RNAlib-2.2.10
part_func_co.h
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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 
59 
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 
79 #include <ViennaRNA/params.h>
80 
84 extern int mirnatog;
85 
89 extern double F_monomer[2];
90 
95  /* free energies for: */
96  double F0AB;
97  double FAB;
98  double FcAB;
99  double FA;
100  double FB;
101 };
102 
107  double A0;
108  double B0;
109  double ABc;
110  double AAc;
111  double BBc;
112  double Ac;
113  double Bc;
114 };
115 
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 
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
double A0
start concentration A
Definition: part_func_co.h:107
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.
double B0
start concentration B
Definition: part_func_co.h:108
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:39
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:424
double ABc
End concentration AB.
Definition: part_func_co.h:109
void update_co_pf_params(int length)
Recalculate energy parameters.
FLT_OR_DBL * export_co_bppm(void)
Get a pointer to the base pair probability array.
double F0AB
Null model without DuplexInit.
Definition: part_func_co.h:96
double FA
monomer A
Definition: part_func_co.h:99
Data structure for concentration dependency computations.
Definition: part_func_co.h:106
int mirnatog
Toggles no intrabp in 2nd mol.
vrna_plist_t * get_plist(vrna_plist_t *pl, int length, double cut_off)
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
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...
void init_co_pf_fold(int length)
double FB
monomer B
Definition: part_func_co.h:100
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.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:164
void update_co_pf_params_par(int length, vrna_exp_param_t *parameters)
Recalculate energy parameters.
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_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...
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...
void free_co_pf_arrays(void)
Free the memory occupied by co_pf_fold()
double FcAB
true hybrid states only
Definition: part_func_co.h:98
Data structure returned by vrna_pf_dimer()
Definition: part_func_co.h:94
double F_monomer[2]
Free energies of the two monomers.
vrna_dimer_pf_t co_pf_fold(char *sequence, char *structure)
Calculate partition function and base pair probabilities.
double FAB
all states with DuplexInit correction
Definition: part_func_co.h:97