RNAlib-2.1.1: /mount/gensoft2/src/ViennaRNA/ViennaRNA-2.1.1/H/2Dpfold.h Source File

00001 /*
00002       minimum free energy
00003       RNA secondary structure with
00004       basepair distance d to reference structure prediction
00005 
00006 */
00007 #ifndef __VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H__
00008 #define __VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H__
00009 
00010 #include "data_structures.h"
00011 
00012 #ifdef __GNUC__
00013 #define DEPRECATED(func) func __attribute__ ((deprecated))
00014 #else
00015 #define DEPRECATED(func) func
00016 #endif
00017 
00042 TwoDpfold_vars  *get_TwoDpfold_variables( const char *seq,
00043                                           const char *structure1,
00044                                           char *structure2,
00045                                           int circ);
00046 
00059 TwoDpfold_vars  *get_TwoDpfold_variables_from_MFE(TwoDfold_vars *mfe_vars);
00060 
00071 void            destroy_TwoDpfold_variables(TwoDpfold_vars *vars);
00072 
00094 TwoDpfold_solution  *TwoDpfoldList( TwoDpfold_vars *vars,
00095                                     int maxDistance1,
00096                                     int maxDistance2);
00097  /* End of group kl_neighborhood_pf */
00099 
00123 char            *TwoDpfold_pbacktrack(TwoDpfold_vars *vars,
00124                                       int d1,
00125                                       int d2);
00126 
00146 char            *TwoDpfold_pbacktrack5( TwoDpfold_vars *vars,
00147                                           int d1,
00148                                           int d2,
00149                                           unsigned int length);
00150  /* End of group kl_neighborhood_stochbt */
00152 
00158 DEPRECATED(FLT_OR_DBL          **TwoDpfold(TwoDpfold_vars *our_variables,
00159                                 int maxDistance1,
00160                                 int maxDistance2));
00161 
00167 DEPRECATED(FLT_OR_DBL          **TwoDpfold_circ(
00168                                 TwoDpfold_vars *our_variables,
00169                                 int maxDistance1,
00170                                 int maxDistance2));
00171 
00172 
00173 #endif