RNAlib-2.2.9

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Data Structures | Macros | Typedefs | Enumerations | Functions
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_t * | vrna_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_t * | vrna_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...