RNAlib-2.1.9
2Dpfold.h
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1 /*
2  minimum free energy
3  RNA secondary structure with
4  basepair distance d to reference structure prediction
5 
6 */
7 #ifndef __VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H__
8 #define __VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H__
9 
10 #include "data_structures.h"
11 
12 #ifdef __GNUC__
13 #define DEPRECATED(func) func __attribute__ ((deprecated))
14 #else
15 #define DEPRECATED(func) func
16 #endif
17 
42 TwoDpfold_vars *get_TwoDpfold_variables( const char *seq,
43  const char *structure1,
44  char *structure2,
45  int circ);
46 
59 TwoDpfold_vars *get_TwoDpfold_variables_from_MFE(TwoDfold_vars *mfe_vars);
60 
71 void destroy_TwoDpfold_variables(TwoDpfold_vars *vars);
72 
94 TwoDpfold_solution *TwoDpfoldList( TwoDpfold_vars *vars,
95  int maxDistance1,
96  int maxDistance2);
97  /* End of group kl_neighborhood_pf */
99 
123 char *TwoDpfold_pbacktrack(TwoDpfold_vars *vars,
124  int d1,
125  int d2);
126 
146 char *TwoDpfold_pbacktrack5( TwoDpfold_vars *vars,
147  int d1,
148  int d2,
149  unsigned int length);
150  /* End of group kl_neighborhood_stochbt */
152 
158 DEPRECATED(FLT_OR_DBL **TwoDpfold(TwoDpfold_vars *our_variables,
159  int maxDistance1,
160  int maxDistance2));
161 
167 DEPRECATED(FLT_OR_DBL **TwoDpfold_circ(
168  TwoDpfold_vars *our_variables,
169  int maxDistance1,
170  int maxDistance2));
171 
172 
173 #endif