RNAlib-2.1.9h
params.h
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1#ifndef __VIENNA_RNA_PACKAGE_PARAMS_H__
2#define __VIENNA_RNA_PACKAGE_PARAMS_H__
3
4#include "energy_const.h"
5#include "data_structures.h"
6
7#ifdef __GNUC__
8#define DEPRECATED(func) func __attribute__ ((deprecated))
9#else
10#define DEPRECATED(func) func
11#endif
12
37
54
55paramT *scale_parameters_hybrid(void);
56
57paramT *get_scaled_parameters_hybrid( double temperature,
59
60paramT *get_parameter_copy(paramT *par);
61
69
94 double betaScale,
96 double pf_scale);
97
107
115
116pf_paramT *get_boltzmann_factors_hybrid(double temperature,
117 double betaScale,
119 double pf_scale);
120
121pf_paramT *get_scaled_alipf_parameters(unsigned int n_seq);
122
129PUBLIC pf_paramT *get_boltzmann_factors_ali(unsigned int n_seq,
130 double temperature,
131 double betaScale,
133 double pf_scale);
134
139DEPRECATED(paramT *copy_parameters(void));
140DEPRECATED(paramT *set_parameters(paramT *dest));
141DEPRECATED(pf_paramT *scale_pf_parameters(void));
142DEPRECATED(pf_paramT *copy_pf_param(void));
143DEPRECATED(pf_paramT *set_pf_param(paramT *dest));
144
145
146#endif
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
double temperature
Rescale energy parameters to a temperature in degC.
double pf_scale
A scaling factor used by pf_fold() to avoid overflows.
paramT * get_scaled_parameters(double temperature, model_detailsT md)
Get precomputed energy contributions for all the known loop types.
paramT * scale_parameters(void)
Get precomputed energy contributions for all the known loop types.
PUBLIC pf_paramT * get_boltzmann_factors_ali(unsigned int n_seq, double temperature, double betaScale, model_detailsT md, double pf_scale)
Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) w...
pf_paramT * get_scaled_pf_parameters(void)
pf_paramT * get_boltzmann_factor_copy(pf_paramT *parameters)
Get a copy of already precomputed Boltzmann factors.
pf_paramT * get_scaled_pf_parameters_hybrid(void)
Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant)
pf_paramT * get_boltzmann_factors(double temperature, double betaScale, model_detailsT md, double pf_scale)
Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent th...
The data structure that contains the complete model details used throughout the calculations.
Definition data_structures.h:102
The datastructure that contains temperature scaled energy parameters.
Definition data_structures.h:122
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition data_structures.h:203