RNAlib-2.1.7
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 
53  model_detailsT md);
54 
55 paramT *get_parameter_copy(paramT *par);
56 
64 
89  double betaScale,
90  model_detailsT md,
91  double pf_scale);
92 
102 
108 pf_paramT *get_scaled_alipf_parameters(unsigned int n_seq);
109 
116 PUBLIC pf_paramT *get_boltzmann_factors_ali(unsigned int n_seq,
117  double temperature,
118  double betaScale,
119  model_detailsT md,
120  double pf_scale);
121 
126 DEPRECATED(paramT *copy_parameters(void));
127 DEPRECATED(paramT *set_parameters(paramT *dest));
128 DEPRECATED(pf_paramT *scale_pf_parameters(void));
129 DEPRECATED(pf_paramT *copy_pf_param(void));
130 DEPRECATED(pf_paramT *set_pf_param(paramT *dest));
131 
132 
133 
134 #endif
pf_paramT * get_boltzmann_factor_copy(pf_paramT *parameters)
Get a copy of already precomputed Boltzmann factors.
pf_paramT * get_scaled_pf_parameters(void)
The datastructure that contains temperature scaled energy parameters.
Definition: data_structures.h:126
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: data_structures.h:171
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_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...
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
pf_paramT * get_scaled_alipf_parameters(unsigned int n_seq)
Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) ...
double pf_scale
A scaling factor used by pf_fold() to avoid overflows.
The data structure that contains the complete model details used throughout the calculations.
Definition: data_structures.h:106
paramT * scale_parameters(void)
Get precomputed energy contributions for all the known loop types.
double temperature
Rescale energy parameters to a temperature in degC.
paramT * get_scaled_parameters(double temperature, model_detailsT md)
Get precomputed energy contributions for all the known loop types.