RNAlib-2.0.6
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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