RNAlib-2.2.7
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 
66 typedef struct vrna_dimer_pf_s cofoldF;
67 typedef struct vrna_dimer_conc_s ConcEnt;
68 
69 #endif
70 
72 #include <ViennaRNA/params.h>
73 
77 extern int mirnatog;
78 
82 extern double F_monomer[2];
83 
88  /* free energies for: */
89  double F0AB;
90  double FAB;
91  double FcAB;
92  double FA;
93  double FB;
94 };
95 
100  double A0;
101  double B0;
102  double ABc;
103  double AAc;
104  double BBc;
105  double Ac;
106  double Bc;
107 };
108 
124  char *structure);
125 
144 void vrna_pf_dimer_probs(double FAB,
145  double FA,
146  double FB,
147  vrna_plist_t *prAB,
148  const vrna_plist_t *prA,
149  const vrna_plist_t *prB,
150  int Alength,
151  const vrna_exp_param_t *exp_params);
152 
173  double FcAA,
174  double FcBB,
175  double FEA,
176  double FEB,
177  const double *startconc,
178  const vrna_exp_param_t *exp_params);
179 
184 /*
185 #################################################
186 # DEPRECATED FUNCTIONS #
187 #################################################
188 */
189 
208 DEPRECATED(vrna_dimer_pf_t co_pf_fold( char *sequence, char *structure));
209 
229 DEPRECATED(vrna_dimer_pf_t co_pf_fold_par(char *sequence, char *structure, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained));
230 
236 DEPRECATED(vrna_plist_t *get_plist( vrna_plist_t *pl,
237  int length,
238  double cut_off));
239 
259 DEPRECATED(void compute_probabilities(double FAB, double FEA, double FEB, vrna_plist_t *prAB, vrna_plist_t *prA, vrna_plist_t *prB, int Alength));
260 
281 DEPRECATED(vrna_dimer_conc_t *get_concentrations(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc));
282 
287 DEPRECATED(void init_co_pf_fold(int length));
288 
302 DEPRECATED(FLT_OR_DBL *export_co_bppm(void));
303 
311 DEPRECATED(void free_co_pf_arrays(void));
312 
323 DEPRECATED(void update_co_pf_params(int length));
324 
344 DEPRECATED(void update_co_pf_params_par(int length, vrna_exp_param_t *parameters));
345 
346 #endif
double A0
start concentration A
Definition: part_func_co.h:100
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:101
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:390
double ABc
End concentration AB.
Definition: part_func_co.h:102
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:89
double FA
monomer A
Definition: part_func_co.h:92
Definition: part_func_co.h:99
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:93
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:91
Definition: part_func_co.h:87
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:90