--- /dev/null
+#ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_UP_H__
+#define __VIENNA_RNA_PACKAGE_PART_FUNC_UP_H__
+
+#include "data_structures.h"
+
+#define RNA_UP_MODE_1 1U
+#define RNA_UP_MODE_2 2U
+#define RNA_UP_MODE_3 4U
+
+/**
+ * \addtogroup up_cofold
+ * \brief Partition Function Cofolding as a stepwise process
+ *
+ * @{
+ * \file part_func_up.h
+ * \brief Partition Function Cofolding as stepwise process
+ *
+ * In this approach to cofolding the interaction between two RNA molecules is
+ * seen as a stepwise process. In a first step, the target molecule has to
+ * adopt a structure in which a binding site is accessible. In a second step,
+ * the ligand molecule will hybridize with a region accessible to an
+ * interaction. Consequently the algorithm is designed as a two step process:
+ * The first step is the calculation of the probability
+ * that a region within the target is unpaired, or equivalently, the
+ * calculation of the free energy needed to expose a region. In the second step
+ * we compute the free energy of an interaction for every possible binding site.
+ */
+
+/**
+ * \brief Calculate the partition function over all unpaired regions
+ * of a maximal length.
+ *
+ * You have to call function pf_fold() providing the same sequence before calling
+ * pf_unstru(). If you want to calculate unpaired regions for a constrained structure, set
+ * variable 'structure' in function 'pf_fold()' to the constrain string.
+ * It returns a #pu_contrib struct containing four arrays of dimension
+ * [i = 1 to length(sequence)][j = 0 to u-1] containing all possible contributions
+ * to the probabilities of unpaired regions of maximum length u.
+ * Each array in #pu_contrib contains one of the contributions to the
+ * total probability of being unpaired: The probability of being unpaired
+ * within an exterior loop is in array #pu_contrib->E, the probability
+ * of being unpaired within a hairpin loop is in array #pu_contrib->H,
+ * the probability of being unpaired within an interior loop is in array
+ * #pu_contrib->I and probability of being unpaired within a multi-loop
+ * is in array #pu_contrib->M. The total probability of being unpaired
+ * is the sum of the four arrays of #pu_contrib.
+ *
+ * This function frees everything allocated automatically. To
+ * free the output structure call free_pu_contrib().
+ *
+ * \param sequence
+ * \param max_w
+ * \return
+ */
+pu_contrib *pf_unstru(char *sequence,
+ int max_w);
+
+/**
+ * \brief Calculates the probability of a local interaction between two sequences.
+ *
+ * The function considers the probability that the
+ * region of interaction is unpaired within 's1' and 's2'. The
+ * longer sequence has to be given as 's1'. The shorter sequence has to
+ * be given as 's2'. Function pf_unstru() has to be called
+ * for 's1' and 's2', where the probabilities of being unpaired
+ * have to be given in 'p_c' and 'p_c2', respectively. If you do
+ * not want to include the probabilities of being unpaired for 's2' set
+ * 'p_c2' to NULL. If variable 'cstruc' is not NULL,
+ * constrained folding is done: The available constrains for intermolecular
+ * interaction are: '.' (no constrain), 'x' (the base has no intermolecular
+ * interaction) and '|' (the corresponding base has to be paired
+ * intermolecularily).\n
+ * The parameter 'w' determines the maximal length of the interaction. The
+ * parameters 'incr5' and 'incr3' allows inclusion of
+ * unpaired residues left ('incr5') and right ('incr3') of the region
+ * of interaction in 's1'. If the 'incr' options are used, function
+ * pf_unstru() has to be called with
+ * w=w+incr5+incr3 for the longer sequence 's1'.
+ *
+ * It returns a structure of type #interact which
+ * contains the probability of the best local interaction including residue i
+ * in Pi and the minimum free energy in Gi, where i is the position in sequence
+ * 's1'. The member Gikjl of structure #interact is
+ * the best interaction between region [k,i] k<i in longer sequence
+ * 's1' and region [j,l] j<l in 's2'. Gikjl_wo is Gikjl without the
+ * probability of beeing unpaired.\n
+ * Use free_interact() to free the returned structure, all
+ * other stuff is freed inside pf_interact().
+ *
+ * \param s1
+ * \param s2
+ * \param p_c
+ * \param p_c2
+ * \param max_w
+ * \param cstruc
+ * \param incr3
+ * \param incr5
+ * \return
+ */
+interact *pf_interact(const char *s1,
+ const char *s2,
+ pu_contrib *p_c,
+ pu_contrib *p_c2,
+ int max_w,
+ char *cstruc,
+ int incr3,
+ int incr5);
+
+/**
+ * \brief Frees the output of function pf_interact().
+ */
+void free_interact(interact *pin);
+
+/**
+ * \brief
+ */
+int Up_plot(pu_contrib *p_c,
+ pu_contrib *p_c_sh,
+ interact *pint,
+ char *ofile,
+ int **unpaired_values,
+ char *select_contrib,
+ char *head,
+ unsigned int mode);
+
+/**
+ * \brief
+ */
+pu_contrib *get_pu_contrib_struct( unsigned int n,
+ unsigned int w);
+
+/**
+ * \brief Frees the output of function pf_unstru().
+ */
+void free_pu_contrib_struct(pu_contrib *pu);
+
+/**
+ * @}
+ */
+
+#endif
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