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# H/part_func_co.h

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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