1 #ifndef VIENNA_RNA_PACKAGE_PARAMS_H 2 #define VIENNA_RNA_PACKAGE_PARAMS_H 4 #ifdef VRNA_WARN_DEPRECATED 5 # if defined(__clang__) 6 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg))) 7 # elif defined(__GNUC__) 8 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg))) 10 # define DEPRECATED(func, msg) func 13 # define DEPRECATED(func, msg) func 44 #define VRNA_GQUAD_MAX_STACK_SIZE 7 45 #define VRNA_GQUAD_MIN_STACK_SIZE 2 46 #define VRNA_GQUAD_MAX_LINKER_LENGTH 15 47 #define VRNA_GQUAD_MIN_LINKER_LENGTH 1 48 #define VRNA_GQUAD_MIN_BOX_SIZE ((4 * VRNA_GQUAD_MIN_STACK_SIZE) + \ 49 (3 * VRNA_GQUAD_MIN_LINKER_LENGTH)) 50 #define VRNA_GQUAD_MAX_BOX_SIZE ((4 * VRNA_GQUAD_MAX_STACK_SIZE) + \ 51 (3 * VRNA_GQUAD_MAX_LINKER_LENGTH)) 62 int mismatchExt[
NBPAIRS + 1][5][5];
63 int mismatchI[
NBPAIRS + 1][5][5];
64 int mismatch1nI[
NBPAIRS + 1][5][5];
65 int mismatch23I[
NBPAIRS + 1][5][5];
66 int mismatchH[
NBPAIRS + 1][5][5];
67 int mismatchM[
NBPAIRS + 1][5][5];
81 char Tetraloops[1401];
89 int gquad [VRNA_GQUAD_MAX_STACK_SIZE + 1]
90 [3 * VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
106 double exphairpin[31];
108 double expinternal[
MAXLOOP + 1];
109 double expmismatchExt[
NBPAIRS + 1][5][5];
110 double expmismatchI[
NBPAIRS + 1][5][5];
111 double expmismatch23I[
NBPAIRS + 1][5][5];
112 double expmismatch1nI[
NBPAIRS + 1][5][5];
113 double expmismatchH[
NBPAIRS + 1][5][5];
114 double expmismatchM[
NBPAIRS + 1][5][5];
115 double expdangle5[
NBPAIRS + 1][5];
116 double expdangle3[
NBPAIRS + 1][5];
120 double expninio[5][
MAXLOOP + 1];
123 double expMLintern[
NBPAIRS + 1];
126 double expDuplexInit;
130 char Tetraloops[1401];
131 double expTriloop[40];
133 char Hexaloops[1801];
135 double expMultipleCA;
136 double expMultipleCB;
137 double expgquad[VRNA_GQUAD_MAX_STACK_SIZE + 1]
138 [3 * VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
362 unsigned int options);
365 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 380 "Use vrna_params_copy() instead");
392 "Use vrna_params() instead");
423 "Use vrna_exp_params() instead");
436 "Use vrna_exp_params_copy() instead");
446 "Use vrna_exp_params_comparative() instead");
461 "Use vrna_exp_params_comparative() instead");
475 "Use vrna_params() instead");
495 "Usee vrna_params() instead");
497 DEPRECATED(
vrna_param_t *copy_parameters(
void),
"Use vrna_params_copy() instead");
499 DEPRECATED(
vrna_exp_param_t *scale_pf_parameters(
void),
"Use vrna_exp_params() instead");
500 DEPRECATED(
vrna_exp_param_t *copy_pf_param(
void),
"Use vrna_exp_params_copy() instead");
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.
vrna_md_t model_details
Model details to be used in the recursions.
Definition: basic.h:94
#define NBPAIRS
Definition: constants.h:25
double pf_scale
Scaling factor to avoid over-/underflows.
Definition: basic.h:141
Energy parameter constants.
vrna_md_t model_details
Model details to be used in the recursions.
Definition: basic.h:151
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
double temperature
Temperature used for loop contribution scaling.
Definition: basic.h:143
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: basic.h:56
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.
#define MAXLOOP
Definition: constants.h:29
char param_file[256]
The filename the parameters were derived from, or empty string if they represent the default...
Definition: basic.h:95
vrna_param_t * vrna_params_copy(vrna_param_t *par)
Get a copy of the provided free energy parameters.
Various data structures and pre-processor macros.
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:177
double alpha
Scaling factor for the thermodynamic temperature.
Definition: basic.h:144
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: basic.h:101
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: basic.h:92
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.
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: basic.h:102
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.