RNAlib-2.4.0
params.h
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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 };
97 
102  int id;
105  double expstack[NBPAIRS + 1][NBPAIRS + 1];
106  double exphairpin[31];
107  double expbulge[MAXLOOP + 1];
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];
117  double expint11[NBPAIRS + 1][NBPAIRS + 1][5][5];
118  double expint21[NBPAIRS + 1][NBPAIRS + 1][5][5][5];
119  double expint22[NBPAIRS + 1][NBPAIRS + 1][5][5][5][5];
120  double expninio[5][MAXLOOP + 1];
121  double lxc;
122  double expMLbase;
123  double expMLintern[NBPAIRS + 1];
124  double expMLclosing;
125  double expTermAU;
126  double expDuplexInit;
127  double exptetra[40];
128  double exptri[40];
129  double exphex[40];
130  char Tetraloops[1401];
131  double expTriloop[40];
132  char Triloops[241];
133  char Hexaloops[1801];
134  double expTripleC;
135  double expMultipleCA;
136  double expMultipleCB;
137  double expgquad[VRNA_GQUAD_MAX_STACK_SIZE + 1]
138  [3 * VRNA_GQUAD_MAX_LINKER_LENGTH + 1];
139 
140  double kT;
141  double pf_scale;
143  double temperature;
144  double alpha;
152 };
153 
154 
166 vrna_param_t *
168 
169 
181 vrna_param_t *
183 
184 
209 
210 
225 vrna_exp_params_comparative(unsigned int n_seq,
226  vrna_md_t *md);
227 
228 
242 
243 
256 void
258  vrna_param_t *par);
259 
260 
278 void
280  vrna_exp_param_t *params);
281 
282 
320 void
322  double *mfe);
323 
324 
339  vrna_md_t *md_p);
340 
341 
357  vrna_md_t *md_p);
358 
359 
360 void vrna_params_prepare(vrna_fold_compound_t *vc,
361  unsigned int options);
362 
363 
364 #ifdef VRNA_BACKWARD_COMPAT
365 
370 typedef struct vrna_param_s paramT;
371 
377 
378 DEPRECATED(vrna_param_t *get_parameter_copy(vrna_param_t *par));
379 
389 DEPRECATED(vrna_exp_param_t *get_scaled_pf_parameters(void));
390 
417  double betaScale,
418  vrna_md_t md,
419  double pf_scale));
420 
432 
440 DEPRECATED(vrna_exp_param_t *get_scaled_alipf_parameters(unsigned int n_seq));
441 
450 DEPRECATED(vrna_exp_param_t *get_boltzmann_factors_ali(unsigned int n_seq,
451  double temperature,
452  double betaScale,
453  vrna_md_t md,
454  double pf_scale));
455 
467 DEPRECATED(vrna_param_t *scale_parameters(void));
468 
486  vrna_md_t md));
487 
488 DEPRECATED(vrna_param_t *copy_parameters(void));
489 DEPRECATED(vrna_param_t *set_parameters(vrna_param_t *dest));
490 DEPRECATED(vrna_exp_param_t *scale_pf_parameters(void));
491 DEPRECATED(vrna_exp_param_t *copy_pf_param(void));
492 DEPRECATED(vrna_exp_param_t *set_pf_param(vrna_param_t *dest));
493 
494 #endif
495 
501 #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:141
vrna_md_t model_details
Model details to be used in the recursions.
Definition: params.h:151
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:463
double temperature
Temperature used for loop contribution scaling.
Definition: params.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: 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.
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.
double alpha
Scaling factor for the thermodynamic temperature.
Definition: params.h:144
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:101
double pf_scale
A scaling factor used by pf_fold() to avoid overflows.
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:189
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: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.