RNAlib-2.2.0RC0
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 
11 
12 #ifdef __GNUC__
13 #define DEPRECATED(func) func __attribute__ ((deprecated))
14 #else
15 #define DEPRECATED(func) func
16 #endif
17 
43 vrna_TwoDpfold_get_vars(const char *seq,
44  const char *structure1,
45  char *structure2,
46  int circ);
47 
65 DEPRECATED(TwoDpfold_vars *
66 get_TwoDpfold_variables(const char *seq,
67  const char *structure1,
68  char *structure2,
69  int circ));
70 
85 
100 DEPRECATED(TwoDpfold_vars *
102 
103 
114 void
116 
129 DEPRECATED(void
131 
155  int maxDistance1,
156  int maxDistance2);
157 
181 DEPRECATED(TwoDpfold_solution *
183  int maxDistance1,
184  int maxDistance2));
185  /* End of group kl_neighborhood_pf */
187 
211 char *
213  int d1,
214  int d2);
215 
235 DEPRECATED(char *
237  int d1,
238  int d2));
239 
259 char *
261  int d1,
262  int d2,
263  unsigned int length);
264 
286 DEPRECATED(char *
288  int d1,
289  int d2,
290  unsigned int length));
291  /* End of group kl_neighborhood_stochbt */
293 
299 DEPRECATED(FLT_OR_DBL **TwoDpfold(TwoDpfold_vars *our_variables,
300  int maxDistance1,
301  int maxDistance2));
302 
308 DEPRECATED(FLT_OR_DBL **TwoDpfold_circ(
309  TwoDpfold_vars *our_variables,
310  int maxDistance1,
311  int maxDistance2));
312 
313 #endif
TwoDpfold_vars * get_TwoDpfold_variables(const char *seq, const char *structure1, char *structure2, int circ)
Get a datastructure containing all necessary attributes and global folding switches.
char * vrna_TwoDpfold_pbacktrack(TwoDpfold_vars *vars, int d1, int d2)
Sample secondary structure representatives from a set of distance classes according to their Boltzman...
TwoDpfold_vars * get_TwoDpfold_variables_from_MFE(TwoDfold_vars *mfe_vars)
Get the datastructure containing all necessary attributes and global folding switches from a pre-fill...
char * vrna_TwoDpfold_pbacktrack5(TwoDpfold_vars *vars, int d1, int d2, unsigned int length)
Sample secondary structure representatives with a specified length from a set of distance classes acc...
Solution element returned from TwoDpfoldList.
Definition: data_structures.h:851
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
Variables compound for 2Dfold MFE folding.
Definition: data_structures.h:729
void destroy_TwoDpfold_variables(TwoDpfold_vars *vars)
Free all memory occupied by a TwoDpfold_vars datastructure.
TwoDpfold_solution * TwoDpfoldList(TwoDpfold_vars *vars, int maxDistance1, int maxDistance2)
Compute the partition function for all distance classes.
TwoDpfold_solution * vrna_TwoDpfold(TwoDpfold_vars *vars, int maxDistance1, int maxDistance2)
Compute the partition function for all distance classes.
TwoDpfold_vars * vrna_TwoDpfold_get_vars_from_MFE(TwoDfold_vars *mfe_vars)
Get the datastructure containing all necessary attributes and global folding switches from a pre-fill...
int circ
backward compatibility variable.. this does not effect anything
char * TwoDpfold_pbacktrack5(TwoDpfold_vars *vars, int d1, int d2, unsigned int length)
Sample secondary structure representatives with a specified length from a set of distance classes acc...
char * TwoDpfold_pbacktrack(TwoDpfold_vars *vars, int d1, int d2)
Sample secondary structure representatives from a set of distance classes according to their Boltzman...
TwoDpfold_vars * vrna_TwoDpfold_get_vars(const char *seq, const char *structure1, char *structure2, int circ)
Get a datastructure containing all necessary attributes and global folding switches.
void vrna_TwoDpfold_destroy_vars(TwoDpfold_vars *vars)
Free all memory occupied by a TwoDpfold_vars datastructure.
Variables compound for 2Dfold partition function folding.
Definition: data_structures.h:863