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perturbation_fold.h
Go to the documentation of this file.
1 #ifndef VIENNA_RNA_PACKAGE_PERTURBATION_FOLD_H
2 #define VIENNA_RNA_PACKAGE_PERTURBATION_FOLD_H
3
4 #include "data_structures.h"
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
96 typedef void (*progress_callback)(int iteration, double score, double *epsilon);
97
137 void vrna_sc_minimize_pertubation(vrna_fold_compound_t *vc,
138 const double *q_prob_unpaired,
139 int objective_function,
140 double sigma_squared,
141 double tau_squared,
142 int algorithm,
143 int sample_size,
144 double *epsilon,
145 double initialStepSize,
146 double minStepSize,
147 double minImprovement,
148 double minimizerTolerance,
149 progress_callback callback);
150
151 #endif
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:424
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