RNAlib-2.5.1
fold_vars.h File Reference

Here all all declarations of the global variables used throughout RNAlib. More...

+ Include dependency graph for fold_vars.h:
+ This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Variables

int fold_constrained
 Global switch to activate/deactivate folding with structure constraints.
 
int csv
 generate comma seperated output
 
char * RibosumFile
 
int james_rule
 
int logML
 
int cut_point
 Marks the position (starting from 1) of the first nucleotide of the second molecule within the concatenated sequence. More...
 
bondTbase_pair
 Contains a list of base pairs after a call to fold(). More...
 
FLT_OR_DBLpr
 A pointer to the base pair probability matrix. More...
 
int * iindx
 index array to move through pr. More...
 

Detailed Description

Here all all declarations of the global variables used throughout RNAlib.

Variable Documentation

◆ RibosumFile

char* RibosumFile
extern

warning this variable will vanish in the future ribosums will be compiled in instead

◆ james_rule

int james_rule
extern

interior loops of size 2 get energy 0.8Kcal and no mismatches, default 1

◆ logML

int logML
extern

use logarithmic multiloop energy function

◆ cut_point

int cut_point
extern

Marks the position (starting from 1) of the first nucleotide of the second molecule within the concatenated sequence.

To evaluate the energy of a duplex structure (a structure formed by two strands), concatenate the to sequences and set it to the first base of the second strand in the concatenated sequence. The default value of -1 stands for single molecule folding. The cut_point variable is also used by vrna_file_PS_rnaplot() and PS_dot_plot() to mark the chain break in postscript plots.

◆ base_pair

bondT* base_pair
extern

Contains a list of base pairs after a call to fold().

base_pair[0].i contains the total number of pairs.

Deprecated:
Do not use this variable anymore!

◆ pr

FLT_OR_DBL* pr
extern

A pointer to the base pair probability matrix.

Deprecated:
Do not use this variable anymore!

◆ iindx

int* iindx
extern

index array to move through pr.

The probability for base i and j to form a pair is in pr[iindx[i]-j].

Deprecated:
Do not use this variable anymore!