--- /dev/null
+#ifndef __VIENNA_RNA_PACKAGE_FOLD_VARS_H__
+#define __VIENNA_RNA_PACKAGE_FOLD_VARS_H__
+
+#include "data_structures.h"
+
+/**
+ * \file fold_vars.h
+ * \brief Here all all declarations of the global variables used throughout RNAlib
+ */
+
+
+#define PUBLIC
+#define PRIVATE static
+
+/**
+ * \brief Global switch to activate/deactivate folding with structure constraints
+ */
+extern int fold_constrained;
+
+/**
+ * \brief Global switch to avoid/allow helices of length 1
+ *
+ * Disallow all pairs which can only occur as lonely pairs (i.e. as helix
+ * of length 1). This avoids lonely base pairs in the predicted structures in
+ * most cases.
+ */
+extern int noLonelyPairs;
+
+/**
+ * \brief Switch the energy model for dangling end contributions (0, 1, 2, 3)
+ *
+ * If set to 0 no stabilizing energies are assigned to bases adjacent to
+ * helices in free ends and multiloops (so called dangling ends). Normally
+ * (dangles = 1) dangling end energies are assigned only to unpaired
+ * bases and a base cannot participate simultaneously in two dangling ends. In
+ * the partition function algorithm pf_fold() these checks are neglected.
+ * If #dangles is set to 2, all folding routines will follow this convention.
+ * This treatment of dangling ends gives more favorable energies to helices
+ * directly adjacent to one another, which can be beneficial since such
+ * helices often do engage in stabilizing interactions through co-axial
+ * stacking.\n
+ * If dangles = 3 co-axial stacking is explicitly included for
+ * adjacent helices in mutli-loops. The option affects only mfe folding
+ * and energy evaluation (fold() and energy_of_structure()), as
+ * well as suboptimal folding (subopt()) via re-evaluation of energies.
+ * Co-axial stacking with one intervening mismatch is not considered so far.
+ *
+ * Default is 2 in most algorithms, partition function algorithms can only handle 0 and 2
+ */
+extern int dangles;
+
+/**
+ * \brief Global switch to forbid/allow GU base pairs at all
+ */
+extern int noGU;
+
+/**
+ * \brief GU allowed only inside stacks if set to 1
+ */
+extern int no_closingGU;
+
+/**
+ * \brief Include special stabilizing energies for some tri-, tetra- and hexa-loops;
+ *
+ * default is 1.
+ */
+extern int tetra_loop;
+
+/**
+ * \brief 0 = BP; 1=any mit GC; 2=any mit AU-parameter
+ *
+ * If set to 1 or 2: fold sequences from an artificial alphabet ABCD..., where A
+ * pairs B, C pairs D, etc. using either GC (1) or AU parameters (2);
+ * default is 0, you probably don't want to change it.
+ */
+extern int energy_set;
+
+/**
+ * \brief backward compatibility variable.. this does not effect anything
+ */
+extern int circ;
+
+/**
+ * \brief generate comma seperated output
+ */
+extern int csv;
+
+/**
+ * use old alifold energies (with gaps)
+ */
+extern int oldAliEn;
+/**
+ * use ribosum matrices
+ */
+extern int ribo;
+
+/**
+ * warning this variable will vanish in the future
+ * ribosums will be compiled in instead
+ */
+extern char *RibosumFile;
+
+/**
+ * \brief contains allowed non standard base pairs
+ *
+ * Lists additional base pairs that will be allowed to form in addition to
+ * GC, CG, AU, UA, GU and UG. Nonstandard base pairs are given a stacking
+ * energy of 0.
+ */
+extern char *nonstandards;
+
+/**
+ * \brief Rescale energy parameters to a temperature in degC.
+ *
+ * Default is 37C. You have to call the update_..._params() functions after
+ * changing this parameter.
+ */
+extern double temperature;
+
+/**
+ * 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 PS_rna_plot() 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;
+
+/**
+ * \brief A scaling factor used by pf_fold() to avoid overflows.
+ *
+ * Should be set to approximately \f$exp{((-F/kT)/length)}\f$, where \f$F\f$ is an estimate
+ * for the ensemble free energy, for example the minimum free energy. You must
+ * call update_pf_params() after changing this parameter.\n
+ * If pf_scale is -1 (the default) , an estimate will be provided
+ * automatically when computing partition functions, e.g. pf_fold()
+ * The automatic estimate is usually insufficient for sequences more
+ * than a few hundred bases long.
+ */
+extern double pf_scale;
+
+/**
+ * \brief do backtracking, i.e. compute secondary structures or base pair probabilities
+ *
+ * If 0, do not calculate pair probabilities in pf_fold(); this is about
+ * twice as fast. Default is 1.
+ */
+extern int do_backtrack;
+
+/**
+ * \brief A backtrack array marker for inverse_fold()
+ *
+ * If set to 'C': force (1,N) to be paired,
+ * 'M' fold as if the sequence were inside a multi-loop. Otherwise ('F') the
+ * usual mfe structure is computed.
+ */
+extern char backtrack_type;
+
+/**
+ * \brief Allow G-quadruplex formation
+ */
+extern int gquad;
+
+
+char * option_string(void);
+
+/**
+ * \brief Set default model details
+ *
+ * Use this function if you wish to initialize a #model_detailsT data structure with
+ * its default values, i.e. the global model settings
+ *
+ * \see
+ *
+ * \param md A pointer to the data structure that shall be initialized
+ */
+void set_model_details(model_detailsT *md);
+
+#endif
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