RNAlib-2.2.5
vrna_md_s Struct Reference

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 window_size
 Size of the sliding window for locally optimal structure predition.
 
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.
 
int rtype [8]
 Reverse base pair type array.
 
short alias [MAXALPHA+1]
 alias of an integer nucleotide representation
 
int pair [MAXALPHA+1][MAXALPHA+1]
 Integer representation of a base pair.
 

Detailed Description

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

For convenience reasons, we provide the type name vrna_md_t to address this data structure without the use of the struct keyword

See also
vrna_md_set_default(), set_model_details(), vrna_md_update(), vrna_md_t

Field Documentation

int vrna_md_s::dangles

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

If set to 0 no stabilizing energies are assigned to bases adjacent to helices in free ends and multiloops (so called dangling ends). Normally (dangles = 1) dangling end energies are assigned only to unpaired bases and a base cannot participate simultaneously in two dangling ends. In the partition function algorithm vrna_pf() these checks are neglected. To provide comparability between free energy minimization and partition function algorithms, the default setting is 2. This treatment of dangling ends gives more favorable energies to helices directly adjacent to one another, which can be beneficial since such helices often do engage in stabilizing interactions through co-axial stacking.
If set to 3 co-axial stacking is explicitly included for adjacent helices in mutli-loops. The option affects only mfe folding and energy evaluation (vrna_mfe() and vrna_eval_structure()), as well as suboptimal folding (vrna_subopt()) via re-evaluation of energies. Co-axial stacking with one intervening mismatch is not considered so far.

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