dot-bracket notation |
m1 | first coordinate of base pair |
m2 | second coordinate of base pair |
int energy_of_move_pt | ( | short * | pt, |
short * | s, | ||
short * | s1, | ||
int | m1, | ||
int | m2 | ||
) |
#include <ViennaRNA/eval.h>
Calculate energy of a move (closing or opening of a base pair)
If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).
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 |
int loop_energy | ( | short * | ptable, |
short * | s, | ||
short * | s1, | ||
int | i | ||
) |
#include <ViennaRNA/eval.h>
Calculate energy of a loop.
ptable | the pair table of the secondary structure |
s | encoded RNA sequence |
s1 | encoded RNA sequence |
i | position of covering base pair |
float energy_of_struct | ( | const char * | string, |
const char * | structure | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA
string | RNA sequence |
structure | secondary structure in dot-bracket notation |
int energy_of_struct_pt | ( | const char * | string, |
short * | ptable, | ||
short * | s, | ||
short * | s1 | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded RNA
string | RNA sequence |
ptable | the pair table of the secondary structure |
s | encoded RNA sequence |
s1 | encoded RNA sequence |
float energy_of_circ_struct | ( | const char * | string, |
const char * | structure | ||
) |
#include <ViennaRNA/eval.h>
Calculate the free energy of an already folded circular RNA
string | RNA sequence |
structure | secondary structure in dot-bracket notation |