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2Dpfold.h
Go to the documentation of this file.
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