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