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# H/part_func.h

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    00001 #ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_H__
    00002 #define __VIENNA_RNA_PACKAGE_PART_FUNC_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
    00012
    00029 // Initializing the RNA-protein binding matirx InvKd,  April 2013 added by Yi-Hsuan Lin
    00030 //void init_InvKd(char *sequence,  int RBPnum);
    00031 //void free_InvKd();
    00032 //double takeInvKd(int, int , int);
    00033
    00037 extern  int st_back;
    00038
    00039 /*
    00040 #################################################
    00041 # PARTITION FUNCTION COMPUTATION                #
    00042 #################################################
    00043 */
    00044
    00076 float   pf_fold_par(  const char *sequence,
    00077                       char *structure,
    00078                       pf_paramT *parameters,
    00079                       int calculate_bppm,
    00080                       int is_constrained,
    00081                       int is_circular);
    00082
    00110 float   pf_fold(const char *sequence,
    00111                 char *structure);
    00112
    00122 float   pf_circ_fold( const char *sequence,
    00123                       char *structure);
    00124
    00137 char    *pbacktrack(char *sequence);
    00138
    00151 char    *pbacktrack_circ(char *sequence);
    00152
    00165 void  free_pf_arrays(void);
    00166
    00173 void  update_pf_params(int length);
    00174
    00175 void update_pf_params_par(int length, pf_paramT *parameters);
    00176
    00189 FLT_OR_DBL  *export_bppm(void);
    00190
    00191 /*
    00192 #################################################
    00193 # OTHER PARTITION FUNCTION RELATED DECLARATIONS #
    00194 #################################################
    00195 */
    00196
    00214 void  assign_plist_from_pr( plist **pl,
    00215                             FLT_OR_DBL *probs,
    00216                             int length,
    00217                             double cutoff);
    00218
    00235 int get_pf_arrays(short **S_p,
    00236                   short **S1_p,
    00237                   char **ptype_p,
    00238                   FLT_OR_DBL **qb_p,
    00239                   FLT_OR_DBL **qm_p,
    00240                   FLT_OR_DBL **q1k_p,
    00241                   FLT_OR_DBL **qln_p);
    00242
    00246 double get_subseq_F(int i, int j);
    00247
    00263 char  *get_centroid_struct_pl(int length,
    00264                               double *dist,
    00265                               plist *pl);
    00266
    00282 char  *get_centroid_struct_pr(int length,
    00283                               double *dist,
    00284                               FLT_OR_DBL *pr);
    00285
    00296 double  mean_bp_distance(int length);
    00297
    00313 double  mean_bp_distance_pr(int length,
    00314                             FLT_OR_DBL *pr);
    00315
    00319 void  bppm_to_structure(char *structure,
    00320                         FLT_OR_DBL *pr,
    00321                         unsigned int length);
    00322
    00323 plist *stackProb(double cutoff);
    00324
    00328 char    bppm_symbol(const float *x);
    00329
    00330
    00331 /*
    00332 #################################################
    00333 # DEPRECATED FUNCTIONS                          #
    00334 #################################################
    00335 */
    00336
    00342 DEPRECATED(void init_pf_fold(int length));
    00343
    00348 DEPRECATED(char *centroid(int length,
    00349                           double *dist));     /* mean pair distance of ensemble */
    00350
    00356 DEPRECATED(double mean_bp_dist(int length));
    00357
    00361 DEPRECATED(double expLoopEnergy(int u1,
    00362                                 int u2,
    00363                                 int type,
    00364                                 int type2,
    00365                                 short si1,
    00366                                 short sj1,
    00367                                 short sp1,
    00368                                 short sq1));
    00369
    00373 DEPRECATED(double expHairpinEnergy( int u,
    00374                                     int type,
    00375                                     short si1,
    00376                                     short sj1,
    00377                                     const char *string));
    00378
    00379 #endif