RNAlib-2.2.0-RC3
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 
5 #include <ViennaRNA/params.h>
6 
7 #ifdef __GNUC__
8 #define DEPRECATED(func) func __attribute__ ((deprecated))
9 #else
10 #define DEPRECATED(func) func
11 #endif
12 
56 extern int mirnatog;
57 
61 extern double F_monomer[2];
62 
77  char *structure);
78 
97 void vrna_co_pf_dimer_probs( double FAB,
98  double FA,
99  double FB,
100  struct plist *prAB,
101  const plist *prA,
102  const plist *prB,
103  int Alength,
104  const vrna_exp_param_t *exp_params);
105 
126  double FcAA,
127  double FcBB,
128  double FEA,
129  double FEB,
130  const double *startconc,
131  const vrna_exp_param_t *exp_params);
132 
137 /*
138 #################################################
139 # DEPRECATED FUNCTIONS #
140 #################################################
141 */
142 
161 DEPRECATED(cofoldF co_pf_fold( char *sequence, char *structure));
162 
180 DEPRECATED(cofoldF co_pf_fold_par(char *sequence, char *structure, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained));
181 
187 DEPRECATED(plist *get_plist( struct plist *pl,
188  int length,
189  double cut_off));
190 
210 DEPRECATED(void compute_probabilities(double FAB, double FEA, double FEB, struct plist *prAB, struct plist *prA, struct plist *prB, int Alength));
211 
232 DEPRECATED(ConcEnt *get_concentrations(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc));
233 
238 DEPRECATED(void init_co_pf_fold(int length));
239 
249 DEPRECATED(FLT_OR_DBL *export_co_bppm(void));
250 
254 DEPRECATED(void free_co_pf_arrays(void));
255 
266 DEPRECATED(void update_co_pf_params(int length));
267 
287 DEPRECATED(void update_co_pf_params_par(int length, vrna_exp_param_t *parameters));
288 
289 #endif
cofoldF co_pf_fold(char *sequence, char *structure)
Calculate partition function and base pair probabilities.
Definition: data_structures.h:128
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.
void vrna_co_pf_dimer_probs(double FAB, double FA, double FB, struct plist *prAB, const plist *prA, const plist *prB, int Alength, const vrna_exp_param_t *exp_params)
Compute Boltzmann probabilities of dimerization without homodimers.
ConcEnt * vrna_co_pf_get_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...
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:698
int mirnatog
Toggles no intrabp in 2nd mol.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:45
void init_co_pf_fold(int length)
cofoldF vrna_co_pf_fold(vrna_fold_compound *vc, char *structure)
Calculate partition function and base pair probabilities of nucleic acid/nucleic acid dimers...
plist * get_plist(struct plist *pl, int length, double cut_off)
void update_co_pf_params_par(int length, vrna_exp_param_t *parameters)
Recalculate energy parameters.
cofoldF 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.
void free_co_pf_arrays(void)
Free the memory occupied by co_pf_fold()
double F_monomer[2]
Free energies of the two monomers.
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:86
void compute_probabilities(double FAB, double FEA, double FEB, struct plist *prAB, struct plist *prA, struct plist *prB, int Alength)
Compute Boltzmann probabilities of dimerization without homodimers.
ConcEnt * 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...
Definition: data_structures.h:140