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