RNAlib-2.2.10
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
 interaction data structure for RNAup More...
 
struct  pu_out
 Collection of all free_energy of beeing unpaired values for output. More...
 
struct  constrain
 constraints for cofolding More...
 
struct  duplexT
 Data structure for RNAduplex. More...
 
struct  node
 Data structure for RNAsnoop (fold energy list) More...
 
struct  snoopT
 Data structure for RNAsnoop. More...
 
struct  dupVar
 Data structure used in RNApkplex. More...
 
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_DEFAULT   0U
 Option flag to specify default settings/requirements.
 
#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_HYBRID   4U
 Option flag to specify requirement of dimer DP matrices.
 
#define VRNA_OPTION_EVAL_ONLY   8U
 Option flag to specify that neither MFE, nor PF DP matrices are required. More...
 
#define VRNA_OPTION_WINDOW   16U
 Option flag to specify requirement of DP matrices for local folding approaches.
 

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 interact interact
 interaction data structure for RNAup
 
typedef struct pu_out pu_out
 Collection of all free_energy of beeing unpaired values for output.
 
typedef struct constrain constrain
 constraints for cofolding
 
typedef struct node folden
 Data structure for RNAsnoop (fold energy list)
 
typedef struct dupVar dupVar
 Data structure used in RNApkplex.
 

Enumerations

Functions

void vrna_C11_features (void)
 Dummy symbol to check whether the library was build using C11/C++11 features. More...
 
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...