RNAlib-2.1.9h
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
43 const char *structure1,
44 char *structure2,
45 int circ);
46
60
72
95 int maxDistance1,
96 int maxDistance2);
97 /* End of group kl_neighborhood_pf */
99
124 int d1,
125 int d2);
126
147 int d1,
148 int d2,
149 unsigned int length);
150 /* End of group kl_neighborhood_stochbt */
152
158DEPRECATED(FLT_OR_DBL **TwoDpfold(TwoDpfold_vars *our_variables,
159 int maxDistance1,
160 int maxDistance2));
161
167DEPRECATED(FLT_OR_DBL **TwoDpfold_circ(
168 TwoDpfold_vars *our_variables,
169 int maxDistance1,
170 int maxDistance2));
171
172
173#endif
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
int circ
backward compatibility variable.. this does not effect anything
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.
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...
TwoDpfold_solution * TwoDpfoldList(TwoDpfold_vars *vars, int maxDistance1, int maxDistance2)
Compute the partition function for all distance classes.
void destroy_TwoDpfold_variables(TwoDpfold_vars *vars)
Free all memory occupied by a TwoDpfold_vars datastructure.
char * TwoDpfold_pbacktrack(TwoDpfold_vars *vars, int d1, int d2)
Sample secondary structure representatives from a set of distance classes according to their Boltzman...
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...
Variables compound for 2Dfold MFE folding.
Definition data_structures.h:605
Solution element returned from TwoDpfoldList.
Definition data_structures.h:727
Variables compound for 2Dfold partition function folding.
Definition data_structures.h:739