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# H/fold.h

Go to the documentation of this file.

    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