RNAlib-2.4.3
params.h
Go to the documentation of this file.
1 #ifndef VIENNA_RNA_PACKAGE_PARAMS_H
2 #define VIENNA_RNA_PACKAGE_PARAMS_H
3 
4 #ifdef VRNA_WARN_DEPRECATED
5 # ifdef __GNUC__
6 # define DEPRECATED(func) func __attribute__ ((deprecated))
7 # else
8 # define DEPRECATED(func) func
9 # endif
10 #else
11 # define DEPRECATED(func) func
12 #endif
13 
14 /* make this interface backward compatible with RNAlib < 2.2.0 */
15 #define VRNA_BACKWARD_COMPAT
16 
37 typedef struct vrna_param_s vrna_param_t;
40 
41 #include <ViennaRNA/energy_const.h>
43 #include <ViennaRNA/model.h>
44 
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))
53 
57 struct vrna_param_s {
58  int id;
59  int stack[NBPAIRS + 1][NBPAIRS + 1];
60  int hairpin[31];
61  int bulge[MAXLOOP + 1];
62  int internal_loop[MAXLOOP + 1];
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];
69  int dangle5[NBPAIRS + 1][5];
70  int dangle3[NBPAIRS + 1][5];
71  int int11[NBPAIRS + 1][NBPAIRS + 1][5][5];
72  int int21[NBPAIRS + 1][NBPAIRS + 1][5][5][5];
73  int int22[NBPAIRS + 1][NBPAIRS + 1][5][5][5][5];
74  int ninio[5];
75  double lxc;
76  int MLbase;
77  int MLintern[NBPAIRS + 1];
78  int MLclosing;
79  int TerminalAU;
80  int DuplexInit;
81  int Tetraloop_E[200];
82  char Tetraloops[1401];
83  int Triloop_E[40];
84  char Triloops[241];
85  int Hexaloop_E[40];
86  char Hexaloops[1801];
87  int TripleC;
88  int MultipleCA;
89  int MultipleCB;
90  int gquad [VRNA_GQUAD_MAX_STACK_SIZE + 1]
91  [3 * VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
92 
93  double temperature;
96  char param_file[256];
97 };
98 
103  int id;
106  double expstack[NBPAIRS + 1][NBPAIRS + 1];
107  double exphairpin[31];
108  double expbulge[MAXLOOP + 1];
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];
118  double expint11[NBPAIRS + 1][NBPAIRS + 1][5][5];
119  double expint21[NBPAIRS + 1][NBPAIRS + 1][5][5][5];
120  double expint22[NBPAIRS + 1][NBPAIRS + 1][5][5][5][5];
121  double expninio[5][MAXLOOP + 1];
122  double lxc;
123  double expMLbase;
124  double expMLintern[NBPAIRS + 1];
125  double expMLclosing;
126  double expTermAU;
127  double expDuplexInit;
128  double exptetra[40];
129  double exptri[40];
130  double exphex[40];
131  char Tetraloops[1401];
132  double expTriloop[40];
133  char Triloops[241];
134  char Hexaloops[1801];
135  double expTripleC;
136  double expMultipleCA;
137  double expMultipleCB;
138  double expgquad[VRNA_GQUAD_MAX_STACK_SIZE + 1]
139  [3 * VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
140 
141  double kT;
142  double pf_scale;
144  double temperature;
145  double alpha;
153  char param_file[256];
154 };
155 
156 
168 vrna_param_t *
170 
171 
183 vrna_param_t *
185 
186 
211 
212 
227 vrna_exp_params_comparative(unsigned int n_seq,
228  vrna_md_t *md);
229 
230 
244 
245 
258 void
260  vrna_param_t *par);
261 
262 
280 void
282  vrna_exp_param_t *params);
283 
284 
322 void
324  double *mfe);
325 
326 
341  vrna_md_t *md_p);
342 
343 
359  vrna_md_t *md_p);
360 
361 
362 void vrna_params_prepare(vrna_fold_compound_t *vc,
363  unsigned int options);
364 
365 
366 #ifdef VRNA_BACKWARD_COMPAT
367 
372 typedef struct vrna_param_s paramT;
373 
379 
380 DEPRECATED(vrna_param_t *get_parameter_copy(vrna_param_t *par));
381 
391 DEPRECATED(vrna_exp_param_t *get_scaled_pf_parameters(void));
392 
419  double betaScale,
420  vrna_md_t md,
421  double pf_scale));
422 
434 
442 DEPRECATED(vrna_exp_param_t *get_scaled_alipf_parameters(unsigned int n_seq));
443 
452 DEPRECATED(vrna_exp_param_t *get_boltzmann_factors_ali(unsigned int n_seq,
453  double temperature,
454  double betaScale,
455  vrna_md_t md,
456  double pf_scale));
457 
469 DEPRECATED(vrna_param_t *scale_parameters(void));
470 
488  vrna_md_t md));
489 
490 DEPRECATED(vrna_param_t *copy_parameters(void));
491 DEPRECATED(vrna_param_t *set_parameters(vrna_param_t *dest));
492 DEPRECATED(vrna_exp_param_t *scale_pf_parameters(void));
493 DEPRECATED(vrna_exp_param_t *copy_pf_param(void));
494 DEPRECATED(vrna_exp_param_t *set_pf_param(vrna_param_t *dest));
495 
496 #endif
497 
503 #endif
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.