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# H/fold_vars.h

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    00001 #ifndef __VIENNA_RNA_PACKAGE_FOLD_VARS_H__
    00002 #define __VIENNA_RNA_PACKAGE_FOLD_VARS_H__
    00003
    00004 #include "data_structures.h"
    00005
    00012 #define PUBLIC
    00013 #define PRIVATE static
    00014
    00015 //Adding new global variables; Sep 2012 by Yi-Hsuan Lin
    00016 /* parameters for nucleocapsid binding */
    00017 extern int footprint; /* binding site size (nucleotides) */
    00018 extern double C_NC[10];//concentrations of RNA-binding proteins
    00019 //extern double ** InvKd;  //position dependent InvKd_0 for proteins
    00020 extern int RBPtype;
    00021 extern double InvKd[10][10000];
    00022 //added new global variables ended//
    00023
    00024
    00025
    00026
    00030 extern int    fold_constrained;
    00031
    00039 extern int    noLonelyPairs;
    00040
    00062 extern int  dangles;
    00063
    00067 extern int  noGU;
    00068
    00072 extern int  no_closingGU;
    00073
    00079 extern int  tetra_loop;
    00080
    00088 extern int  energy_set;
    00089
    00093 extern int  circ;
    00094
    00098 extern int  csv;
    00099
    00103 extern int oldAliEn;
    00107 extern int ribo;
    00108
    00113 extern char *RibosumFile;
    00114
    00122 extern char *nonstandards;
    00123
    00130 extern double temperature;
    00131
    00136 extern int  james_rule;
    00137
    00141 extern int  logML;
    00142
    00154 extern int  cut_point;
    00155
    00162 extern bondT  *base_pair;
    00163
    00169 extern FLT_OR_DBL *pr;
    00170
    00177 extern int   *iindx;
    00178
    00190 extern double pf_scale;
    00191
    00198 extern int    do_backtrack;
    00199
    00207 extern char backtrack_type;
    00208
    00209 char * option_string(void);
    00210
    00221 void set_model_details(model_detailsT *md);
    00222
    00223 #endif