Direct refolding paths between two secondary structures

Overview

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

// typedefs

typedef struct vrna_path_s vrna_path_t
typedef struct vrna_path_s path_t

// structs

struct vrna_path_s

// global functions

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

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

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

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

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

void free_path (vrna_path_t* path)

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

Detailed Documentation

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

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 .
Deprecated Use vrna_path_t instead!

Global 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)

This function uses an inplementation of the findpath algorithm [5] 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:

vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_DEFAULT);

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.

Parameters:

vc The vrna_fold_compound_t with precomputed sequence encoding and model details
s1 The start structure in dot-bracket notation
s2 The target structure in dot-bracket notation
width A number specifying how many strutures are being kept at each step during the search

Returns:

The saddle energy in 10cal/mol

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)

This function uses an inplementation of the findpath algorithm [5] 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:

vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_DEFAULT);

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.

Parameters:

vc The vrna_fold_compound_t with precomputed sequence encoding and model details
s1 The start structure in dot-bracket notation
s2 The target structure in dot-bracket notation
width A number specifying how many strutures are being kept at each step during the search
maxE An upper bound for the saddle point energy in 10cal/mol

Returns:

The saddle energy in 10cal/mol

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

vrna_path_t* vrna_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)

This function uses an inplementation of the findpath algorithm [5] 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:

vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_DEFAULT);

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.

Parameters:

vc The vrna_fold_compound_t with precomputed sequence encoding and model details
s1 The start structure in dot-bracket notation
s2 The target structure in dot-bracket notation
width A 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_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)

This function uses an inplementation of the findpath algorithm [5] 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:

vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_DEFAULT);

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.

Parameters:

vc The vrna_fold_compound_t with precomputed sequence encoding and model details
s1 The start structure in dot-bracket notation
s2 The target structure in dot-bracket notation
width A number specifying how many strutures are being kept at each step during the search
maxE An upper bound for the saddle point energy in 10cal/mol

Returns:

The saddle energy in 10cal/mol

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

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)

Parameters:

seq RNA sequence
s1 A pointer to the character array where the first secondary structure in dot-bracket notation will be written to
s2 A pointer to the character array where the second secondary structure in dot-bracket notation will be written to
width integer how many strutures are being kept during the search

Returns:

the saddle energy in 10cal/mol

void free_path (vrna_path_t* path)
Free memory allocated by get_path() function.

Parameters:

path pointer to memory to be freed
vrna_path_t* get_path (
    const char* seq,
    const char* s1,
    const char* s2,
    int width
    )
Find refolding path between 2 structures (search only direct path)

Parameters:

seq RNA sequence
s1 A pointer to the character array where the first secondary structure in dot-bracket notation will be written to
s2 A pointer to the character array where the second secondary structure in dot-bracket notation will be written to
width integer how many strutures are being kept during the search

Returns:

direct refolding path between two structures