RNAlib-2.2.0-RC2

The model details data structure and its corresponding modifiers. More...

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Data Structures

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

Macros

#define VRNA_MODEL_DEFAULT_TEMPERATURE   37.0
  Default temperature for structure prediction and free energy evaluation in °C More...
 
#define VRNA_MODEL_DEFAULT_PF_SCALE   -1
 Default scaling factor for partition function computations. More...
 
#define VRNA_MODEL_DEFAULT_BETA_SCALE   1.
 Default scaling factor for absolute thermodynamic temperature in Boltzmann factors. More...
 
#define VRNA_MODEL_DEFAULT_DANGLES   2
 Default dangling end model. More...
 
#define VRNA_MODEL_DEFAULT_SPECIAL_HP   1
 Default model behavior for lookup of special tri-, tetra-, and hexa-loops. More...
 
#define VRNA_MODEL_DEFAULT_NO_LP   0
 Default model behavior for so-called 'lonely pairs'. More...
 
#define VRNA_MODEL_DEFAULT_NO_GU   0
 Default model behavior for G-U base pairs. More...
 
#define VRNA_MODEL_DEFAULT_NO_GU_CLOSURE   0
 Default model behavior for G-U base pairs closing a loop. More...
 
#define VRNA_MODEL_DEFAULT_CIRC   0
 Default model behavior to treat a molecule as a circular RNA (DNA) More...
 
#define VRNA_MODEL_DEFAULT_GQUAD   0
 Default model behavior regarding the treatment of G-Quadruplexes. More...
 
#define VRNA_MODEL_DEFAULT_UNIQ_ML   0
 Default behavior of the model regarding unique multibranch loop decomposition. More...
 
#define VRNA_MODEL_DEFAULT_ENERGY_SET   0
 Default model behavior on which energy set to use. More...
 
#define VRNA_MODEL_DEFAULT_BACKTRACK   1
 Default model behavior with regards to backtracking of structures. More...
 
#define VRNA_MODEL_DEFAULT_BACKTRACK_TYPE   'F'
 Default model behavior on what type of backtracking to perform. More...
 
#define VRNA_MODEL_DEFAULT_COMPUTE_BPP   1
 Default model behavior with regards to computing base pair probabilities. More...
 
#define VRNA_MODEL_DEFAULT_MAX_BP_SPAN   -1
 Default model behavior for the allowed maximum base pair span. More...
 
#define VRNA_MODEL_DEFAULT_LOG_ML   0
 Default model behavior on how to evaluate the energy contribution of multibranch loops. More...
 
#define VRNA_MODEL_DEFAULT_ALI_OLD_EN   0
 Default model behavior for consensus structure energy evaluation. More...
 
#define VRNA_MODEL_DEFAULT_ALI_RIBO   0
 Default model behavior for consensus structure covariance contribution assessment. More...
 
#define VRNA_MODEL_DEFAULT_ALI_CV_FACT   1.
 Default model behavior for weighting the covariance score in consensus structure prediction. More...
 
#define VRNA_MODEL_DEFAULT_ALI_NC_FACT   1.
 Default model behavior for weighting the nucleotide conservation? in consensus structure prediction. More...
 
#define MAXALPHA   20
 Maximal length of alphabet.
 

Functions

void vrna_md_set_default (vrna_md_t *md)
 Set default model details. More...
 
void vrna_md_update (vrna_md_t *md)
 Update the model details data structure. More...
 
void vrna_md_set_globals (vrna_md_t *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
 

Detailed Description

The model details data structure and its corresponding modifiers.