perturbation_fold.h

Go to the documentation of this file.

#ifndef VIENNA_RNA_PACKAGE_PERTURBATION_FOLD_H
#define VIENNA_RNA_PACKAGE_PERTURBATION_FOLD_H

#include <ViennaRNA/fold_compound.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