RNAlib-2.2.0RC0
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 
6 #ifdef __GNUC__
7 #define DEPRECATED(func) func __attribute__ ((deprecated))
8 #else
9 #define DEPRECATED(func) func
10 #endif
11 
55 extern int mirnatog;
56 
60 extern double F_monomer[2];
61 
76  char *structure);
77 
96 void vrna_co_pf_dimer_probs( double FAB,
97  double FA,
98  double FB,
99  struct plist *prAB,
100  const plist *prA,
101  const plist *prB,
102  int Alength,
103  const pf_paramT *exp_params);
104 
125  double FcAA,
126  double FcBB,
127  double FEA,
128  double FEB,
129  const double *startconc,
130  const pf_paramT *exp_params);
131 
136 /*
137 #################################################
138 # DEPRECATED FUNCTIONS #
139 #################################################
140 */
141 
160 DEPRECATED(cofoldF co_pf_fold( char *sequence, char *structure));
161 
179 DEPRECATED(cofoldF co_pf_fold_par(char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int is_constrained));
180 
186 DEPRECATED(plist *get_plist( struct plist *pl,
187  int length,
188  double cut_off));
189 
209 DEPRECATED(void compute_probabilities(double FAB, double FEA, double FEB, struct plist *prAB, struct plist *prA, struct plist *prB, int Alength));
210 
231 DEPRECATED(ConcEnt *get_concentrations(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc));
232 
237 DEPRECATED(void init_co_pf_fold(int length));
238 
248 DEPRECATED(FLT_OR_DBL *export_co_bppm(void));
249 
253 DEPRECATED(void free_co_pf_arrays(void));
254 
269 DEPRECATED(void update_co_pf_params(int length));
270 
290 DEPRECATED(void update_co_pf_params_par(int length, pf_paramT *parameters));
291 
292 #endif
cofoldF co_pf_fold(char *sequence, char *structure)
Calculate partition function and base pair probabilities.
Definition: data_structures.h:456
cofoldF co_pf_fold_par(char *sequence, char *structure, pf_paramT *parameters, int calculate_bppm, int is_constrained)
Calculate partition function and base pair probabilities.
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 update_co_pf_params_par(int length, pf_paramT *parameters)
Recalculate energy parameters.
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: data_structures.h:225
Definition: data_structures.h:359
int mirnatog
Toggles no intrabp in 2nd mol.
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:94
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)
ConcEnt * vrna_co_pf_get_concentrations(double FcAB, double FcAA, double FcBB, double FEA, double FEB, const double *startconc, const pf_paramT *exp_params)
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()
void vrna_co_pf_dimer_probs(double FAB, double FA, double FB, struct plist *prAB, const plist *prA, const plist *prB, int Alength, const pf_paramT *exp_params)
Compute Boltzmann probabilities of dimerization without homodimers.
double F_monomer[2]
Free energies of the two monomers.
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:468