RNAlib-2.2.7
Data Structures and Preprocessor Macros

All datastructures and typedefs shared among the Vienna RNA Package can be found here. More...

+ Collaboration diagram for Data Structures and Preprocessor Macros:

Modules

 The Fold Compound
 This module provides interfaces that deal with the most basic data structure used in structure predicting and energy evaluating function of the RNAlib.
 
 The Dynamic Programming Matrices
 This module provides interfaces that deal with creation and destruction of dynamic programming matrices used within the RNAlib.
 

Data Structures

struct  vrna_basepair_s
 Base pair data structure used in subopt.c. More...
 
struct  vrna_plist_s
 this datastructure is used as input parameter in functions of PS_dot.h and others More...
 
struct  vrna_cpair_s
 this datastructure is used as input parameter in functions of PS_dot.c More...
 
struct  vrna_sect_s
 Stack of partial structures for backtracking. More...
 
struct  vrna_bp_stack_s
 Base pair stack element. More...
 
struct  pu_contrib
 contributions to p_u More...
 
struct  interact
 
struct  pu_out
 Collection of all free_energy of beeing unpaired values for output. More...
 
struct  constrain
 constraints for cofolding More...
 
struct  duplexT
 
struct  node
 
struct  snoopT
 
struct  dupVar
 

Typedefs

typedef struct vrna_basepair_s vrna_basepair_t
 Typename for the base pair repesenting data structure vrna_basepair_s.
 
typedef struct vrna_plist_s vrna_plist_t
 Typename for the base pair list repesenting data structure vrna_plist_s.
 
typedef struct vrna_bp_stack_s vrna_bp_stack_t
 Typename for the base pair stack repesenting data structure vrna_bp_stack_s.
 
typedef struct vrna_cpair_s vrna_cpair_t
 Typename for data structure vrna_cpair_s.
 
typedef struct vrna_sect_s vrna_sect_t
 Typename for stack of partial structures vrna_sect_s.
 
typedef double FLT_OR_DBL
 Typename for floating point number in partition function computations.
 
typedef struct vrna_basepair_s PAIR
 Old typename of vrna_basepair_s. More...
 
typedef struct vrna_plist_s plist
 Old typename of vrna_plist_s. More...
 
typedef struct vrna_cpair_s cpair
 Old typename of vrna_cpair_s. More...
 
typedef struct vrna_sect_s sect
 Old typename of vrna_sect_s. More...
 
typedef struct vrna_bp_stack_s bondT
 Old typename of vrna_bp_stack_s. More...
 
typedef struct pu_contrib pu_contrib
 contributions to p_u
 
typedef struct pu_out pu_out
 Collection of all free_energy of beeing unpaired values for output.
 
typedef struct constrain constrain
 constraints for cofolding
 

Detailed Description

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


Data Structure Documentation

struct vrna_basepair_s

Base pair data structure used in subopt.c.

struct vrna_plist_s

this datastructure is used as input parameter in functions of PS_dot.h and others

struct vrna_cpair_s

this datastructure is used as input parameter in functions of PS_dot.c

struct vrna_sect_s

Stack of partial structures for backtracking.

struct vrna_bp_stack_s

Base pair stack element.

struct pu_contrib

contributions to p_u

Data Fields

double ** H
 hairpin loops
 
double ** I
 interior loops
 
double ** M
 multi loops
 
double ** E
 exterior loop
 
int length
 length of the input sequence
 
int w
 longest unpaired region
 
struct interact

Data Fields

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

Collection of all free_energy of beeing unpaired values for output.

Data Fields

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

constraints for cofolding

struct duplexT
struct node
+ Collaboration diagram for node:
struct snoopT
struct dupVar

Typedef Documentation

typedef struct vrna_basepair_s PAIR
typedef struct vrna_plist_s plist

#include <ViennaRNA/data_structures.h>

Old typename of vrna_plist_s.

Deprecated:
Use vrna_plist_t instead!
typedef struct vrna_cpair_s cpair

#include <ViennaRNA/data_structures.h>

Old typename of vrna_cpair_s.

Deprecated:
Use vrna_cpair_t instead!
typedef struct vrna_sect_s sect

#include <ViennaRNA/data_structures.h>

Old typename of vrna_sect_s.

Deprecated:
Use vrna_sect_t instead!
typedef struct vrna_bp_stack_s bondT