RNAlib-2.4.10
Direct Refolding Paths between two Secondary Structures

Heuristics to explore direct, optimal (re-)folding paths between two secondary structures. More...

Detailed Description

Heuristics to explore direct, optimal (re-)folding paths between two secondary structures.

+ 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 *s1, const char *s2, int width)
 Find energy of a saddle point between 2 structures (search only direct path) More...
 
int vrna_path_findpath_saddle_ub (vrna_fold_compound_t *vc, const char *s1, const char *s2, int width, int maxE)
 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 width)
 Find refolding path between 2 structures (search only direct path) More...
 
vrna_path_tvrna_path_findpath_ub (vrna_fold_compound_t *vc, const char *s1, const char *s2, int width, int maxE)
 Find refolding path between 2 structures (search only direct path) More...
 
int find_saddle (const char *seq, const char *s1, const char *s2, int width)
 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 width)
 Find refolding path between 2 structures (search only direct path) More...
 

Data Structure Documentation

◆ vrna_path_s

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

◆ path_t

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

◆ vrna_path_findpath_saddle()

vrna_path_findpath_saddle ( vrna_fold_compound_t vc,
const char *  s1,
const char *  s2,
int  width 
)

#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 [7] 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_path_findpath_saddle_ub(), vrna_fold_compound(), vrna_fold_compound_t, vrna_path_findpath()
Parameters
vcThe vrna_fold_compound_t with precomputed sequence encoding and model details
s1The start structure in dot-bracket notation
s2The target structure in dot-bracket notation
widthA number specifying how many strutures are being kept at each step during the search
Returns
The saddle energy in 10cal/mol
SWIG Wrapper Notes:
This function is attached as an overloaded method path_findpath_saddle() to objects of type fold_compound. The optional parameter width defaults to 1 if it is omitted.

◆ vrna_path_findpath_saddle_ub()

vrna_path_findpath_saddle_ub ( vrna_fold_compound_t vc,
const char *  s1,
const char *  s2,
int  width,
int  maxE 
)

#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 [7] 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:

Warning
The argument maxE ( $E_{max}$) enables one to specify an upper bound, or maximum free energy for the saddle point between the two input structures. If no path with $E_{saddle} < E_{max}$ is found, the function simply returns maxE
See also
vrna_path_findpath_saddle(), vrna_fold_compound(), vrna_fold_compound_t, vrna_path_findpath()
Parameters
vcThe vrna_fold_compound_t with precomputed sequence encoding and model details
s1The start structure in dot-bracket notation
s2The target structure in dot-bracket notation
widthA number specifying how many strutures are being kept at each step during the search
maxEAn upper bound for the saddle point energy in 10cal/mol
Returns
The saddle energy in 10cal/mol
SWIG Wrapper Notes:
This function is attached as an overloaded method path_findpath_saddle() to objects of type fold_compound. The optional parameter width defaults to 1 if it is omitted, while the optional parameter maxE defaults to INF. In case the function did not find a path with $E_{saddle} < E_{max}$ the function returns a NULL object, i.e. undef for Perl and None for Python.

◆ vrna_path_findpath()

vrna_path_findpath ( vrna_fold_compound_t vc,
const char *  s1,
const char *  s2,
int  width 
)

#include <ViennaRNA/findpath.h>

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

This function uses an inplementation of the findpath algorithm [7] 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_path_findpath_ub(), vrna_fold_compound(), vrna_fold_compound_t, vrna_path_findpath_saddle()
Parameters
vcThe vrna_fold_compound_t with precomputed sequence encoding and model details
s1The start structure in dot-bracket notation
s2The target structure in dot-bracket notation
widthA number specifying how many strutures are being kept at each step during the search
Returns
The saddle energy in 10cal/mol
SWIG Wrapper Notes:
This function is attached as an overloaded method path_findpath() to objects of type fold_compound. The optional parameter width defaults to 1 if it is omitted.

◆ vrna_path_findpath_ub()

vrna_path_findpath_ub ( vrna_fold_compound_t vc,
const char *  s1,
const char *  s2,
int  width,
int  maxE 
)

#include <ViennaRNA/findpath.h>

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

This function uses an inplementation of the findpath algorithm [7] 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:

Warning
The argument maxE enables one to specify an upper bound, or maximum free energy for the saddle point between the two input structures. If no path with $E_{saddle} < E_{max}$ is found, the function simply returns NULL
See also
vrna_path_findpath(), vrna_fold_compound(), vrna_fold_compound_t, vrna_path_findpath_saddle()
Parameters
vcThe vrna_fold_compound_t with precomputed sequence encoding and model details
s1The start structure in dot-bracket notation
s2The target structure in dot-bracket notation
widthA number specifying how many strutures are being kept at each step during the search
maxEAn upper bound for the saddle point energy in 10cal/mol
Returns
The saddle energy in 10cal/mol
SWIG Wrapper Notes:
This function is attached as an overloaded method path_findpath() to objects of type fold_compound. The optional parameter width defaults to 1 if it is omitted, while the optional parameter maxE defaults to INF. In case the function did not find a path with $E_{saddle} < E_{max}$ the function returns an empty list.

◆ find_saddle()

int find_saddle ( const char *  seq,
const char *  s1,
const char *  s2,
int  width 
)

#include <ViennaRNA/findpath.h>

Find energy of a saddle point 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
widthinteger how many strutures are being kept during the search
Returns
the saddle energy in 10cal/mol

◆ free_path()

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

◆ get_path()

vrna_path_t* get_path ( const char *  seq,
const char *  s1,
const char *  s2,
int  width 
)

#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
widthinteger how many strutures are being kept during the search
Returns
direct refolding path between two structures