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part_func_co.h
Go to the documentation of this file.
1 #ifndef VIENNA_RNA_PACKAGE_PART_FUNC_CO_H
2 #define VIENNA_RNA_PACKAGE_PART_FUNC_CO_H
3
4 #ifdef DEPRECATION_WARNINGS
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
58 typedef struct vrna_dimer_pf_s vrna_dimer_pf_t;
59
61 typedef struct vrna_dimer_conc_s vrna_dimer_conc_t;
62
63
64 #ifdef VRNA_BACKWARD_COMPAT
65
69 typedef struct vrna_dimer_pf_s cofoldF;
70
74 typedef struct vrna_dimer_conc_s ConcEnt;
75
76 #endif
77
78 #include <ViennaRNA/data_structures.h>
79 #include <ViennaRNA/params.h>
80
84 extern int mirnatog;
85
89 extern double F_monomer[2];
90
94 struct vrna_dimer_pf_s {
95 /* free energies for: */
96 double F0AB;
97 double FAB;
98 double FcAB;
99 double FA;
100 double FB;
101 };
102
106 struct vrna_dimer_conc_s {
107 double A0;
108 double B0;
109 double ABc;
110 double AAc;
111 double BBc;
112 double Ac;
113 double Bc;
114 };
115
129 vrna_dimer_pf_t
130 vrna_pf_dimer(vrna_fold_compound_t *vc,
131 char *structure);
132
151 void vrna_pf_dimer_probs(double FAB,
152 double FA,
153 double FB,
154 vrna_plist_t *prAB,
155 const vrna_plist_t *prA,
156 const vrna_plist_t *prB,
157 int Alength,
158 const vrna_exp_param_t *exp_params);
159
179 vrna_dimer_conc_t *vrna_pf_dimer_concentrations(double FcAB,
180 double FcAA,
181 double FcBB,
182 double FEA,
183 double FEB,
184 const double *startconc,
185 const vrna_exp_param_t *exp_params);
186
191 /*
192 #################################################
193 # DEPRECATED FUNCTIONS #
194 #################################################
195 */
196
215 DEPRECATED(vrna_dimer_pf_t co_pf_fold( char *sequence, char *structure));
216
236 DEPRECATED(vrna_dimer_pf_t co_pf_fold_par(char *sequence, char *structure, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained));
237
243 DEPRECATED(vrna_plist_t *get_plist( vrna_plist_t *pl,
244 int length,
245 double cut_off));
246
266 DEPRECATED(void compute_probabilities(double FAB, double FEA, double FEB, vrna_plist_t *prAB, vrna_plist_t *prA, vrna_plist_t *prB, int Alength));
267
288 DEPRECATED(vrna_dimer_conc_t *get_concentrations(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc));
289
294 DEPRECATED(void init_co_pf_fold(int length));
295
309 DEPRECATED(FLT_OR_DBL *export_co_bppm(void));
310
318 DEPRECATED(void free_co_pf_arrays(void));
319
330 DEPRECATED(void update_co_pf_params(int length));
331
351 DEPRECATED(void update_co_pf_params_par(int length, vrna_exp_param_t *parameters));
352
353 #endif
vrna_dimer_conc_s::A0
double A0
start concentration A
Definition: part_func_co.h:107
compute_probabilities
void compute_probabilities(double FAB, double FEA, double FEB, vrna_plist_t *prAB, vrna_plist_t *prA, vrna_plist_t *prB, int Alength)
Compute Boltzmann probabilities of dimerization without homodimers.
vrna_dimer_conc_s::B0
double B0
start concentration B
Definition: part_func_co.h:108
FLT_OR_DBL
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:39
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:424
vrna_dimer_conc_s::ABc
double ABc
End concentration AB.
Definition: part_func_co.h:109
update_co_pf_params
void update_co_pf_params(int length)
Recalculate energy parameters.
export_co_bppm
FLT_OR_DBL * export_co_bppm(void)
Get a pointer to the base pair probability array.
vrna_dimer_pf_s::F0AB
double F0AB
Null model without DuplexInit.
Definition: part_func_co.h:96
vrna_dimer_pf_s::FA
double FA
monomer A
Definition: part_func_co.h:99
vrna_dimer_conc_s
Data structure for concentration dependency computations.
Definition: part_func_co.h:106
mirnatog
int mirnatog
Toggles no intrabp in 2nd mol.
get_plist
vrna_plist_t * get_plist(vrna_plist_t *pl, int length, double cut_off)
data_structures.h
params.h
vrna_exp_param_s
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
vrna_pf_dimer
vrna_dimer_pf_t vrna_pf_dimer(vrna_fold_compound_t *vc, char *structure)
Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers...
init_co_pf_fold
void init_co_pf_fold(int length)
vrna_dimer_pf_s::FB
double FB
monomer B
Definition: part_func_co.h:100
co_pf_fold_par
vrna_dimer_pf_t co_pf_fold_par(char *sequence, char *structure, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained)
Calculate partition function and base pair probabilities.
vrna_plist_s
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:164
update_co_pf_params_par
void update_co_pf_params_par(int length, vrna_exp_param_t *parameters)
Recalculate energy parameters.
vrna_pf_dimer_probs
void vrna_pf_dimer_probs(double FAB, double FA, double FB, vrna_plist_t *prAB, const vrna_plist_t *prA, const vrna_plist_t *prB, int Alength, const vrna_exp_param_t *exp_params)
Compute Boltzmann probabilities of dimerization without homodimers.
vrna_pf_dimer_concentrations
vrna_dimer_conc_t * vrna_pf_dimer_concentrations(double FcAB, double FcAA, double FcBB, double FEA, double FEB, const double *startconc, const vrna_exp_param_t *exp_params)
Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibri...
get_concentrations
vrna_dimer_conc_t * get_concentrations(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc)
Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibri...
free_co_pf_arrays
void free_co_pf_arrays(void)
Free the memory occupied by co_pf_fold()
vrna_dimer_pf_s::FcAB
double FcAB
true hybrid states only
Definition: part_func_co.h:98
vrna_dimer_pf_s
Data structure returned by vrna_pf_dimer()
Definition: part_func_co.h:94
F_monomer
double F_monomer[2]
Free energies of the two monomers.
co_pf_fold
vrna_dimer_pf_t co_pf_fold(char *sequence, char *structure)
Calculate partition function and base pair probabilities.
vrna_dimer_pf_s::FAB
double FAB
all states with DuplexInit correction
Definition: part_func_co.h:97