1 #ifndef VIENNA_RNA_PACKAGE_PARAMS_H
2 #define VIENNA_RNA_PACKAGE_PARAMS_H
4 #ifdef DEPRECATION_WARNINGS
6 # define DEPRECATED(func) func __attribute__ ((deprecated))
8 # define DEPRECATED(func) func
11 # define DEPRECATED(func) func
15 #define VRNA_BACKWARD_COMPAT
40 #define VRNA_GQUAD_MAX_STACK_SIZE 7
41 #define VRNA_GQUAD_MIN_STACK_SIZE 2
42 #define VRNA_GQUAD_MAX_LINKER_LENGTH 15
43 #define VRNA_GQUAD_MIN_LINKER_LENGTH 1
44 #define VRNA_GQUAD_MIN_BOX_SIZE ((4*VRNA_GQUAD_MIN_STACK_SIZE)+(3*VRNA_GQUAD_MIN_LINKER_LENGTH))
45 #define VRNA_GQUAD_MAX_BOX_SIZE ((4*VRNA_GQUAD_MAX_STACK_SIZE)+(3*VRNA_GQUAD_MAX_LINKER_LENGTH))
56 int mismatchExt[
NBPAIRS+1][5][5];
58 int mismatch1nI[
NBPAIRS+1][5][5];
59 int mismatch23I[
NBPAIRS+1][5][5];
75 char Tetraloops[1401];
83 int gquad [VRNA_GQUAD_MAX_STACK_SIZE + 1]
84 [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
99 double exphairpin[31];
102 double expmismatchExt[
NBPAIRS+1][5][5];
103 double expmismatchI[
NBPAIRS+1][5][5];
104 double expmismatch23I[
NBPAIRS+1][5][5];
105 double expmismatch1nI[
NBPAIRS+1][5][5];
106 double expmismatchH[
NBPAIRS+1][5][5];
107 double expmismatchM[
NBPAIRS+1][5][5];
108 double expdangle5[
NBPAIRS+1][5];
109 double expdangle3[
NBPAIRS+1][5];
119 double expDuplexInit;
123 char Tetraloops[1401];
124 double expTriloop[40];
126 char Hexaloops[1801];
128 double expMultipleCA;
129 double expMultipleCB;
130 double expgquad[VRNA_GQUAD_MAX_STACK_SIZE + 1]
131 [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
344 #ifdef VRNA_BACKWARD_COMPAT
vrna_param_t * vrna_params(vrna_md_t *md)
Get a data structure containing prescaled free energy parameters.
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_md_t model_details
Model details to be used in the recursions.
Definition: params.h:88
double pf_scale
Scaling factor to avoid over-/underflows.
Definition: params.h:134
vrna_md_t model_details
Model details to be used in the recursions.
Definition: params.h:144
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:390
double temperature
Temperature used for loop contribution scaling.
Definition: params.h:136
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) ...
double temperature
Rescale energy parameters to a temperature in degC.
The model details data structure and its corresponding modifiers.
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:50
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) ...
void vrna_exp_params_subst(vrna_fold_compound_t *vc, vrna_exp_param_t *params)
Update the energy parameters for subsequent partition function computations.
void vrna_exp_params_reset(vrna_fold_compound_t *vc, vrna_md_t *md_p)
Reset Boltzmann factors for partition function computations within a vrna_fold_compound_t according t...
vrna_param_t * vrna_params_copy(vrna_param_t *par)
Get a copy of the provided free energy parameters.
void vrna_exp_params_rescale(vrna_fold_compound_t *vc, double *mfe)
Rescale Boltzmann factors for partition function computations.
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:187
double alpha
Scaling factor for the thermodynamic temperature.
Definition: params.h:137
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
double pf_scale
A scaling factor used by pf_fold() to avoid overflows.
vrna_exp_param_t * get_scaled_pf_parameters(void)
double temperature
Temperature used for loop contribution scaling.
Definition: params.h:86
vrna_exp_param_t * vrna_exp_params_comparative(unsigned int n_seq, vrna_md_t *md)
Get a data structure containing prescaled free energy parameters already transformed to Boltzmann fac...
vrna_exp_param_t * get_boltzmann_factor_copy(vrna_exp_param_t *parameters)
Get a copy of already precomputed Boltzmann factors.
#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...
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...
void vrna_params_reset(vrna_fold_compound_t *vc, vrna_md_t *md_p)
Reset free energy parameters within a vrna_fold_compound_t according to provided, or default model de...
int id
An identifier for the data structure.
Definition: params.h:95
vrna_exp_param_t * vrna_exp_params(vrna_md_t *md)
Get a data structure containing prescaled free energy parameters already transformed to Boltzmann fac...
vrna_param_t * scale_parameters(void)
Get precomputed energy contributions for all the known loop types.
void vrna_params_subst(vrna_fold_compound_t *vc, vrna_param_t *par)
Update/Reset energy parameters data structure within a vrna_fold_compound_t.