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# /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h

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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
    00061 extern  int logML;
    00062
    00064 extern  int uniq_ML;
    00065
    00067 extern  int cut_point;
    00068
    00073 extern  int eos_debug;
    00074
    00075
    00119 float fold_par( const char *sequence,
    00120                 char *structure,
    00121                 paramT *parameters,
    00122                 int is_constrained,
    00123                 int is_circular);
    00124
    00143 float fold( const char *sequence,
    00144             char *structure);
    00145
    00164 float circfold( const char *sequence,
    00165                 char *structure);
    00166
    00167
    00195 float energy_of_structure(const char *string,
    00196                           const char *structure,
    00197                           int verbosity_level);
    00198
    00214 float energy_of_struct_par( const char *string,
    00215                             const char *structure,
    00216                             paramT *parameters,
    00217                             int verbosity_level);
    00218
    00237 float energy_of_circ_structure( const char *string,
    00238                                 const char *structure,
    00239                                 int verbosity_level);
    00240
    00256 float energy_of_circ_struct_par(const char *string,
    00257                                 const char *structure,
    00258                                 paramT *parameters,
    00259                                 int verbosity_level);
    00260
    00261
    00262 float energy_of_gquad_structure(const char *string,
    00263                                 const char *structure,
    00264                                 int verbosity_level);
    00265
    00286 int energy_of_structure_pt( const char *string,
    00287                             short *ptable,
    00288                             short *s,
    00289                             short *s1,
    00290                             int verbosity_level);
    00291
    00309 int energy_of_struct_pt_par(const char *string,
    00310                             short *ptable,
    00311                             short *s,
    00312                             short *s1,
    00313                             paramT *parameters,
    00314                             int verbosity_level);
    00315
    00322 void  free_arrays(void);
    00323
    00324
    00330 void  parenthesis_structure(char *structure,
    00331                             bondT *bp,
    00332                             int length);
    00333
    00340 void parenthesis_zuker( char *structure,
    00341                         bondT *bp,
    00342                         int length);
    00343
    00344 void letter_structure(char *structure,
    00345                       bondT *bp,
    00346                       int length);
    00347
    00348
    00354 void  update_fold_params(void);
    00355
    00361 void update_fold_params_par(paramT *parameters);
    00362
    00368 char  *backtrack_fold_from_pair(char *sequence,
    00369                                 int i,
    00370                                 int j);
    00371
    00385 float energy_of_move( const char *string,
    00386                       const char *structure,
    00387                       int m1,
    00388                       int m2);
    00389
    00390
    00406 int energy_of_move_pt(short *pt,
    00407                    short *s,
    00408                    short *s1,
    00409                    int m1,
    00410                    int m2);
    00411
    00421 int   loop_energy(short *ptable,
    00422                   short *s,
    00423                   short *s1,
    00424                   int i);
    00425
    00431 void export_fold_arrays(int **f5_p,
    00432                         int **c_p,
    00433                         int **fML_p,
    00434                         int **fM1_p,
    00435                         int **indx_p,
    00436                         char **ptype_p);
    00437
    00443 void export_fold_arrays_par(int **f5_p,
    00444                             int **c_p,
    00445                             int **fML_p,
    00446                             int **fM1_p,
    00447                             int **indx_p,
    00448                             char **ptype_p,
    00449                             paramT **P_p);
    00450
    00456 void export_circfold_arrays(int *Fc_p,
    00457                             int *FcH_p,
    00458                             int *FcI_p,
    00459                             int *FcM_p,
    00460                             int **fM2_p,
    00461                             int **f5_p,
    00462                             int **c_p,
    00463                             int **fML_p,
    00464                             int **fM1_p,
    00465                             int **indx_p,
    00466                             char **ptype_p);
    00467
    00473 void export_circfold_arrays_par(int *Fc_p,
    00474                                 int *FcH_p,
    00475                                 int *FcI_p,
    00476                                 int *FcM_p,
    00477                                 int **fM2_p,
    00478                                 int **f5_p,
    00479                                 int **c_p,
    00480                                 int **fML_p,
    00481                                 int **fM1_p,
    00482                                 int **indx_p,
    00483                                 char **ptype_p,
    00484                                 paramT **P_p);
    00485
    00486
    00504 void assign_plist_from_db(plist **pl,
    00505                           const char *struc,
    00506                           float pr);
    00507
    00508 /* finally moved the loop energy function declarations to this header...  */
    00509 /* BUT: The functions only exist for backward compatibility reasons!      */
    00510 /* You better include "loop_energies.h" and call the functions:           */
    00511 /* E_Hairpin() and E_IntLoop() which are (almost) threadsafe as they get  */
    00512 /* a pointer to the energy parameter datastructure as additional argument */
    00513
    00518 DEPRECATED(int LoopEnergy(int n1,
    00519                           int n2,
    00520                           int type,
    00521                           int type_2,
    00522                           int si1,
    00523                           int sj1,
    00524                           int sp1,
    00525                           int sq1));
    00526
    00531 DEPRECATED(int HairpinE(int size,
    00532                         int type,
    00533                         int si1,
    00534                         int sj1,
    00535                         const char *string));
    00536
    00542 DEPRECATED(void initialize_fold(int length));
    00543
    00558 DEPRECATED(float energy_of_struct(const char *string,
    00559                                   const char *structure));
    00560
    00577 DEPRECATED(int energy_of_struct_pt( const char *string,
    00578                                     short *ptable,
    00579                                     short *s,
    00580                                     short *s1));
    00581
    00596 DEPRECATED(float energy_of_circ_struct( const char *string,
    00597                                         const char *structure));
    00598
    00599 #endif