RNAlib-2.2.7
data_structures.h File Reference
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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
 
struct  vrna_fc_s
 The most basic data structure required by many functions throughout the RNAlib. More...
 

Macros

#define VRNA_STATUS_MFE_PRE   (unsigned char)1
 Status message indicating that MFE computations are about to begin. More...
 
#define VRNA_STATUS_MFE_POST   (unsigned char)2
 Status message indicating that MFE computations are finished. More...
 
#define VRNA_STATUS_PF_PRE   (unsigned char)3
 Status message indicating that Partition function computations are about to begin. More...
 
#define VRNA_STATUS_PF_POST   (unsigned char)4
 Status message indicating that Partition function computations are finished. More...
 
#define VRNA_OPTION_MFE   1U
 Option flag to specify requirement of Minimum Free Energy (MFE) DP matrices and corresponding set of energy parameters. More...
 
#define VRNA_OPTION_PF   2U
 Option flag to specify requirement of Partition Function (PF) DP matrices and corresponding set of Boltzmann factors. More...
 
#define VRNA_OPTION_EVAL_ONLY   8U
 Option flag to specify that neither MFE, nor PF DP matrices are required. More...
 

Typedefs

typedef struct vrna_fc_s vrna_fold_compound_t
 Typename for the fold_compound data structure vrna_fc_s.
 
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 void( vrna_callback_free_auxdata) (void *data)
 Callback to free memory allocated for auxiliary user-provided data. More...
 
typedef void( vrna_callback_recursion_status) (unsigned char status, void *data)
 Callback to perform specific user-defined actions before, or after recursive computations. More...
 
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
 

Enumerations

enum  vrna_fc_type_e { VRNA_VC_TYPE_SINGLE, VRNA_VC_TYPE_ALIGNMENT }
 An enumerator that is used to specify the type of a vrna_fold_compound_t. More...
 

Functions

vrna_fold_compound_tvrna_fold_compound (const char *sequence, vrna_md_t *md_p, unsigned int options)
 Retrieve a vrna_fold_compound_t data structure for single sequences and hybridizing sequences. More...
 
vrna_fold_compound_tvrna_fold_compound_comparative (const char **sequences, vrna_md_t *md_p, unsigned int options)
 Retrieve a vrna_fold_compound_t data structure for sequence alignments. More...
 
void vrna_fold_compound_free (vrna_fold_compound_t *vc)
 Free memory occupied by a vrna_fold_compound_t. More...
 
void vrna_fold_compound_add_auxdata (vrna_fold_compound_t *vc, void *data, vrna_callback_free_auxdata *f)
 Add auxiliary data to the vrna_fold_compound_t. More...
 
void vrna_fold_compound_add_callback (vrna_fold_compound_t *vc, vrna_callback_recursion_status *f)
 Add a recursion status callback to the vrna_fold_compound_t. More...