(Abstract) Data Structures

All datastructures and typedefs shared among the ViennaRNA Package can be found here.

Common Data Structures

Typedefs

typedef struct vrna_elem_prob_s vrna_plist_t
#include <ViennaRNA/datastructures/basic.h>

Typename for the base pair list repesenting data structure vrna_elem_prob_s.

typedef struct vrna_cpair_s vrna_cpair_t
#include <ViennaRNA/datastructures/basic.h>

Typename for data structure vrna_cpair_s.

typedef struct vrna_data_linear_s vrna_data_lin_t
#include <ViennaRNA/datastructures/basic.h>
typedef struct vrna_color_s vrna_color_t
#include <ViennaRNA/datastructures/basic.h>
typedef double FLT_OR_DBL
#include <ViennaRNA/datastructures/basic.h>

Typename for floating point number in partition function computations.

typedef struct vrna_basepair_s PAIR
#include <ViennaRNA/datastructures/basic.h>

Old typename of vrna_basepair_s.

Deprecated:

Use vrna_basepair_t instead!

typedef struct vrna_elem_prob_s plist
#include <ViennaRNA/datastructures/basic.h>

Old typename of vrna_elem_prob_s.

Deprecated:

Use vrna_ep_t or vrna_elem_prob_s instead!

typedef struct vrna_cpair_s cpair
#include <ViennaRNA/datastructures/basic.h>

Old typename of vrna_cpair_s.

Deprecated:

Use vrna_cpair_t instead!

typedef struct vrna_sect_s sect
#include <ViennaRNA/datastructures/basic.h>

Old typename of vrna_sect_s.

Deprecated:

Use vrna_sect_t instead!

typedef vrna_bp_stack_t bondT
#include <ViennaRNA/datastructures/basic.h>

Old typename of #vrna_bp_stack_s.

Deprecated:

Use vrna_bp_stack_t instead!

typedef struct pu_contrib pu_contrib
#include <ViennaRNA/datastructures/basic.h>

contributions to p_u

typedef struct interact interact
#include <ViennaRNA/datastructures/basic.h>

interaction data structure for RNAup

typedef struct pu_out pu_out
#include <ViennaRNA/datastructures/basic.h>

Collection of all free_energy of beeing unpaired values for output.

typedef struct constrain constrain
#include <ViennaRNA/datastructures/basic.h>

constraints for cofolding

typedef struct node folden
#include <ViennaRNA/datastructures/basic.h>

Data structure for RNAsnoop (fold energy list)

typedef struct dupVar dupVar
#include <ViennaRNA/datastructures/basic.h>

Data structure used in RNApkplex.

struct vrna_basepair_t
#include <ViennaRNA/datastructures/basic.h>

Typename for base pair element.

Deprecated:

Use vrna_bp_t instead!

Public Members

int i
int j
struct vrna_bp_stack_t
#include <ViennaRNA/datastructures/basic.h>

Typename for the base pair stack element.

Public Members

unsigned int i
unsigned int j
struct pu_contrib
#include <ViennaRNA/datastructures/basic.h>

contributions to p_u

Public Members

double **H

hairpin loops

double **I

internal loops

double **M

multi loops

double **E

exterior loop

int length

length of the input sequence

int w

longest unpaired region

struct interact
#include <ViennaRNA/datastructures/basic.h>

interaction data structure for RNAup

Public Members

double *Pi

probabilities of interaction

double *Gi

free energies of interaction

double Gikjl

full free energy for interaction between [k,i] k<i in longer seq and [j,l] j<l in shorter seq

double Gikjl_wo

Gikjl without contributions for prob_unpaired.

int i

k<i in longer seq

int k

k<i in longer seq

int j

j<l in shorter seq

int l

j<l in shorter seq

int length

length of longer sequence

struct pu_out
#include <ViennaRNA/datastructures/basic.h>

Collection of all free_energy of beeing unpaired values for output.

Public Members

int len

sequence length

int u_vals

number of different -u values

int contribs

[-c “SHIME”]

char **header

header line

double **u_values

(the -u values * [-c “SHIME”]) * seq len

struct constrain
#include <ViennaRNA/datastructures/basic.h>

constraints for cofolding

Public Members

int *indx
char *ptype
struct duplexT
#include <ViennaRNA/datastructures/basic.h>

Data structure for RNAduplex.

Public Members

int i
int j
int end
char *structure
double energy
double energy_backtrack
double opening_backtrack_x
double opening_backtrack_y
int offset
double dG1
double dG2
double ddG
int tb
int te
int qb
int qe
struct node
#include <ViennaRNA/datastructures/basic.h>

Data structure for RNAsnoop (fold energy list)

Public Members

int k
int energy
struct node *next
struct snoopT
#include <ViennaRNA/datastructures/basic.h>

Data structure for RNAsnoop.

Public Members

int i
int j
int u
char *structure
float energy
float Duplex_El
float Duplex_Er
float Loop_E
float Loop_D
float pscd
float psct
float pscg
float Duplex_Ol
float Duplex_Or
float Duplex_Ot
float fullStemEnergy
struct dupVar
#include <ViennaRNA/datastructures/basic.h>

Data structure used in RNApkplex.

Public Members

int i
int j
int end
char *pk_helix
char *structure
double energy
int offset
double dG1
double dG2
double ddG
int tb
int te
int qb
int qe
int inactive
int processed