1 #ifndef __VIENNA_RNA_PACKAGE_FOLD_VARS_H__
2 #define __VIENNA_RNA_PACKAGE_FOLD_VARS_H__
13 #define PRIVATE static
157 extern FLT_OR_DBL *
pr;
207 char * option_string(
void);
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 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.
Base pair.
Definition: data_structures.h:88
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:106
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.
double temperature
Rescale energy parameters to a temperature in degC.