RNAlib-2.1.9h
fold_vars.h
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1 #ifndef __VIENNA_RNA_PACKAGE_FOLD_VARS_H__
2 #define __VIENNA_RNA_PACKAGE_FOLD_VARS_H__
3 
4 #include "data_structures.h"
5 
12 #define PUBLIC
13 #define PRIVATE static
14 
18 extern int fold_constrained;
19 
27 extern int noLonelyPairs;
28 
50 extern int dangles;
51 
55 extern int noGU;
56 
60 extern int no_closingGU;
61 
67 extern int tetra_loop;
68 
76 extern int energy_set;
77 
81 extern int circ;
82 
86 extern int csv;
87 
91 extern int oldAliEn;
95 extern int ribo;
96 
101 extern char *RibosumFile;
102 
110 extern char *nonstandards;
111 
118 extern double temperature;
119 
124 extern int james_rule;
125 
129 extern int logML;
130 
142 extern int cut_point;
143 
150 extern bondT *base_pair;
151 
157 extern FLT_OR_DBL *pr;
158 
165 extern int *iindx;
166 
178 extern double pf_scale;
179 
186 extern int do_backtrack;
187 
195 extern char backtrack_type;
196 
200 extern int gquad;
201 
205 extern int canonicalBPonly;
206 
207 char * option_string(void);
208 
220 
221 #endif
int tetra_loop
Include special stabilizing energies for some tri-, tetra- and hexa-loops;.
int do_backtrack
do backtracking, i.e. compute secondary structures or base pair probabilities
double * pr
A pointer to the base pair probability matrix.
int csv
generate comma seperated output
int cut_point
Marks the position (starting from 1) of the first nucleotide of the second molecule within the concat...
int circ
backward compatibility variable.. this does not effect anything
char * nonstandards
contains allowed non standard base pairs
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
char backtrack_type
A backtrack array marker for inverse_fold()
int gquad
Allow G-quadruplex formation.
int oldAliEn
int noLonelyPairs
Global switch to avoid/allow helices of length 1.
bondT * base_pair
Contains a list of base pairs after a call to fold().
int fold_constrained
Global switch to activate/deactivate folding with structure constraints.
int ribo
int james_rule
char * RibosumFile
Base pair.
Definition: data_structures.h:84
int canonicalBPonly
double pf_scale
A scaling factor used by pf_fold() to avoid overflows.
The data structure that contains the complete model details used throughout the calculations.
Definition: data_structures.h:102
int no_closingGU
GU allowed only inside stacks if set to 1.
int noGU
Global switch to forbid/allow GU base pairs at all.
int dangles
Switch the energy model for dangling end contributions (0, 1, 2, 3)
int energy_set
0 = BP; 1=any mit GC; 2=any mit AU-parameter
void set_model_details(model_detailsT *md)
Set default model details.
int * iindx
index array to move through pr.
int logML
double temperature
Rescale energy parameters to a temperature in degC.