1 #ifndef VIENNA_RNA_PACKAGE_PARAMS_H
2 #define VIENNA_RNA_PACKAGE_PARAMS_H
5 #define DEPRECATED(func) func __attribute__ ((deprecated))
7 #define DEPRECATED(func) func
11 #define VRNA_BACKWARD_COMPAT
31 #define VRNA_GQUAD_MAX_STACK_SIZE 7
32 #define VRNA_GQUAD_MIN_STACK_SIZE 2
33 #define VRNA_GQUAD_MAX_LINKER_LENGTH 15
34 #define VRNA_GQUAD_MIN_LINKER_LENGTH 1
35 #define VRNA_GQUAD_MIN_BOX_SIZE ((4*VRNA_GQUAD_MIN_STACK_SIZE)+(3*VRNA_GQUAD_MIN_LINKER_LENGTH))
36 #define VRNA_GQUAD_MAX_BOX_SIZE ((4*VRNA_GQUAD_MAX_STACK_SIZE)+(3*VRNA_GQUAD_MAX_LINKER_LENGTH))
47 int mismatchExt[
NBPAIRS+1][5][5];
49 int mismatch1nI[
NBPAIRS+1][5][5];
50 int mismatch23I[
NBPAIRS+1][5][5];
66 char Tetraloops[1401];
74 int gquad [VRNA_GQUAD_MAX_STACK_SIZE + 1]
75 [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
91 double exphairpin[31];
94 double expmismatchExt[
NBPAIRS+1][5][5];
95 double expmismatchI[
NBPAIRS+1][5][5];
96 double expmismatch23I[
NBPAIRS+1][5][5];
97 double expmismatch1nI[
NBPAIRS+1][5][5];
98 double expmismatchH[
NBPAIRS+1][5][5];
99 double expmismatchM[
NBPAIRS+1][5][5];
100 double expdangle5[
NBPAIRS+1][5];
101 double expdangle3[
NBPAIRS+1][5];
111 double expDuplexInit;
115 char Tetraloops[1401];
116 double expTriloop[40];
118 char Hexaloops[1801];
120 double expMultipleCA;
121 double expMultipleCB;
122 double expgquad[VRNA_GQUAD_MAX_STACK_SIZE + 1]
123 [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
220 #ifdef VRNA_BACKWARD_COMPAT
222 #define paramT vrna_param_t
223 #define pf_paramT vrna_exp_param_t
vrna_param_t * get_scaled_parameters(double temperature, vrna_md_t md)
Get precomputed energy contributions for all the known loop types.
#define MAXLOOP
Definition: energy_const.h:28
vrna_exp_param_t * get_scaled_alipf_parameters(unsigned int n_seq)
Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) ...
The model details data structure and its corresponding modifiers.
vrna_md_t model_details
Model details to be used in the recursions.
Definition: params.h:79
vrna_exp_param_t * vrna_exp_params_copy(vrna_exp_param_t *par)
Get a copy of the provided free energy parameters (provided as Boltzmann factors) ...
vrna_param_t * vrna_params_copy(vrna_param_t *par)
Get a copy of the provided free energy parameters.
vrna_exp_param_t * vrna_exp_params_get(vrna_md_t *md)
Get a data structure containing prescaled free energy parameters already transformed to Boltzmann fac...
double alpha
Scaling factor for the thermodynamic temperature.
Definition: params.h:129
double temperature
Temperature used for loop contribution scaling.
Definition: params.h:128
vrna_exp_param_t * get_scaled_pf_parameters(void)
vrna_md_t model_details
Model details to be used in the recursions.
Definition: params.h:136
double temperature
Temperature used for loop contribution scaling.
Definition: params.h:77
vrna_exp_param_t * get_boltzmann_factor_copy(vrna_exp_param_t *parameters)
Get a copy of already precomputed Boltzmann factors.
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:41
vrna_exp_param_t * vrna_exp_params_ali_get(unsigned int n_seq, vrna_md_t *md)
Get a data structure containing prescaled free energy parameters already transformed to Boltzmann fac...
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:169
#define NBPAIRS
Definition: energy_const.h:24
vrna_exp_param_t * get_boltzmann_factors_ali(unsigned int n_seq, double temperature, double betaScale, vrna_md_t md, double pf_scale)
Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) w...
double temperature
Rescale energy parameters to a temperature in degC.
double pf_scale
Scaling factor to avoid over-/underflows.
Definition: params.h:126
vrna_exp_param_t * get_boltzmann_factors(double temperature, double betaScale, vrna_md_t md, double pf_scale)
Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent th...
double pf_scale
A scaling factor used by pf_fold() to avoid overflows.
vrna_param_t * vrna_params_get(vrna_md_t *md)
Get a data structure containing prescaled free energy parameters.
int id
An identifier for the data structure.
Definition: params.h:87
vrna_param_t * scale_parameters(void)
Get precomputed energy contributions for all the known loop types.
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:86