struct vrna_md_s

#include <ViennaRNA/model.h>

Overview

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

// fields

double temperature
double betaScale
int dangles
int special_hp
int noLP
int noGU
int noGUclosure
int logML
int circ
int gquad
int uniq_ML
int energy_set
int backtrack
char backtrack_type
int compute_bpp
char nonstandards[64]
int max_bp_span
int min_loop_size
int window_size
int oldAliEn
int ribo
double cv_fact
double nc_fact
double sfact
int rtype[8]
short alias[MAXALPHA+1]
int pair[MAXALPHA+1][MAXALPHA+1]

Detailed Documentation

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

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()

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)

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 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 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.

Note

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

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.