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