RNAlib-2.2.0-RC3

The data structure that contains the complete model details used throughout the calculations. More...

Data Fields

double temperature
 The temperature used to scale the thermodynamic parameters.
 
double betaScale
 A scaling factor for the thermodynamic temperature of the Boltzmann factors.
 
int dangles
 Specifies the dangle model used in any energy evaluation (0,1,2 or 3) More...
 
int special_hp
 Include special hairpin contributions for tri, tetra and hexaloops.
 
int noLP
 Only consider canonical structures, i.e. no 'lonely' base pairs.
 
int noGU
 Do not allow GU pairs.
 
int noGUclosure
 Do not allow loops to be closed by GU pair.
 
int logML
 Use logarithmic scaling for multi loops.
 
int circ
 Assume RNA to be circular instead of linear.
 
int gquad
 Include G-quadruplexes in structure prediction.
 
int canonicalBPonly
 remove non-canonical bp's from constraint structures
 
int uniq_ML
 Flag to ensure unique multibranch loop decomposition during folding.
 
int energy_set
 Specifies the energy set that defines set of compatible base pairs.
 
int backtrack
 Specifies whether or not secondary structures should be backtraced.
 
char backtrack_type
 Specifies in which matrix to backtrack.
 
int compute_bpp
 Specifies whether or not backward recursions for base pair probability (bpp) computation will be performed.
 
char nonstandards [33]
 contains allowed non standard bases
 
int max_bp_span
 maximum allowed base pair span
 
int min_loop_size
 Minimum size of hairpin loops. More...
 
int oldAliEn
 Use old alifold energy model.
 
int ribo
 Use ribosum scoring table in alifold energy model.
 
double cv_fact
 Covariance scaling factor for consensus structure prediction.
 
double sfact
 Scaling factor for partition function scaling.
 

Detailed Description

The data structure that contains the complete model details used throughout the calculations.

See also
vrna_md_set_default(), vrna_md_set_globals(), vrna_md_update()

Field Documentation

int vrna_md_t::dangles

Specifies the dangle model used in any energy evaluation (0,1,2 or 3)

Note
Some function do not implement all dangle model but only a subset of (0,1,2,3). Read the documentaion of the particular recurrences or energy evaluation function for information about the provided dangle model.
int vrna_md_t::min_loop_size

Minimum size of hairpin loops.

Note
The default value for this field is TURN, however, it may be 0 in cofolding context.

The documentation for this struct was generated from the following file: