// typedefs typedef void () vrna_subopt_callback ( const char *stucture, float energy, void *data ) // global variables double print_energy int subopt_sorted // global functions vrna_subopt_solution_t* vrna_subopt ( vrna_fold_compound_t* vc, int delta, int sorted, FILE* fp ) void vrna_subopt_cb ( vrna_fold_compound_t* vc, int delta, vrna_subopt_callback* cb, void* data ) SOLUTION* subopt ( char* seq, char* structure, int delta, FILE* fp ) SOLUTION* subopt_par ( char* seq, char* structure, vrna_param_t* parameters, int delta, int is_constrained, int is_circular, FILE* fp ) SOLUTION* subopt_circ ( char* seq, char* sequence, int delta, FILE* fp )
typedef void () vrna_subopt_callback ( const char *stucture, float energy, void *data )
Notes on Callback Functions This function will be called for each suboptimal secondary structure that is successfully backtraced.
Parameters:
structure | The suboptimal secondary structure in dot-bracket notation |
energy | The free energy of the secondary structure in kcal/mol |
data | Some arbitrary, auxiliary data address as passed to vrna_subopt_cb() |
See also:
double print_energy
int subopt_sorted
vrna_subopt_solution_t* vrna_subopt ( vrna_fold_compound_t* vc, int delta, int sorted, FILE* fp )
This function produces all suboptimal secondary structures within ‘delta’ * 0.01 kcal/mol of the optimum, see [21] . The results are either directly written to a ‘fp’ (if ‘fp’ is not NULL), or (fp==NULL) returned in a vrna_subopt_solution_t * list terminated by an entry were the ‘structure’ member is NULL.
SWIG Wrapper Notes This function is attached as method subopt() to objects of type fold_compound
Parameters:
vc | |
delta | |
sorted | Sort results by energy in ascending order |
fp |
Returns:
Note
This function requires all multibranch loop DP matrices for unique multibranch loop backtracing. Therefore, the supplied vrna_fold_compound_t vc
(argument 1) must be initialized with vrna_md_t.uniq_ML = 1, for instance like this:
vrna_md_t md; vrna_md_set_default(&md); md.uniq_ML = 1; vrna_fold_compound_t *vc=vrna_fold_compound("GGGGGGAAAAAACCCCCC", &md, VRNA_OPTION_DEFAULT);
See also:
void vrna_subopt_cb ( vrna_fold_compound_t* vc, int delta, vrna_subopt_callback* cb, void* data )
This is the most generic implementation of the suboptimal structure generator according to Wuchty et al. 1999 [21] . Identical to vrna_subopt() , it computes all secondary structures within an energy band delta
arround the MFE. However, this function does not print the resulting structures and their corresponding free energies to a file pointer, or returns them as a list. Instead, it calls a user-provided callback function which it passes the structure in dot-bracket format, the corresponding free energy in kcal/mol, and a user-provided data structure each time a structure was backtracked successfully. This function indicates the final output, i.e. the end of the backtracking procedure by passing NULL instead of an actual dot-bracket string to the callback.
SWIG Wrapper Notes This function is attached as method subopt_cb() to objects of type fold_compound
Parameters:
vc | fold compount with the sequence data |
delta | Energy band arround the MFE in 10cal/mol, i.e. deka-calories |
cb | Pointer to a callback function that handles the backtracked structure and its free energy in kcal/mol |
data | Pointer to some data structure that is passed along to the callback |
Note
This function requires all multibranch loop DP matrices for unique multibranch loop backtracing. Therefore, the supplied vrna_fold_compound_t vc
(argument 1) must be initialized with vrna_md_t.uniq_ML = 1, for instance like this:
vrna_md_t md; vrna_md_set_default(&md); md.uniq_ML = 1; vrna_fold_compound_t *vc=vrna_fold_compound("GGGGGGAAAAAACCCCCC", &md, VRNA_OPTION_DEFAULT);
See also:
SOLUTION* subopt ( char* seq, char* structure, int delta, FILE* fp )
This function produces all suboptimal secondary structures within ‘delta’ * 0.01 kcal/mol of the optimum. The results are either directly written to a ‘fp’ (if ‘fp’ is not NULL), or (fp==NULL) returned in a SOLUTION * list terminated by an entry were the ‘structure’ pointer is NULL.
Parameters:
seq | |
structure | |
delta | |
fp |
Returns:
SOLUTION* subopt_par ( char* seq, char* structure, vrna_param_t* parameters, int delta, int is_constrained, int is_circular, FILE* fp )
SOLUTION* subopt_circ ( char* seq, char* sequence, int delta, FILE* fp )
This function is similar to subopt() but calculates secondary structures assuming the RNA sequence to be circular instead of linear
Parameters:
seq | |
sequence | |
delta | |
fp |
Returns: