RNAlib-2.3.1
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 multiloops.
 
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 multi-branch 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 [64]
 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 prediction.
 
int oldAliEn
 Use old alifold energy model.
 
int ribo
 Use ribosum scoring table in alifold energy model.
 
double cv_fact
 Co-variance scaling factor for consensus structure prediction.
 
double nc_fact
 Scaling factor to weight co-variance contributions of non-canonical pairs.
 
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
SWIG Wrapper Notes:

This data structure is wrapped as an object md with multiple related functions attached as methods.

A new set of default parameters can be obtained by calling the constructure of md:

  • md() – Initialize with default settings

The resulting object has a list of attached methods which directly correspond to functions that mainly operate on the corresponding C data structure:

Note, that default parameters can be modified by directly setting any of the following global variables. Internally, getting/setting default parameters using their global variable representative translates into calls of the following functions, therefore these wrappers for these functions do not exist in the scripting language interface(s):

global variable C getter C setter
temperature vrna_md_defaults_temperature_get() vrna_md_defaults_temperature()
dangles vrna_md_defaults_dangles_get() vrna_md_defaults_dangles()
betaScale vrna_md_defaults_betaScale_get() vrna_md_defaults_betaScale()
tetra_loop this is an alias of special_hp
special_hp vrna_md_defaults_special_hp_get() vrna_md_defaults_special_hp()
noLonelyPairs this is an alias of noLP
noLP vrna_md_defaults_noLP_get() vrna_md_defaults_noLP()
noGU vrna_md_defaults_noGU_get() vrna_md_defaults_noGU()
no_closingGU this is an alias of noGUclosure
noGUclosure vrna_md_defaults_noGUclosure_get() vrna_md_defaults_noGUclosure()
logML vrna_md_defaults_logML_get() vrna_md_defaults_logML()
circ vrna_md_defaults_circ_get() vrna_md_defaults_circ()
gquad vrna_md_defaults_gquad_get() vrna_md_defaults_gquad()
uniq_ML vrna_md_defaults_uniq_ML_get() vrna_md_defaults_uniq_ML()
energy_set vrna_md_defaults_energy_set_get() vrna_md_defaults_energy_set()
backtrack vrna_md_defaults_backtrack_get() vrna_md_defaults_backtrack()
backtrack_type vrna_md_defaults_backtrack_type_get() vrna_md_defaults_backtrack_type()
do_backtrack this is an alias of compute_bpp
compute_bpp vrna_md_defaults_compute_bpp_get() vrna_md_defaults_compute_bpp()
max_bp_span vrna_md_defaults_max_bp_span_get() vrna_md_defaults_max_bp_span()
min_loop_size vrna_md_defaults_min_loop_size_get() vrna_md_defaults_min_loop_size()
window_size vrna_md_defaults_window_size_get() vrna_md_defaults_window_size()
oldAliEn vrna_md_defaults_oldAliEn_get() vrna_md_defaults_oldAliEn()
ribo vrna_md_defaults_ribo_get() vrna_md_defaults_ribo()
cv_fact vrna_md_defaults_cv_fact_get() vrna_md_defaults_cv_fact()
nc_fact vrna_md_defaults_nc_fact_get() vrna_md_defaults_nc_fact()
sfact vrna_md_defaults_sfact_get() vrna_md_defaults_sfact()

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 multiloops. 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 documentation 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: