RNAlib-2.2.0RC0
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The model details data structure and its corresponding modifiers. More...
Go to the source code of this file.
Data Structures | |
struct | model_detailsT |
The data structure that contains the complete model details used throughout the calculations. More... | |
Macros | |
#define | MAXALPHA 20 |
Maximal length of alphabet. | |
Functions | |
void | vrna_md_set_default (model_detailsT *md) |
Set default model details. More... | |
void | vrna_md_update (model_detailsT *md) |
Update the model details. | |
void | set_model_details (model_detailsT *md) |
Set default model details. More... | |
Variables | |
double | temperature |
Rescale energy parameters to a temperature in degC. More... | |
double | pf_scale |
A scaling factor used by pf_fold() to avoid overflows. More... | |
int | dangles |
Switch the energy model for dangling end contributions (0, 1, 2, 3) More... | |
int | tetra_loop |
Include special stabilizing energies for some tri-, tetra- and hexa-loops;. More... | |
int | noLonelyPairs |
Global switch to avoid/allow helices of length 1. More... | |
int | noGU |
Global switch to forbid/allow GU base pairs at all. | |
int | no_closingGU |
GU allowed only inside stacks if set to 1. | |
int | circ |
backward compatibility variable.. this does not effect anything | |
int | gquad |
Allow G-quadruplex formation. | |
int | canonicalBPonly |
int | uniq_ML |
do ML decomposition uniquely (for subopt) | |
int | energy_set |
0 = BP; 1=any mit GC; 2=any mit AU-parameter More... | |
int | do_backtrack |
do backtracking, i.e. compute secondary structures or base pair probabilities More... | |
char | backtrack_type |
A backtrack array marker for inverse_fold() More... | |
char * | nonstandards |
contains allowed non standard base pairs More... | |
int | max_bp_span |
Maximum allowed base pair span. More... | |
int | oldAliEn |
use old alifold energies (with gaps) | |
int | ribo |
use ribosum matrices | |
int | logML |
if nonzero use logarithmic ML energy in energy_of_struct | |
The model details data structure and its corresponding modifiers.
void vrna_md_set_default | ( | model_detailsT * | md | ) |
Set default model details.
Use this function if you wish to initialize a model_detailsT data structure with its default values, i.e. the global model settings
md | A pointer to the data structure that shall be initialized |
void set_model_details | ( | model_detailsT * | md | ) |
Set default model details.
Use this function if you wish to initialize a model_detailsT data structure with its default values, i.e. the global model settings
md | A pointer to the data structure that shall be initialized |
double temperature |
Rescale energy parameters to a temperature in degC.
Default is 37C. You have to call the update_..._params() functions after changing this parameter.
double pf_scale |
A scaling factor used by pf_fold() to avoid overflows.
Should be set to approximately , where
is an estimate for the ensemble free energy, for example the minimum free energy. You must call update_pf_params() after changing this parameter.
If pf_scale is -1 (the default) , an estimate will be provided automatically when computing partition functions, e.g. pf_fold() The automatic estimate is usually insufficient for sequences more than a few hundred bases long.
int dangles |
Switch the energy model for dangling end contributions (0, 1, 2, 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 pf_fold() these checks are neglected. If dangles is set to 2, all folding routines will follow this convention. 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 dangles = 3 co-axial stacking is explicitly included for adjacent helices in mutli-loops. The option affects only mfe folding and energy evaluation (fold() and energy_of_structure()), as well as suboptimal folding (subopt()) via re-evaluation of energies. Co-axial stacking with one intervening mismatch is not considered so far.
Default is 2 in most algorithms, partition function algorithms can only handle 0 and 2
int tetra_loop |
Include special stabilizing energies for some tri-, tetra- and hexa-loops;.
default is 1.
int noLonelyPairs |
Global switch to avoid/allow helices of length 1.
Disallow all pairs which can only occur as lonely pairs (i.e. as helix of length 1). This avoids lonely base pairs in the predicted structures in most cases.
int canonicalBPonly |
Do not use this variable, it will eventually be removed in one of the next versions
int energy_set |
0 = BP; 1=any mit GC; 2=any mit AU-parameter
If set to 1 or 2: fold sequences from an artificial alphabet ABCD..., where A pairs B, C pairs D, etc. using either GC (1) or AU parameters (2); default is 0, you probably don't want to change it.
int do_backtrack |
do backtracking, i.e. compute secondary structures or base pair probabilities
If 0, do not calculate pair probabilities in pf_fold(); this is about twice as fast. Default is 1.
char backtrack_type |
A backtrack array marker for inverse_fold()
If set to 'C': force (1,N) to be paired, 'M' fold as if the sequence were inside a multi-loop. Otherwise ('F') the usual mfe structure is computed.
char* nonstandards |
contains allowed non standard base pairs
Lists additional base pairs that will be allowed to form in addition to GC, CG, AU, UA, GU and UG. Nonstandard base pairs are given a stacking energy of 0.
int max_bp_span |
Maximum allowed base pair span.
A value of -1 indicates no restriction for distant base pairs.