RNAlib-2.2.0-RC3
data_structures.h File Reference
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Data Structures

struct  plist
 this datastructure is used as input parameter in functions of PS_dot.h and others More...
 
struct  cpair
 this datastructure is used as input parameter in functions of PS_dot.c More...
 
struct  sect
 Stack of partial structures for backtracking. More...
 
struct  bondT
 Base pair. More...
 
struct  bondTEn
 Base pair with associated energy. More...
 
struct  PAIR
 Base pair data structure used in subopt.c. More...
 
struct  INTERVAL
 Sequence interval stack element used in subopt.c. More...
 
struct  SOLUTION
 Solution element from subopt.c. More...
 
struct  cofoldF
 
struct  ConcEnt
 
struct  pairpro
 
struct  pair_info
 A base pair info structure. More...
 
struct  move_t
 
struct  intermediate_t
 
struct  path_t
 
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  folden
 
struct  snoopT
 
struct  dupVar
 
struct  vrna_mx_mfe_t
 Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the vrna_fold_compound. More...
 
struct  vrna_mx_pf_t
 Partition function (PF) Dynamic Programming (DP) matrices data structure required within the vrna_fold_compound. More...
 
struct  vrna_fold_compound
 The most basic data structure required by many functions throughout the RNAlib. More...
 

Macros

#define MAXDOS   1000
 Maximum density of states discretization for subopt.
 
#define VRNA_OPTION_MFE   1
 Option flag to specify requirement of Minimum Free Energy (MFE) DP matrices and corresponding set of energy parameters. More...
 
#define VRNA_OPTION_PF   2
 Option flag to specify requirement of Partition Function (PF) DP matrices and corresponding set of Boltzmann factors. More...
 
#define VRNA_OPTION_EVAL_ONLY   8
 Option flag to specify that neither MFE, nor PF DP matrices are required. More...
 

Enumerations

enum  vrna_mx_t { VRNA_MX_DEFAULT, VRNA_MX_LFOLD, VRNA_MX_2DFOLD }
 An enumerator that is used to specify the type of a polymorphic Dynamic Programming (DP) matrix data structure. More...
 
enum  vrna_vc_t { VRNA_VC_TYPE_SINGLE, VRNA_VC_TYPE_ALIGNMENT }
 An enumerator that is used to specify the type of a vrna_fold_compound. More...
 

Functions

vrna_fold_compoundvrna_get_fold_compound (const char *sequence, vrna_md_t *md_p, unsigned int options)
 Retrieve a vrna_fold_compound data structure for single sequences and hybridizing sequences. More...
 
vrna_fold_compoundvrna_get_fold_compound_ali (const char **sequences, vrna_md_t *md_p, unsigned int options)
 Retrieve a vrna_fold_compound data structure for sequence alignments. More...
 
void vrna_params_update (vrna_fold_compound *vc, vrna_param_t *par)
 Update/Reset energy parameters data structure within a vrna_fold_compound. More...
 
void vrna_exp_params_update (vrna_fold_compound *vc, vrna_exp_param_t *params)
 Update the energy parameters for subsequent partition function computations. More...
 
void vrna_exp_params_rescale (vrna_fold_compound *vc, double *mfe)
 Rescale Boltzmann factors for partition function computations. More...
 
void vrna_free_fold_compound (vrna_fold_compound *vc)
 Free memory occupied by a vrna_fold_compound. More...
 
void vrna_free_mfe_matrices (vrna_fold_compound *vc)
 Free memory occupied by the Minimum Free Energy (MFE) Dynamic Programming (DP) matrices. More...
 
void vrna_free_pf_matrices (vrna_fold_compound *vc)
 Free memory occupied by the Partition Function (PF) Dynamic Programming (DP) matrices. More...