1 #ifndef VIENNA_RNA_PACKAGE_PARAMS_H 2 #define VIENNA_RNA_PACKAGE_PARAMS_H 4 #ifdef VRNA_WARN_DEPRECATED 6 # define DEPRECATED(func) func __attribute__ ((deprecated)) 8 # define DEPRECATED(func) func 11 # define DEPRECATED(func) func 15 #define VRNA_BACKWARD_COMPAT 45 #define VRNA_GQUAD_MAX_STACK_SIZE 7 46 #define VRNA_GQUAD_MIN_STACK_SIZE 2 47 #define VRNA_GQUAD_MAX_LINKER_LENGTH 15 48 #define VRNA_GQUAD_MIN_LINKER_LENGTH 1 49 #define VRNA_GQUAD_MIN_BOX_SIZE ((4 * VRNA_GQUAD_MIN_STACK_SIZE) + \ 50 (3 * VRNA_GQUAD_MIN_LINKER_LENGTH)) 51 #define VRNA_GQUAD_MAX_BOX_SIZE ((4 * VRNA_GQUAD_MAX_STACK_SIZE) + \ 52 (3 * VRNA_GQUAD_MAX_LINKER_LENGTH)) 63 int mismatchExt[
NBPAIRS + 1][5][5];
64 int mismatchI[
NBPAIRS + 1][5][5];
65 int mismatch1nI[
NBPAIRS + 1][5][5];
66 int mismatch23I[
NBPAIRS + 1][5][5];
67 int mismatchH[
NBPAIRS + 1][5][5];
68 int mismatchM[
NBPAIRS + 1][5][5];
82 char Tetraloops[1401];
90 int gquad [VRNA_GQUAD_MAX_STACK_SIZE + 1]
91 [3 * VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
107 double exphairpin[31];
109 double expinternal[
MAXLOOP + 1];
110 double expmismatchExt[
NBPAIRS + 1][5][5];
111 double expmismatchI[
NBPAIRS + 1][5][5];
112 double expmismatch23I[
NBPAIRS + 1][5][5];
113 double expmismatch1nI[
NBPAIRS + 1][5][5];
114 double expmismatchH[
NBPAIRS + 1][5][5];
115 double expmismatchM[
NBPAIRS + 1][5][5];
116 double expdangle5[
NBPAIRS + 1][5];
117 double expdangle3[
NBPAIRS + 1][5];
121 double expninio[5][
MAXLOOP + 1];
124 double expMLintern[
NBPAIRS + 1];
127 double expDuplexInit;
131 char Tetraloops[1401];
132 double expTriloop[40];
134 char Hexaloops[1801];
136 double expMultipleCA;
137 double expMultipleCB;
138 double expgquad[VRNA_GQUAD_MAX_STACK_SIZE + 1]
139 [3 * VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
363 unsigned int options);
366 #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:29
vrna_md_t model_details
Model details to be used in the recursions.
Definition: params.h:95
double pf_scale
Scaling factor to avoid over-/underflows.
Definition: params.h:142
vrna_md_t model_details
Model details to be used in the recursions.
Definition: params.h:152
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:130
double temperature
Temperature used for loop contribution scaling.
Definition: params.h:144
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.
The datastructure that contains temperature scaled energy parameters.
Definition: params.h:57
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.
char param_file[256]
The filename the parameters were derived from, or empty string if they represent the default...
Definition: params.h:96
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.
Energy parameter constants.
Various data structures and pre-processor macros.
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:189
double alpha
Scaling factor for the thermodynamic temperature.
Definition: params.h:145
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:102
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:93
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...
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_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:25
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:103
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.