RNAlib-2.2.0-RC2
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Go to the source code of this file.
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 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_compound * | vrna_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_compound * | vrna_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_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... | |