// global functions vrna_move_t* vrna_path ( vrna_fold_compound_t* vc, short* pt, unsigned int steps, unsigned int options ) vrna_move_t* vrna_path_gradient ( vrna_fold_compound_t* vc, short* pt, unsigned int options ) vrna_move_t* vrna_path_random ( vrna_fold_compound_t* vc, short* pt, unsigned int steps, unsigned int options ) // macros #define VRNA_PATH_DEFAULT #define VRNA_PATH_NO_TRANSITION_OUTPUT #define VRNA_PATH_RANDOM #define VRNA_PATH_STEEPEST_DESCENT
vrna_move_t* vrna_path ( vrna_fold_compound_t* vc, short* pt, unsigned int steps, unsigned int options )
This function computes, given a start structure in pair table format, a transition path, updates the pair table to the final structure of the path. Finally, if not requested otherwise by using the VRNA_PATH_NO_TRANSITION_OUTPUT flag in the options
field, this function returns a list of individual transitions that lead from the start to the final structure if requested.
The currently available transition paths are
The type of transitions must be set through the options
parameter
SWIG Wrapper Notes This function is attached as an overloaded method path() to objects of type fold_compound . The optional parameter options
defaults to VRNA_PATH_DEFAULT if it is omitted.
Parameters:
vc | A vrna_fold_compound_t containing the energy parameters and model details |
pt | The pair table containing the start structure. Used to update to the final structure after execution of this function |
options | Options to modify the behavior of this function |
Returns:
A list of transition moves (default), or NULL (if options & VRNA_PATH_NO_TRANSITION_OUTPUT )
Note
Since the result is written to the input structure you may want to use vrna_ptable_copy() before calling this function to keep the initial structure
vrna_move_t* vrna_path_gradient ( vrna_fold_compound_t* vc, short* pt, unsigned int options )
This function computes, given a start structure in pair table format, a steepest descent path, updates the pair table to the final structure of the path. Finally, if not requested otherwise by using the VRNA_PATH_NO_TRANSITION_OUTPUT flag in the options
field, this function returns a list of individual transitions that lead from the start to the final structure if requested.
SWIG Wrapper Notes This function is attached as an overloaded method path_gradient() to objects of type fold_compound . The optional parameter options
defaults to VRNA_PATH_DEFAULT if it is omitted.
Parameters:
vc | A vrna_fold_compound_t containing the energy parameters and model details |
pt | The pair table containing the start structure. Used to update to the final structure after execution of this function |
options | Options to modify the behavior of this function |
Returns:
A list of transition moves (default), or NULL (if options & VRNA_PATH_NO_TRANSITION_OUTPUT )
Note
Since the result is written to the input structure you may want to use vrna_ptable_copy() before calling this function to keep the initial structure
vrna_move_t* vrna_path_random ( vrna_fold_compound_t* vc, short* pt, unsigned int steps, unsigned int options )
This function generates, given a start structure in pair table format, a random walk / path, updates the pair table to the final structure of the path. Finally, if not requested otherwise by using the VRNA_PATH_NO_TRANSITION_OUTPUT flag in the options
field, this function returns a list of individual transitions that lead from the start to the final structure if requested.
SWIG Wrapper Notes This function is attached as an overloaded method path_gradient() to objects of type fold_compound . The optional parameter options
defaults to VRNA_PATH_DEFAULT if it is omitted.
Parameters:
vc | A vrna_fold_compound_t containing the energy parameters and model details |
pt | The pair table containing the start structure. Used to update to the final structure after execution of this function |
steps | The length of the path, i.e. the total number of transitions / moves |
options | Options to modify the behavior of this function |
Returns:
A list of transition moves (default), or NULL (if options & VRNA_PATH_NO_TRANSITION_OUTPUT )
Note
Since the result is written to the input structure you may want to use vrna_ptable_copy() before calling this function to keep the initial structure
#define VRNA_PATH_DEFAULT
See also:
vrna_path() , VRNA_PATH_STEEPEST_DESCENT , VRNA_MOVESET_DEFAULT
#define VRNA_PATH_NO_TRANSITION_OUTPUT
See also:
#define VRNA_PATH_STEEPEST_DESCENT
See also: