RNAlib-2.6.3
 
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The model details data structure and its corresponding modifiers. More...

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Data Structures

struct  vrna_md_s
 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
 
#define VRNA_MODEL_DEFAULT_PF_SCALE   -1
 Default scaling factor for partition function computations.
 
#define VRNA_MODEL_DEFAULT_BETA_SCALE   1.
 Default scaling factor for absolute thermodynamic temperature in Boltzmann factors.
 
#define VRNA_MODEL_DEFAULT_DANGLES   2
 Default dangling end model.
 
#define VRNA_MODEL_DEFAULT_SPECIAL_HP   1
 Default model behavior for lookup of special tri-, tetra-, and hexa-loops.
 
#define VRNA_MODEL_DEFAULT_NO_LP   0
 Default model behavior for so-called 'lonely pairs'.
 
#define VRNA_MODEL_DEFAULT_NO_GU   0
 Default model behavior for G-U base pairs.
 
#define VRNA_MODEL_DEFAULT_NO_GU_CLOSURE   0
 Default model behavior for G-U base pairs closing a loop.
 
#define VRNA_MODEL_DEFAULT_CIRC   0
 Default model behavior to treat a molecule as a circular RNA (DNA)
 
#define VRNA_MODEL_DEFAULT_GQUAD   0
 Default model behavior regarding the treatment of G-Quadruplexes.
 
#define VRNA_MODEL_DEFAULT_UNIQ_ML   0
 Default behavior of the model regarding unique multi-branch loop decomposition.
 
#define VRNA_MODEL_DEFAULT_ENERGY_SET   0
 Default model behavior on which energy set to use.
 
#define VRNA_MODEL_DEFAULT_BACKTRACK   1
 Default model behavior with regards to backtracking of structures.
 
#define VRNA_MODEL_DEFAULT_BACKTRACK_TYPE   'F'
 Default model behavior on what type of backtracking to perform.
 
#define VRNA_MODEL_DEFAULT_COMPUTE_BPP   1
 Default model behavior with regards to computing base pair probabilities.
 
#define VRNA_MODEL_DEFAULT_MAX_BP_SPAN   -1
 Default model behavior for the allowed maximum base pair span.
 
#define VRNA_MODEL_DEFAULT_WINDOW_SIZE   -1
 Default model behavior for the sliding window approach.
 
#define VRNA_MODEL_DEFAULT_LOG_ML   0
 Default model behavior on how to evaluate the energy contribution of multi-branch loops.
 
#define VRNA_MODEL_DEFAULT_ALI_OLD_EN   0
 Default model behavior for consensus structure energy evaluation.
 
#define VRNA_MODEL_DEFAULT_ALI_RIBO   0
 Default model behavior for consensus structure co-variance contribution assessment.
 
#define VRNA_MODEL_DEFAULT_ALI_CV_FACT   1.
 Default model behavior for weighting the co-variance score in consensus structure prediction.
 
#define VRNA_MODEL_DEFAULT_ALI_NC_FACT   1.
 Default model behavior for weighting the nucleotide conservation? in consensus structure prediction.
 
#define VRNA_MODEL_DEFAULT_SALT   1.021
 Default model salt concentration (M)
 
#define VRNA_MODEL_DEFAULT_SALT_MLLOWER   6
 Default model lower bound of multiloop size for salt correction fiting.
 
#define VRNA_MODEL_DEFAULT_SALT_MLUPPER   24
 Default model upper bound of multiloop size for salt correction fiting.
 
#define VRNA_MODEL_DEFAULT_SALT_DPXINIT   99999
 Default model value to turn off user-provided salt correction for duplex initializtion.
 
#define VRNA_MODEL_DEFAULT_HELICAL_RISE   VRNA_MODEL_HELICAL_RISE_RNA
 Default helical rise.
 
#define VRNA_MODEL_DEFAULT_BACKBONE_LENGTH   VRNA_MODEL_BACKBONE_LENGTH_RNA
 Default backbone length.
 
#define MAXALPHA   20
 Maximal length of alphabet.
 

Typedefs

typedef struct vrna_md_s vrna_md_t
 Typename for the model details data structure vrna_md_s.
 

Functions

void vrna_md_set_default (vrna_md_t *md)
 Apply default model details to a provided vrna_md_t data structure.
 
void vrna_md_update (vrna_md_t *md)
 Update the model details data structure.
 
vrna_md_tvrna_md_copy (vrna_md_t *md_to, const vrna_md_t *md_from)
 Copy/Clone a vrna_md_t model.
 
char * vrna_md_option_string (vrna_md_t *md)
 Get a corresponding commandline parameter string of the options in a vrna_md_t.
 
void vrna_md_defaults_reset (vrna_md_t *md_p)
 Reset the global default model details to a specific set of parameters, or their initial values.
 
void vrna_md_defaults_temperature (double T)
 Set default temperature for energy evaluation of loops.
 
double vrna_md_defaults_temperature_get (void)
 Get default temperature for energy evaluation of loops.
 
void vrna_md_defaults_betaScale (double b)
 Set default scaling factor of thermodynamic temperature in Boltzmann factors.
 
double vrna_md_defaults_betaScale_get (void)
 Get default scaling factor of thermodynamic temperature in Boltzmann factors.
 
void vrna_md_defaults_dangles (int d)
 Set default dangle model for structure prediction.
 
int vrna_md_defaults_dangles_get (void)
 Get default dangle model for structure prediction.
 
void vrna_md_defaults_special_hp (int flag)
 Set default behavior for lookup of tabulated free energies for special hairpin loops, such as Tri-, Tetra-, or Hexa-loops.
 
int vrna_md_defaults_special_hp_get (void)
 Get default behavior for lookup of tabulated free energies for special hairpin loops, such as Tri-, Tetra-, or Hexa-loops.
 
void vrna_md_defaults_noLP (int flag)
 Set default behavior for prediction of canonical secondary structures.
 
int vrna_md_defaults_noLP_get (void)
 Get default behavior for prediction of canonical secondary structures.
 
void vrna_md_defaults_noGU (int flag)
 Set default behavior for treatment of G-U wobble pairs.
 
int vrna_md_defaults_noGU_get (void)
 Get default behavior for treatment of G-U wobble pairs.
 
void vrna_md_defaults_noGUclosure (int flag)
 Set default behavior for G-U pairs as closing pair for loops.
 
int vrna_md_defaults_noGUclosure_get (void)
 Get default behavior for G-U pairs as closing pair for loops.
 
void vrna_md_defaults_logML (int flag)
 Set default behavior recomputing free energies of multi-branch loops using a logarithmic model.
 
int vrna_md_defaults_logML_get (void)
 Get default behavior recomputing free energies of multi-branch loops using a logarithmic model.
 
void vrna_md_defaults_circ (int flag)
 Set default behavior whether input sequences are circularized.
 
int vrna_md_defaults_circ_get (void)
 Get default behavior whether input sequences are circularized.
 
void vrna_md_defaults_gquad (int flag)
 Set default behavior for treatment of G-Quadruplexes.
 
int vrna_md_defaults_gquad_get (void)
 Get default behavior for treatment of G-Quadruplexes.
 
void vrna_md_defaults_uniq_ML (int flag)
 Set default behavior for creating additional matrix for unique multi-branch loop prediction.
 
int vrna_md_defaults_uniq_ML_get (void)
 Get default behavior for creating additional matrix for unique multi-branch loop prediction.
 
void vrna_md_defaults_energy_set (int e)
 Set default energy set.
 
int vrna_md_defaults_energy_set_get (void)
 Get default energy set.
 
void vrna_md_defaults_backtrack (int flag)
 Set default behavior for whether to backtrack secondary structures.
 
int vrna_md_defaults_backtrack_get (void)
 Get default behavior for whether to backtrack secondary structures.
 
void vrna_md_defaults_backtrack_type (char t)
 Set default backtrack type, i.e. which DP matrix is used.
 
char vrna_md_defaults_backtrack_type_get (void)
 Get default backtrack type, i.e. which DP matrix is used.
 
void vrna_md_defaults_compute_bpp (int flag)
 Set the default behavior for whether to compute base pair probabilities after partition function computation.
 
int vrna_md_defaults_compute_bpp_get (void)
 Get the default behavior for whether to compute base pair probabilities after partition function computation.
 
void vrna_md_defaults_max_bp_span (int span)
 Set default maximal base pair span.
 
int vrna_md_defaults_max_bp_span_get (void)
 Get default maximal base pair span.
 
void vrna_md_defaults_min_loop_size (int size)
 Set default minimal loop size.
 
int vrna_md_defaults_min_loop_size_get (void)
 Get default minimal loop size.
 
void vrna_md_defaults_window_size (int size)
 Set default window size for sliding window structure prediction approaches.
 
int vrna_md_defaults_window_size_get (void)
 Get default window size for sliding window structure prediction approaches.
 
void vrna_md_defaults_oldAliEn (int flag)
 Set default behavior for whether to use old energy model for comparative structure prediction.
 
int vrna_md_defaults_oldAliEn_get (void)
 Get default behavior for whether to use old energy model for comparative structure prediction.
 
void vrna_md_defaults_ribo (int flag)
 Set default behavior for whether to use Ribosum Scoring in comparative structure prediction.
 
int vrna_md_defaults_ribo_get (void)
 Get default behavior for whether to use Ribosum Scoring in comparative structure prediction.
 
void vrna_md_defaults_cv_fact (double factor)
 Set the default co-variance scaling factor used in comparative structure prediction.
 
double vrna_md_defaults_cv_fact_get (void)
 Get the default co-variance scaling factor used in comparative structure prediction.
 
void vrna_md_defaults_nc_fact (double factor)
 
double vrna_md_defaults_nc_fact_get (void)
 
void vrna_md_defaults_sfact (double factor)
 Set the default scaling factor used to avoid under-/overflows in partition function computation.
 
double vrna_md_defaults_sfact_get (void)
 Get the default scaling factor used to avoid under-/overflows in partition function computation.
 
void vrna_md_defaults_salt (double salt)
 Set the default salt concentration.
 
double vrna_md_defaults_salt_get (void)
 Get the default salt concentration.
 
void vrna_md_defaults_saltMLLower (int lower)
 Set the default multiloop size lower bound for loop salt correciton linear fitting.
 
int vrna_md_defaults_saltMLLower_get (void)
 Get the default multiloop size lower bound for loop salt correciton linear fitting.
 
void vrna_md_defaults_saltMLUpper (int upper)
 Set the default multiloop size upper bound for loop salt correciton linear fitting.
 
int vrna_md_defaults_saltMLUpper_get (void)
 Get the default multiloop size upper bound for loop salt correciton linear fitting.
 
void vrna_md_defaults_saltDPXInit (int value)
 Set user-provided salt correciton for duplex initialization If value is 99999 the default value from fitting is used.
 
int vrna_md_defaults_saltDPXInit_get (void)
 Get user-provided salt correciton for duplex initialization If value is 99999 the default value from fitting is used.
 
void set_model_details (vrna_md_t *md)
 Set default model details.
 

Variables

double temperature
 Rescale energy parameters to a temperature in degC.
 
double pf_scale
 A scaling factor used by pf_fold() to avoid overflows.
 
int dangles
 Switch the energy model for dangling end contributions (0, 1, 2, 3)
 
int tetra_loop
 Include special stabilizing energies for some tri-, tetra- and hexa-loops;.
 
int noLonelyPairs
 Global switch to avoid/allow helices of length 1.
 
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 uniq_ML
 do ML decomposition uniquely (for subopt)
 
int energy_set
 0 = BP; 1=any with GC; 2=any with AU-parameter
 
int do_backtrack
 do backtracking, i.e. compute secondary structures or base pair probabilities
 
char backtrack_type
 A backtrack array marker for inverse_fold()
 
char * nonstandards
 contains allowed non standard base pairs
 
int max_bp_span
 Maximum allowed base pair span.
 
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

 
double salt
 salt concentration
 
int saltDPXInit
 Salt correction for duplex initialization.
 

Detailed Description

The model details data structure and its corresponding modifiers.