#ifndef VIENNA_RNA_PACKAGE_FOLD_VARS_H
#define VIENNA_RNA_PACKAGE_FOLD_VARS_H
#include <ViennaRNA/data_structures.h>
/* For now, we include model.h by default to provide backwards compatibility
However, this will most likely change, since fold_vars.h is scheduled to
vanish from the sources at latest in ViennaRNA Package v3
*/
#include <ViennaRNA/model.h>
/**
* \file fold_vars.h
* \brief Here all all declarations of the global variables used throughout RNAlib
*/
#ifdef DEPRECATION_WARNINGS
# ifdef __GNUC__
# define DEPRECATED(func) func __attribute__ ((deprecated))
# else
# define DEPRECATED(func) func
# endif
#else
# define DEPRECATED(func) func
#endif
/**
* \brief Global switch to activate/deactivate folding with structure constraints
*/
extern int fold_constrained;
/**
* \brief generate comma seperated output
*/
extern int csv;
/**
* warning this variable will vanish in the future
* ribosums will be compiled in instead
*/
extern char *RibosumFile;
/**
* interior loops of size 2 get energy 0.8Kcal and
* no mismatches, default 1
*/
extern int james_rule;
/**
* use logarithmic multiloop energy function
*/
extern int logML;
/**
* \brief Marks the position (starting from 1) of the first
* nucleotide of the second molecule within the concatenated sequence.
*
* To evaluate the energy of a duplex structure (a structure formed by two
* strands), concatenate the to sequences and set it to the
* first base of the second strand in the concatenated sequence.
* The default value of -1 stands for single molecule folding. The
* cut_point variable is also used by vrna_file_PS_rnaplot() and
* PS_dot_plot() to mark the chain break in postscript plots.
*/
extern int cut_point;
/**
* \brief Contains a list of base pairs after a call to fold().
*
* base_pair[0].i contains the total number of pairs.
* \deprecated Do not use this variable anymore!
*/
extern bondT *base_pair;
/**
* \brief A pointer to the base pair probability matrix
*
* \deprecated Do not use this variable anymore!
*/
extern FLT_OR_DBL *pr;
/**
* \brief index array to move through pr.
*
* The probability for base i and j to form a pair is in pr[iindx[i]-j].
* \deprecated Do not use this variable anymore!
*/
extern int *iindx;
#endif