RNAlib-2.1.3
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 #include "data_structures.h"
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 
80 cofoldF co_pf_fold( char *sequence,
81  char *structure);
82 
100 cofoldF co_pf_fold_par( char *sequence,
101  char *structure,
102  pf_paramT *parameters,
103  int calculate_bppm,
104  int is_constrained);
105 
115 FLT_OR_DBL *export_co_bppm(void);
116 
120 void free_co_pf_arrays(void);
121 
136 void update_co_pf_params(int length);
137 
157 void update_co_pf_params_par(int length,
158  pf_paramT *parameters);
159 
177 void compute_probabilities(double FAB,
178  double FEA,
179  double FEB,
180  struct plist *prAB,
181  struct plist *prA,
182  struct plist *prB,
183  int Alength);
184 
203 ConcEnt *get_concentrations(double FEAB,
204  double FEAA,
205  double FEBB,
206  double FEA,
207  double FEB,
208  double *startconc);
209 
210 
215 /*
216 #################################################
217 # DEPRECATED FUNCTIONS #
218 #################################################
219 */
220 
226 DEPRECATED(plist *get_plist( struct plist *pl,
227  int length,
228  double cut_off));
233 DEPRECATED(void init_co_pf_fold(int length));
234 
235 #endif