1 #ifndef VIENNA_RNA_PACKAGE_FOLD_VARS_H 2 #define VIENNA_RNA_PACKAGE_FOLD_VARS_H 3 4 #include <ViennaRNA/datastructures/basic.h> 5 /* For now, we include model.h by default to provide backwards compatibility 6 However, this will most likely change, since fold_vars.h is scheduled to 7 vanish from the sources at latest in ViennaRNA Package v3 8 */ 9 #include <ViennaRNA/model.h> 10 11 12 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 13 14 /** 15 * \file fold_vars.h 16 * \brief Here all all declarations of the global variables used throughout RNAlib 17 */ 18 19 /** 20 * \brief Global switch to activate/deactivate folding with structure constraints 21 */ 22 extern int fold_constrained; 23 24 /** 25 * \brief generate comma seperated output 26 */ 27 extern int csv; 28 29 /** 30 * warning this variable will vanish in the future 31 * ribosums will be compiled in instead 32 */ 33 extern char *RibosumFile; 34 35 /** 36 * interior loops of size 2 get energy 0.8Kcal and 37 * no mismatches, default 1 38 */ 39 extern int james_rule; 40 41 /** 42 * use logarithmic multiloop energy function 43 */ 44 extern int logML; 45 46 /** 47 * \brief Marks the position (starting from 1) of the first 48 * nucleotide of the second molecule within the concatenated sequence. 49 * 50 * To evaluate the energy of a duplex structure (a structure formed by two 51 * strands), concatenate the to sequences and set it to the 52 * first base of the second strand in the concatenated sequence. 53 * The default value of -1 stands for single molecule folding. The 54 * cut_point variable is also used by vrna_file_PS_rnaplot() and 55 * PS_dot_plot() to mark the chain break in postscript plots. 56 */ 57 extern int cut_point; 58 59 /** 60 * \brief Contains a list of base pairs after a call to fold(). 61 * 62 * base_pair[0].i contains the total number of pairs. 63 * \deprecated Do not use this variable anymore! 64 */ 65 extern bondT *base_pair; 66 67 /** 68 * \brief A pointer to the base pair probability matrix 69 * 70 * \deprecated Do not use this variable anymore! 71 */ 72 extern FLT_OR_DBL *pr; 73 74 /** 75 * \brief index array to move through pr. 76 * 77 * The probability for base i and j to form a pair is in pr[iindx[i]-j]. 78 * \deprecated Do not use this variable anymore! 79 */ 80 extern int *iindx; 81 82 83 #endif 84 85 86 #endif 87