RNAlib-2.4.17
Examples
profiledist.h
expand_Full
char * expand_Full(const char *structure)
Convert the full structure from bracket notation to the expanded notation including root.
RNAstruct.h
Parsing and Coarse Graining of Structures.
vrna_eval_structure
float vrna_eval_structure(vrna_fold_compound_t *vc, const char *structure)
Calculate the free energy of an already folded RNA.
pf_scale
double pf_scale
A scaling factor used by pf_fold() to avoid overflows.
model.h
The model details data structure and its corresponding modifiers.
vrna_elem_prob_s
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:453
vrna_sc_add_up
void vrna_sc_add_up(vrna_fold_compound_t *vc, int i, FLT_OR_DBL energy, unsigned int options)
Add soft constraints for unpaired nucleotides.
vrna_centroid
char * vrna_centroid(vrna_fold_compound_t *vc, double *dist)
Get the centroid structure of the ensemble.
vrna_md_s::gquad
int gquad
Include G-quadruplexes in structure prediction.
Definition: model.h:214
alignments.h
Various utility- and helper-functions for sequence alignments and comparative structure prediction.
vrna_exp_params_rescale
void vrna_exp_params_rescale(vrna_fold_compound_t *vc, double *mfe)
Rescale Boltzmann factors for partition function computations.
fold
float fold(const char *sequence, char *structure)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence.
free_profile
void free_profile(float *T)
free space allocated in Make_bp_profile
vrna_fold_compound_free
void vrna_fold_compound_free(vrna_fold_compound_t *fc)
Free memory occupied by a vrna_fold_compound_t.
alifold.h
Functions for comparative structure prediction using RNA sequence alignments.
vrna_random_string
char * vrna_random_string(int l, const char symbols[])
Create a random string using characters from a specified symbol set.
aligned_line
char * aligned_line[4]
Contains the two aligned structures after a call to one of the distance functions with edit_backtrack...
subopt.h
RNAsubopt and density of states declarations.
export_bppm
FLT_OR_DBL * export_bppm(void)
Get a pointer to the base pair probability array.
vrna_init_rand
void vrna_init_rand(void)
Initialize seed for random number generator.
fold_vars.h
Here all all declarations of the global variables used throughout RNAlib.
vrna_md_s::temperature
double temperature
The temperature used to scale the thermodynamic parameters.
Definition: model.h:181
vrna_subopt_cb
void vrna_subopt_cb(vrna_fold_compound_t *vc, int delta, vrna_subopt_callback *cb, void *data)
Generate suboptimal structures within an energy band arround the MFE.
soft.h
Functions and data structures for secondary structure soft constraints.
FLT_OR_DBL
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
pf_fold
float pf_fold(const char *sequence, char *structure)
Compute the partition function of an RNA sequence.
swString
Some other data structure.
Definition: dist_vars.h:57
vrna_elem_prob_s::p
float p
Probability of the element.
Definition: structures.h:456
string_edit_distance
float string_edit_distance(swString *T1, swString *T2)
Calculate the string edit distance of T1 and T2.
basic.h
General utility- and helper-functions used throughout the ViennaRNA Package.
edit_backtrack
int edit_backtrack
Produce an alignment of the two structures being compared by tracing the editing path giving the mini...
Make_swString
swString * Make_swString(char *string)
Convert a structure into a format suitable for string_edit_distance().
make_tree
Tree * make_tree(char *struc)
Constructs a Tree ( essentially the postorder list ) of the structure 'struc', for use in tree_edit_d...
eval.h
Functions and variables related to energy evaluation of sequence/structure pairs.
tree_edit_distance
float tree_edit_distance(Tree *T1, Tree *T2)
Calculates the edit distance of the two trees.
vrna_md_set_default
void vrna_md_set_default(vrna_md_t *md)
Apply default model details to a provided vrna_md_t data structure.
vrna_fold
float vrna_fold(const char *sequence, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding secondary structure for an RNA sequence.
free_arrays
void free_arrays(void)
Free arrays for mfe folding.
strings.h
General utility- and helper-functions for RNA sequence and structure strings used throughout the Vien...
vrna_md_s
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:180
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:137
treedist.h
Functions for Tree Edit Distances.
Tree
Tree data structure.
Definition: dist_vars.h:49
mfe.h
Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence ...
vrna_pf_fold
float vrna_pf_fold(const char *sequence, char *structure, vrna_ep_t **pl)
Compute Partition function (and base pair probabilities) for an RNA sequence using a comparative met...
space
void * space(unsigned size)
Allocate space safely.
VRNA_OPTION_DEFAULT
#define VRNA_OPTION_DEFAULT
Option flag to specify default settings/requirements.
Definition: fold_compound.h:355
vrna_alifold
float vrna_alifold(const char **sequences, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for an RNA seque...
vrna_mfe
float vrna_mfe(vrna_fold_compound_t *vc, char *structure)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence,...
fold.h
MFE calculations for single RNA sequences.
vrna_elem_prob_s::i
int i
Start position (usually 5' nucleotide that starts the element, e.g. base pair)
Definition: structures.h:454
free_tree
void free_tree(Tree *t)
Free the memory allocated for Tree t.
part_func.h
Partition function implementations.
profile_edit_distance
float profile_edit_distance(const float *T1, const float *T2)
Align the 2 probability profiles T1, T2 .
vrna_pf
float vrna_pf(vrna_fold_compound_t *vc, char *structure)
Compute the partition function for a given RNA sequence, or sequence alignment.
fold_compound.h
The Basic Fold Compound API.
unexpand_aligned_F
void unexpand_aligned_F(char *align[2])
Converts two aligned structures in expanded notation.
vrna_fold_compound
vrna_fold_compound_t * vrna_fold_compound(const char *sequence, const vrna_md_t *md_p, unsigned int options)
Retrieve a vrna_fold_compound_t data structure for single sequences and hybridizing sequences.
stringdist.h
Functions for String Alignment.
data_structures.h
Use ViennaRNA/datastructures/basic.h instead.
temperature
double temperature
Rescale energy parameters to a temperature in degC.
Make_bp_profile_bppm
float * Make_bp_profile_bppm(FLT_OR_DBL *bppm, int length)
condense pair probability matrix into a vector containing probabilities for unpaired,...
vrna_elem_prob_s::j
int j
End position (usually 3' nucleotide that ends the element, e.g. base pair)
Definition: structures.h:455
free_pf_arrays
void free_pf_arrays(void)
Free arrays for the partition function recursions.
inverse.h
Inverse folding routines.
basic.h
Functions to deal with sets of energy parameters.
vrna_alloc
void * vrna_alloc(unsigned size)
Allocate space safely.