2Dpfold.h
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/*
minimum free energy
RNA secondary structure with
basepair distance d to reference structure prediction
*/
#ifndef __VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H__
#define __VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H__
#include "data_structures.h"
#ifdef __GNUC__
#define DEPRECATED(func) func __attribute__ ((deprecated))
#else
#define DEPRECATED(func) func
#endif
TwoDpfold_vars *get_TwoDpfold_variables( const char *seq,
const char *structure1,
char *structure2,
int circ);
TwoDpfold_vars *get_TwoDpfold_variables_from_MFE(TwoDfold_vars *mfe_vars);
void destroy_TwoDpfold_variables(TwoDpfold_vars *vars);
TwoDpfold_solution *TwoDpfoldList( TwoDpfold_vars *vars,
int maxDistance1,
int maxDistance2);
/* End of group kl_neighborhood_pf */
char *TwoDpfold_pbacktrack(TwoDpfold_vars *vars,
int d1,
int d2);
char *TwoDpfold_pbacktrack5( TwoDpfold_vars *vars,
int d1,
int d2,
unsigned int length);
/* End of group kl_neighborhood_stochbt */
DEPRECATED(FLT_OR_DBL **TwoDpfold(TwoDpfold_vars *our_variables,
int maxDistance1,
int maxDistance2));
DEPRECATED(FLT_OR_DBL **TwoDpfold_circ(
TwoDpfold_vars *our_variables,
int maxDistance1,
int maxDistance2));
#endif