RNAlib-2.0.4
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00001 #ifndef __VIENNA_RNA_PACKAGE_FOLD_H__ 00002 #define __VIENNA_RNA_PACKAGE_FOLD_H__ 00003 00004 #include "data_structures.h" 00005 00006 #ifdef __GNUC__ 00007 #define DEPRECATED(func) func __attribute__ ((deprecated)) 00008 #else 00009 #define DEPRECATED(func) func 00010 #endif 00011 00021 extern int logML; 00022 00024 extern int uniq_ML; 00025 00027 extern int cut_point; 00028 00030 extern int eos_debug; 00031 00073 float fold_par( const char *sequence, 00074 char *structure, 00075 paramT *parameters, 00076 int is_constrained, 00077 int is_circular); 00078 00095 float fold( const char *sequence, 00096 char *structure); 00097 00114 float circfold( const char *sequence, 00115 char *structure); 00116 00117 00134 float energy_of_structure(const char *string, 00135 const char *structure, 00136 int verbosity_level); 00137 00151 float energy_of_struct_par( const char *string, 00152 const char *structure, 00153 paramT *parameters, 00154 int verbosity_level); 00155 00172 float energy_of_circ_structure( const char *string, 00173 const char *structure, 00174 int verbosity_level); 00175 00189 float energy_of_circ_struct_par(const char *string, 00190 const char *structure, 00191 paramT *parameters, 00192 int verbosity_level); 00193 00194 00195 00214 int energy_of_structure_pt( const char *string, 00215 short *ptable, 00216 short *s, 00217 short *s1, 00218 int verbosity_level); 00219 00235 int energy_of_struct_pt_par(const char *string, 00236 short *ptable, 00237 short *s, 00238 short *s1, 00239 paramT *parameters, 00240 int verbosity_level); 00241 00245 void free_arrays(void); 00246 00247 00253 void parenthesis_structure(char *structure, 00254 bondT *bp, 00255 int length); 00256 00263 void parenthesis_zuker( char *structure, 00264 bondT *bp, 00265 int length); 00266 00267 void letter_structure(char *structure, 00268 bondT *bp, 00269 int length); 00270 00271 00275 void update_fold_params(void); 00276 00277 void update_fold_params_par(paramT *parameters); 00278 00282 char *backtrack_fold_from_pair(char *sequence, 00283 int i, 00284 int j); 00285 00289 int loop_energy(short *ptable, 00290 short *s, 00291 short *s1, 00292 int i); 00293 00297 void export_fold_arrays(int **f5_p, 00298 int **c_p, 00299 int **fML_p, 00300 int **fM1_p, 00301 int **indx_p, 00302 char **ptype_p); 00303 00307 void export_fold_arrays_par(int **f5_p, 00308 int **c_p, 00309 int **fML_p, 00310 int **fM1_p, 00311 int **indx_p, 00312 char **ptype_p, 00313 paramT **P_p); 00314 00318 void export_circfold_arrays(int *Fc_p, 00319 int *FcH_p, 00320 int *FcI_p, 00321 int *FcM_p, 00322 int **fM2_p, 00323 int **f5_p, 00324 int **c_p, 00325 int **fML_p, 00326 int **fM1_p, 00327 int **indx_p, 00328 char **ptype_p); 00329 00333 void export_circfold_arrays_par(int *Fc_p, 00334 int *FcH_p, 00335 int *FcI_p, 00336 int *FcM_p, 00337 int **fM2_p, 00338 int **f5_p, 00339 int **c_p, 00340 int **fML_p, 00341 int **fM1_p, 00342 int **indx_p, 00343 char **ptype_p, 00344 paramT **P_p); 00345 00346 00364 void assign_plist_from_db(plist **pl, 00365 const char *struc, 00366 float pr); 00367 00368 /* finally moved the loop energy function declarations to this header... */ 00369 /* BUT: The functions only exist for backward compatibility reasons! */ 00370 /* You better include "loop_energies.h" and call the functions: */ 00371 /* E_Hairpin() and E_IntLoop() which are (almost) threadsafe as they get */ 00372 /* a pointer to the energy parameter datastructure as additional argument */ 00373 00378 DEPRECATED(int LoopEnergy(int n1, 00379 int n2, 00380 int type, 00381 int type_2, 00382 int si1, 00383 int sj1, 00384 int sp1, 00385 int sq1)); 00386 00391 DEPRECATED(int HairpinE(int size, 00392 int type, 00393 int si1, 00394 int sj1, 00395 const char *string)); 00396 00402 DEPRECATED(void initialize_fold(int length)); 00403 00418 DEPRECATED(float energy_of_struct(const char *string, 00419 const char *structure)); 00420 00437 DEPRECATED(int energy_of_struct_pt( const char *string, 00438 short *ptable, 00439 short *s, 00440 short *s1)); 00441 00456 DEPRECATED(float energy_of_circ_struct( const char *string, 00457 const char *structure)); 00458 00459 #endif