RNAlib-2.2.0RC0
params.h
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1 #ifndef __VIENNA_RNA_PACKAGE_PARAMS_H__
2 #define __VIENNA_RNA_PACKAGE_PARAMS_H__
3 
6 
7 #ifdef __GNUC__
8 #define DEPRECATED(func) func __attribute__ ((deprecated))
9 #else
10 #define DEPRECATED(func) func
11 #endif
12 
37 
38 
39 paramT *vrna_get_energy_contributions(model_detailsT md);
40 
41 
57  model_detailsT md);
58 
59 paramT *get_parameter_copy(paramT *par);
60 
68 
69 pf_paramT *vrna_get_boltzmann_factors(model_detailsT md);
70 
95  double betaScale,
96  model_detailsT md,
97  double pf_scale);
98 
108 
114 pf_paramT *get_scaled_alipf_parameters(unsigned int n_seq);
115 
122 pf_paramT *get_boltzmann_factors_ali( unsigned int n_seq,
123  double temperature,
124  double betaScale,
125  model_detailsT md,
126  double pf_scale);
127 
128 pf_paramT *vrna_get_boltzmann_factors_ali(unsigned int n_seq,
129  model_detailsT md);
130 
135 DEPRECATED(paramT *copy_parameters(void));
136 DEPRECATED(paramT *set_parameters(paramT *dest));
137 DEPRECATED(pf_paramT *scale_pf_parameters(void));
138 DEPRECATED(pf_paramT *copy_pf_param(void));
139 DEPRECATED(pf_paramT *set_pf_param(paramT *dest));
140 
141 
142 
143 #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:180
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: data_structures.h:225
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.
double pf_scale
A scaling factor used by pf_fold() to avoid overflows.
pf_paramT * get_scaled_alipf_parameters(unsigned int n_seq)
Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) ...
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...
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:206
double temperature
Rescale energy parameters to a temperature in degC.
paramT * scale_parameters(void)
Get precomputed energy contributions for all the known loop types.
paramT * get_scaled_parameters(double temperature, model_detailsT md)
Get precomputed energy contributions for all the known loop types.