perturbation_fold.h
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#ifndef VIENNA_RNA_PACKAGE_PERTURBATION_FOLD_H
#define VIENNA_RNA_PACKAGE_PERTURBATION_FOLD_H
#include "data_structures.h"
#define VRNA_OBJECTIVE_FUNCTION_QUADRATIC 0
#define VRNA_OBJECTIVE_FUNCTION_ABSOLUTE 1
#define VRNA_MINIMIZER_DEFAULT 0
#define VRNA_MINIMIZER_CONJUGATE_FR 1
#define VRNA_MINIMIZER_CONJUGATE_PR 2
#define VRNA_MINIMIZER_VECTOR_BFGS 3
#define VRNA_MINIMIZER_VECTOR_BFGS2 4
#define VRNA_MINIMIZER_STEEPEST_DESCENT 5
typedef void (*progress_callback)(int iteration, double score, double *epsilon);
void vrna_sc_minimize_pertubation(vrna_fold_compound_t *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);
#endif
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:390
data_structures.h
vrna_sc_minimize_pertubation
void vrna_sc_minimize_pertubation(vrna_fold_compound_t *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...
progress_callback
void(* progress_callback)(int iteration, double score, double *epsilon)
Callback for following the progress of the minimization process.
Definition: perturbation_fold.h:96