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 )
typedef struct vrna_path_s vrna_path_t
int vrna_path_findpath_saddle ( vrna_fold_compound_t* vc, const char* s1, const char* s2, int width )
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 )
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 )
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 )
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 )
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)
Parameters:
path | pointer to memory to be freed |
vrna_path_t* get_path ( const char* seq, const char* s1, const char* s2, int width )
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