RNAlib-2.2.0RC0
2Dfold.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_FOLD_H__
8 #define __VIENNA_RNA_PACKAGE_TWO_D_FOLD_H__
9 
33 
34 #ifdef __GNUC__
35 #define DEPRECATED(func) func __attribute__ ((deprecated))
36 #else
37 #define DEPRECATED(func) func
38 #endif
39 
58 vrna_TwoDfold_get_vars( const char *seq,
59  const char *structure1,
60  const char *structure2,
61  int circ);
62 
72 void
74 
101  int distance1,
102  int distance2);
103 
122 char *
123 vrna_TwoDfold_backtrack_f5( unsigned int j,
124  int k,
125  int l,
126  TwoDfold_vars *vars);
127 
147 DEPRECATED(TwoDfold_vars *
148 get_TwoDfold_variables( const char *seq,
149  const char *structure1,
150  const char *structure2,
151  int circ));
152 
164 DEPRECATED(void
166 
193 DEPRECATED(TwoDfold_solution *
195  int distance1,
196  int distance2));
197 
218 DEPRECATED(char *TwoDfold_backtrack_f5(unsigned int j,
219  int k,
220  int l,
221  TwoDfold_vars *vars));
222 
226 DEPRECATED(TwoDfold_solution **TwoDfold(TwoDfold_vars *our_variables,
227  int distance1,
228  int distance2));
229 
230 
231 
235 #endif
void vrna_TwoDfold_destroy_vars(TwoDfold_vars *our_variables)
Destroy a TwoDfold_vars datastructure without memory loss.
TwoDfold_solution * TwoDfoldList(TwoDfold_vars *vars, int distance1, int distance2)
Compute MFE's and representative for distance partitioning.
char * TwoDfold_backtrack_f5(unsigned int j, int k, int l, TwoDfold_vars *vars)
Backtrack a minimum free energy structure from a 5' section of specified length.
void destroy_TwoDfold_variables(TwoDfold_vars *our_variables)
Destroy a TwoDfold_vars datastructure without memory loss.
char * vrna_TwoDfold_backtrack_f5(unsigned int j, int k, int l, TwoDfold_vars *vars)
Backtrack a minimum free energy structure from a 5' section of specified length.
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
TwoDfold_solution * vrna_TwoDfold(TwoDfold_vars *vars, int distance1, int distance2)
Compute MFE's and representative for distance partitioning.
Variables compound for 2Dfold MFE folding.
Definition: data_structures.h:729
TwoDfold_vars * vrna_TwoDfold_get_vars(const char *seq, const char *structure1, const char *structure2, int circ)
Get a structure of type TwoDfold_vars prefilled with current global settings.
int circ
backward compatibility variable.. this does not effect anything
TwoDfold_vars * get_TwoDfold_variables(const char *seq, const char *structure1, const char *structure2, int circ)
Get a structure of type TwoDfold_vars prefilled with current global settings.
Solution element returned from TwoDfoldList.
Definition: data_structures.h:717