RNAlib-2.6.3
 
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perturbation_fold.h
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1#ifndef VIENNA_RNA_PACKAGE_PERTURBATION_FOLD_H
2#define VIENNA_RNA_PACKAGE_PERTURBATION_FOLD_H
3
5
24#define VRNA_OBJECTIVE_FUNCTION_QUADRATIC 0
25
33#define VRNA_OBJECTIVE_FUNCTION_ABSOLUTE 1
34
40#define VRNA_MINIMIZER_DEFAULT 0
41
49#define VRNA_MINIMIZER_CONJUGATE_FR 1
50
58#define VRNA_MINIMIZER_CONJUGATE_PR 2
59
67#define VRNA_MINIMIZER_VECTOR_BFGS 3
68
76#define VRNA_MINIMIZER_VECTOR_BFGS2 4
77
85#define VRNA_MINIMIZER_STEEPEST_DESCENT 5
86
96typedef void (*progress_callback)(int iteration,
97 double score,
98 double *epsilon);
99
142 const double *q_prob_unpaired,
143 int objective_function,
144 double sigma_squared,
145 double tau_squared,
146 int algorithm,
147 int sample_size,
148 double *epsilon,
149 double initialStepSize,
150 double minStepSize,
151 double minImprovement,
152 double minimizerTolerance,
153 progress_callback callback);
154
155
156#endif
The Basic Fold Compound API.
The most basic data structure required by many functions throughout the RNAlib.
Definition fold_compound.h:168
void vrna_sc_minimize_pertubation(vrna_fold_compound_t *fc, 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...
void(* progress_callback)(int iteration, double score, double *epsilon)
Callback for following the progress of the minimization process.
Definition perturbation_fold.h:96