RNAlib-2.2.0RC0
perturbation_fold.h
1 #ifndef __VIENNA_RNA_PACKAGE_PERTURBATION_FOLD_H__
2 #define __VIENNA_RNA_PACKAGE_PERTURBATION_FOLD_H__
3 
4 #include "data_structures.h"
5 
13 #define VRNA_OBJECTIVE_FUNCTION_QUADRATIC 0
14 
22 #define VRNA_OBJECTIVE_FUNCTION_ABSOLUTE 1
23 
29 #define VRNA_MINIMIZER_DEFAULT 0
30 
38 #define VRNA_MINIMIZER_CONJUGATE_FR 1
39 
47 #define VRNA_MINIMIZER_CONJUGATE_PR 2
48 
56 #define VRNA_MINIMIZER_VECTOR_BFGS 3
57 
65 #define VRNA_MINIMIZER_VECTOR_BFGS2 4
66 
74 #define VRNA_MINIMIZER_STEEPEST_DESCENT 5
75 
85 typedef void (*progress_callback)(int iteration, double score, double *epsilon);
86 
121  const double *q_prob_unpaired,
122  int objective_function,
123  double sigma_squared,
124  double tau_squared,
125  int algorithm,
126  int sample_size,
127  double *epsilon,
128  double initialStepSize,
129  double minStepSize,
130  double minImprovement,
131  double minimizerTolerance,
132  progress_callback callback);
133 
134 #endif
void(* progress_callback)(int iteration, double score, double *epsilon)
Callback for following the progress of the minimization process.
Definition: perturbation_fold.h:85
void vrna_find_perturbation_vector(vrna_fold_compound *vc, const double *q_prob_unpaired, int objective_function, double sigma_squared, double tau_squared, int algorithm, int sample_size, double *epsilon, double initialStepSize, double minStepSize, double minImprovement, double minimizerTolerance, progress_callback callback)
Find a vector of perturbation energies that minimizes the discripancies between predicted and observe...
Definition: data_structures.h:359
All datastructures and typedefs shared among the Vienna RNA Package can be found here.