RNAlib-2.2.7
Direct refolding paths between two secondary structures

Implementation of heuristics to explore optimal (re-)folding paths between two secondary structures. More...

+ Collaboration diagram for Direct refolding paths between two secondary structures:

Data Structures

struct  vrna_path_s
 An element of a refolding path list. More...
 

Typedefs

typedef struct vrna_path_s vrna_path_t
 Typename for the refolding path data structure vrna_path_s.
 
typedef struct vrna_path_s path_t
 Old typename of vrna_path_s. More...
 

Functions

int vrna_path_findpath_saddle (vrna_fold_compound_t *vc, const char *struc1, const char *struc2, int max)
 Find energy of a saddle point between 2 structures (search only direct path) More...
 
vrna_path_tvrna_path_findpath (vrna_fold_compound_t *vc, const char *s1, const char *s2, int maxkeep)
 Find refolding path between 2 structures (search only direct path) More...
 
int find_saddle (const char *seq, const char *struc1, const char *struc2, int max)
 Find energy of a saddle point between 2 structures (search only direct path) More...
 
void free_path (vrna_path_t *path)
 Free memory allocated by get_path() function. More...
 
vrna_path_tget_path (const char *seq, const char *s1, const char *s2, int maxkeep)
 Find refolding path between 2 structures (search only direct path) More...
 

Detailed Description

Implementation of heuristics to explore optimal (re-)folding paths between two secondary structures.


Data Structure Documentation

struct vrna_path_s

An element of a refolding path list.

See also
vrna_path_findpath()

Data Fields

double en
 Free energy of current structure.
 
char * s
 Secondary structure in dot-bracket notation.
 

Typedef Documentation

typedef struct vrna_path_s path_t

#include <ViennaRNA/findpath.h>

Old typename of vrna_path_s.

Deprecated:
Use vrna_path_t instead!

Function Documentation

int vrna_path_findpath_saddle ( vrna_fold_compound_t vc,
const char *  struc1,
const char *  struc2,
int  max 
)

#include <ViennaRNA/findpath.h>

Find energy of a saddle point between 2 structures (search only direct path)

This function uses an inplementation of the findpath algorithm [4] for near-optimal direct refolding path prediction.

Model details, and energy parameters are used as provided via the parameter 'vc'. The vrna_fold_compound_t does not require memory for any DP matrices, but requires all most basic init values as one would get from a call like this:

See also
vrna_fold_compound(), vrna_fold_compound_t, vrna_path_findpath()
Parameters
vcThe vrna_fold_compound_t with precomputed sequence encoding and model details
struc1The start structure in dot-brakcet notation
struc2The target structure in dot-bracket notation
maxA number specifying how many strutures are being kept at each step during the search
Returns
The saddle energy in 10cal/mol
vrna_path_t* vrna_path_findpath ( vrna_fold_compound_t vc,
const char *  s1,
const char *  s2,
int  maxkeep 
)

#include <ViennaRNA/findpath.h>

Find refolding path between 2 structures (search only direct path)

This function uses an inplementation of the findpath algorithm [4] for near-optimal direct refolding path prediction.

Model details, and energy parameters are used as provided via the parameter 'vc'. The vrna_fold_compound_t does not require memory for any DP matrices, but requires all most basic init values as one would get from a call like this:

See also
vrna_fold_compound(), vrna_fold_compound_t, vrna_path_findpath_saddle()
Parameters
vcThe vrna_fold_compound_t with precomputed sequence encoding and model details
struc1The start structure in dot-brakcet notation
struc2The target structure in dot-bracket notation
maxA number specifying how many strutures are being kept at each step during the search
Returns
The saddle energy in 10cal/mol
int find_saddle ( const char *  seq,
const char *  struc1,
const char *  struc2,
int  max 
)

#include <ViennaRNA/findpath.h>

Find energy of a saddle point between 2 structures (search only direct path)

Parameters
seqRNA sequence
struc1A pointer to the character array where the first secondary structure in dot-bracket notation will be written to
struc2A pointer to the character array where the second secondary structure in dot-bracket notation will be written to
maxinteger how many strutures are being kept during the search
Returns
the saddle energy in 10cal/mol
void free_path ( vrna_path_t path)

#include <ViennaRNA/findpath.h>

Free memory allocated by get_path() function.

Parameters
pathpointer to memory to be freed
vrna_path_t* get_path ( const char *  seq,
const char *  s1,
const char *  s2,
int  maxkeep 
)

#include <ViennaRNA/findpath.h>

Find refolding path between 2 structures (search only direct path)

Parameters
seqRNA sequence
s1A pointer to the character array where the first secondary structure in dot-bracket notation will be written to
s2A pointer to the character array where the second secondary structure in dot-bracket notation will be written to
maxkeepinteger how many strutures are being kept during the search
Returns
direct refolding path between two structures