RNAlib-2.2.7
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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 | 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 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_WINDOW_SIZE -1 |
Default model behavior for the sliding window approach. 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. | |
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. More... | |
void | vrna_md_update (vrna_md_t *md) |
Update the model details data structure. More... | |
char * | vrna_md_option_string (vrna_md_t *md) |
Get a corresponding commandline parameter string of the options in a vrna_md_t. More... | |
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. More... | |
void | vrna_md_defaults_temperature (double T) |
Set default temperature for energy evaluation of loops. More... | |
double | vrna_md_defaults_temperature_get (void) |
Get default temperature for energy evaluation of loops. More... | |
void | vrna_md_defaults_betaScale (double b) |
Set default scaling factor of thermodynamic temperature in Boltzmann factors. More... | |
double | vrna_md_defaults_betaScale_get (void) |
Get default scaling factor of thermodynamic temperature in Boltzmann factors. More... | |
void | vrna_md_defaults_dangles (int d) |
Set default dangle model for structure prediction. More... | |
int | vrna_md_defaults_dangles_get (void) |
Get default dangle model for structure prediction. More... | |
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. More... | |
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. More... | |
void | vrna_md_defaults_noLP (int flag) |
Set default behavior for prediction of canonical secondary structures. More... | |
int | vrna_md_defaults_noLP_get (void) |
Get default behavior for prediction of canonical secondary structures. More... | |
void | vrna_md_defaults_noGU (int flag) |
Set default behavior for treatment of G-U wobble pairs. More... | |
int | vrna_md_defaults_noGU_get (void) |
Get default behavior for treatment of G-U wobble pairs. More... | |
void | vrna_md_defaults_noGUclosure (int flag) |
Set default behavior for G-U pairs as closing pair for loops. More... | |
int | vrna_md_defaults_noGUclosure_get (void) |
Get default behavior for G-U pairs as closing pair for loops. More... | |
void | vrna_md_defaults_logML (int flag) |
Set default behavior recomputing free energies of multibranch loops using a logarithmic model. More... | |
int | vrna_md_defaults_logML_get (void) |
Get default behavior recomputing free energies of multibranch loops using a logarithmic model. More... | |
void | vrna_md_defaults_circ (int flag) |
Set default behavior whether input sequences are circularized. More... | |
int | vrna_md_defaults_circ_get (void) |
Get default behavior whether input sequences are circularized. More... | |
void | vrna_md_defaults_gquad (int flag) |
Set default behavior for treatment of G-Quadruplexes. More... | |
int | vrna_md_defaults_gquad_get (void) |
Get default behavior for treatment of G-Quadruplexes. More... | |
void | vrna_md_defaults_uniq_ML (int flag) |
Set default behavior for creating additional matrix for unique multibranch loop prediction. More... | |
int | vrna_md_defaults_uniq_ML_get (void) |
Get default behavior for creating additional matrix for unique multibranch loop prediction. More... | |
void | vrna_md_defaults_energy_set (int e) |
Set default energy set. More... | |
int | vrna_md_defaults_energy_set_get (void) |
Get default energy set. More... | |
void | vrna_md_defaults_backtrack (int flag) |
Set default behavior for whether to backtrack secondary structures. More... | |
int | vrna_md_defaults_backtrack_get (void) |
Get default behavior for whether to backtrack secondary structures. More... | |
void | vrna_md_defaults_backtrack_type (char t) |
Set default backtrack type, i.e. which DP matrix is used. More... | |
char | vrna_md_defaults_backtrack_type_get (void) |
Get default backtrack type, i.e. which DP matrix is used. More... | |
void | vrna_md_defaults_compute_bpp (int flag) |
Set the default behavior for whether to compute base pair probabilities after partition function computation. More... | |
int | vrna_md_defaults_compute_bpp_get (void) |
Get the default behavior for whether to compute base pair probabilities after partition function computation. More... | |
void | vrna_md_defaults_max_bp_span (int span) |
Set default maximal base pair span. More... | |
int | vrna_md_defaults_max_bp_span_get (void) |
Get default maximal base pair span. More... | |
void | vrna_md_defaults_min_loop_size (int size) |
Set default minimal loop size. More... | |
int | vrna_md_defaults_min_loop_size_get (void) |
Get default minimal loop size. More... | |
void | vrna_md_defaults_window_size (int size) |
Set default window size for sliding window structure prediction approaches. More... | |
int | vrna_md_defaults_window_size_get (void) |
Get default window size for sliding window structure prediction approaches. More... | |
void | vrna_md_defaults_oldAliEn (int flag) |
Set default behavior for whether to use old energy model for comparative structure prediction. More... | |
int | vrna_md_defaults_oldAliEn_get (void) |
Get default behavior for whether to use old energy model for comparative structure prediction. More... | |
void | vrna_md_defaults_ribo (int flag) |
Set default behavior for whether to use Ribosum Scoring in comparative structure prediction. More... | |
int | vrna_md_defaults_ribo_get (void) |
Get default behavior for whether to use Ribosum Scoring in comparative structure prediction. More... | |
void | vrna_md_defaults_cv_fact (double factor) |
Set the default covariance scaling factor used in comparative structure prediction. More... | |
double | vrna_md_defaults_cv_fact_get (void) |
Get the default covariance scaling factor used in comparative structure prediction. More... | |
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. More... | |
double | vrna_md_defaults_sfact_get (void) |
Get the default scaling factor used to avoid under-/overflows in partition function computation. More... | |
void | set_model_details (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 | |
The model details data structure and its corresponding modifiers.