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00001 /* functions from part_func.c */
00002 /* calculate partition function and base pair probabilities */
00003 #ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_CO_H__
00004 #define __VIENNA_RNA_PACKAGE_PART_FUNC_CO_H__
00005 
00006 #include "data_structures.h"
00007 
00008 #ifdef __GNUC__
00009 #define DEPRECATED(func) func __attribute__ ((deprecated))
00010 #else
00011 #define DEPRECATED(func) func
00012 #endif
00013 
00045 extern int    mirnatog;
00046 
00050 extern double F_monomer[2];
00051 
00070 cofoldF co_pf_fold( char *sequence,
00071                     char *structure);
00072 
00090 cofoldF co_pf_fold_par( char *sequence,
00091                         char *structure,
00092                         pf_paramT *parameters,
00093                         int calculate_bppm,
00094                         int is_constrained);
00095 
00105 FLT_OR_DBL *export_co_bppm(void);
00106 
00110 void    free_co_pf_arrays(void);
00111 
00126 void    update_co_pf_params(int length);
00127 
00147 void    update_co_pf_params_par(int length,
00148                                 pf_paramT *parameters);
00149 
00167 void    compute_probabilities(double FAB,
00168                               double FEA,
00169                               double FEB,
00170                               struct plist  *prAB,
00171                               struct plist  *prA,
00172                               struct plist  *prB,
00173                               int Alength);
00174 
00193 ConcEnt *get_concentrations(double FEAB,
00194                             double FEAA,
00195                             double FEBB,
00196                             double FEA,
00197                             double FEB,
00198                             double *startconc);
00199 
00200 /*
00201 #################################################
00202 # DEPRECATED FUNCTIONS                          #
00203 #################################################
00204 */
00205 
00211 DEPRECATED(plist  *get_plist( struct plist *pl,
00212                               int length,
00213                               double cut_off));
00218 DEPRECATED(void   init_co_pf_fold(int length));
00219 
00220 #endif