#include <ViennaRNA/model.h>
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]
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:
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()
betaScale
vrna_md_defaults_betaScale_get()
tetra_loop
this is an alias of special_hp
special_hp
vrna_md_defaults_special_hp_get()
noLonelyPairs
this is an alias of noLP
noLP
noGU
no_closingGU
this is an alias of noGUclosure
noGUclosure
vrna_md_defaults_noGUclosure_get()
vrna_md_defaults_noGUclosure()
logML
circ
gquad
uniq_ML
vrna_md_defaults_uniq_ML_get()
energy_set
vrna_md_defaults_energy_set_get()
backtrack
vrna_md_defaults_backtrack_get()
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()
ribo
cv_fact
vrna_md_defaults_cv_fact_get()
nc_fact
vrna_md_defaults_nc_fact_get()
sfact
See also:
vrna_md_set_default() , set_model_details() , vrna_md_update() , vrna_md_t
double temperature
double betaScale
int dangles
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
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
Note
The default value for this field is TURN , however, it may be 0 in cofolding context.
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]