H/2Dfold.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_FOLD_H__
#define __VIENNA_RNA_PACKAGE_TWO_D_FOLD_H__

#include "data_structures.h"

#ifdef __GNUC__
#define DEPRECATED(func) func __attribute__ ((deprecated))
#else
#define DEPRECATED(func) func
#endif

TwoDfold_vars *get_TwoDfold_variables(const char *seq,
                                      const char *structure1,
                                      const char *structure2,
                                      int circ);

void          destroy_TwoDfold_variables(TwoDfold_vars *our_variables);

DEPRECATED(TwoDfold_solution **TwoDfold(TwoDfold_vars *our_variables,
                                        int distance1,
                                        int distance2));

TwoDfold_solution *TwoDfoldList(TwoDfold_vars *vars,
                                int distance1,
                                int distance2);

char *TwoDfold_backtrack_f5(unsigned int j,
                            int k,
                            int l,
                            TwoDfold_vars *vars);

#endif

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