RNAlib-2.3.1
SWIG Wrapper Notes

Below, you find an enumeration of special note on how functions, structures, enums, and macro definitions are wrapped.

Global vrna_commands_apply (vrna_fold_compound_t *vc, vrna_cmd_t *commands, unsigned int options)
This function is attached as method commands_apply() to objects of type fold_compound
Global vrna_enumerate_necklaces (const unsigned int *type_counts)
This function is available as global function enumerate_necklaces() which accepts lists input, an produces list of lists output.
Global vrna_eval_covar_structure (vrna_fold_compound_t *vc, const char *structure)
This function is attached as method eval_covar_structure() to objects of type fold_compound
Global vrna_eval_hp_loop (vrna_fold_compound_t *vc, int i, int j)
This function is attached as method eval_hp_loop() to objects of type fold_compound
Global vrna_eval_int_loop (vrna_fold_compound_t *vc, int i, int j, int k, int l)
This function is attached as method eval_int_loop() to objects of type fold_compound
Global vrna_eval_loop_pt (vrna_fold_compound_t *vc, int i, const short *pt)
This function is attached as method eval_loop_pt() to objects of type fold_compound
Global vrna_eval_move (vrna_fold_compound_t *vc, const char *structure, int m1, int m2)
This function is attached as method eval_move() to objects of type fold_compound
Global vrna_eval_move_pt (vrna_fold_compound_t *vc, short *pt, int m1, int m2)
This function is attached as method eval_move_pt() to objects of type fold_compound
Global vrna_eval_structure (vrna_fold_compound_t *vc, const char *structure)
This function is attached as method eval_structure() to objects of type fold_compound
Global vrna_eval_structure_pt (vrna_fold_compound_t *vc, const short *pt)
This function is attached as method eval_structure_pt() to objects of type fold_compound
Global vrna_eval_structure_pt_verbose (vrna_fold_compound_t *vc, const short *pt, FILE *file)
This function is attached as method eval_structure_pt_verbose() to objects of type fold_compound
Global vrna_eval_structure_verbose (vrna_fold_compound_t *vc, const char *structure, FILE *file)
This function is attached as method eval_structure_verbose() to objects of type fold_compound
Global vrna_exp_params_rescale (vrna_fold_compound_t *vc, double *mfe)

This function is attached to vrna_fc_s objects as overloaded exp_params_rescale() method.

When no parameter is passed to this method, the resulting action is the same as passing NULL as second parameter to vrna_exp_params_rescale(), i.e. default scaling of the partition function. Passing an energy in kcal/mol, e.g. as retrieved by a previous call to the mfe() method, instructs all subsequent calls to scale the partition function accordingly.

Global vrna_exp_params_reset (vrna_fold_compound_t *vc, vrna_md_t *md_p)

This function is attached to vrna_fc_s objects as overloaded exp_params_reset() method.

When no parameter is passed to this method, the resulting action is the same as passing NULL as second parameter to vrna_exp_params_reset(), i.e. global default model settings are used. Passing an object of type vrna_md_s resets the fold compound according to the specifications stored within the vrna_md_s object.

Class vrna_fc_s

This data structure is wrapped as an object fold_compound with several related functions attached as methods.

A new fold_compound can be obtained by calling one of its constructors:

  • fold_compound(seq) – Initialize with a single sequence, or two concatenated sequences separated by an ampersand character '&' (for cofolding)
  • fold_compound(aln) – Initialize with a sequence alignment aln stored as a list of sequences (with gap characters)

The resulting object has a list of attached methods which in most cases directly correspond to functions that mainly operate on the corresponding C data structure:

  • type() – Get the type of the fold_compound (See vrna_fc_type_e)
  • length() – Get the length of the sequence(s) or alignment stored within the fold_compound
Global vrna_file_commands_apply (vrna_fold_compound_t *vc, const char *filename, unsigned int options)
This function is attached as method file_commands_apply() to objects of type fold_compound
Global vrna_hc_add_bp (vrna_fold_compound_t *vc, int i, int j, char option)
This function is attached as method hc_add_bp() to objects of type fold_compound
Global vrna_hc_add_bp_nonspecific (vrna_fold_compound_t *vc, int i, int d, char option)
This function is attached as method hc_add_bp_nonspecific() to objects of type fold_compound
Global vrna_hc_add_from_db (vrna_fold_compound_t *vc, const char *constraint, unsigned int options)
This function is attached as method hc_add_from_db() to objects of type fold_compound
Global vrna_hc_add_up (vrna_fold_compound_t *vc, int i, char option)
This function is attached as method hc_add_up() to objects of type fold_compound
Global vrna_hc_init (vrna_fold_compound_t *vc)
This function is attached as method hc_init() to objects of type fold_compound
Class vrna_md_s

This data structure is wrapped as an object md with multiple related functions attached as methods.

A new set of default parameters can be obtained by calling the constructure of md:

  • md() – Initialize with default settings

The resulting object has a list of attached methods which directly correspond to functions that mainly operate on the corresponding C data structure:

Note, that default parameters can be modified by directly setting any of the following global variables. Internally, getting/setting default parameters using their global variable representative translates into calls of the following functions, therefore these wrappers for these functions do not exist in the scripting language interface(s):

global variable C getter C setter
temperature vrna_md_defaults_temperature_get() vrna_md_defaults_temperature()
dangles vrna_md_defaults_dangles_get() vrna_md_defaults_dangles()
betaScale vrna_md_defaults_betaScale_get() vrna_md_defaults_betaScale()
tetra_loop this is an alias of special_hp
special_hp vrna_md_defaults_special_hp_get() vrna_md_defaults_special_hp()
noLonelyPairs this is an alias of noLP
noLP vrna_md_defaults_noLP_get() vrna_md_defaults_noLP()
noGU vrna_md_defaults_noGU_get() vrna_md_defaults_noGU()
no_closingGU this is an alias of noGUclosure
noGUclosure vrna_md_defaults_noGUclosure_get() vrna_md_defaults_noGUclosure()
logML vrna_md_defaults_logML_get() vrna_md_defaults_logML()
circ vrna_md_defaults_circ_get() vrna_md_defaults_circ()
gquad vrna_md_defaults_gquad_get() vrna_md_defaults_gquad()
uniq_ML vrna_md_defaults_uniq_ML_get() vrna_md_defaults_uniq_ML()
energy_set vrna_md_defaults_energy_set_get() vrna_md_defaults_energy_set()
backtrack vrna_md_defaults_backtrack_get() vrna_md_defaults_backtrack()
backtrack_type vrna_md_defaults_backtrack_type_get() vrna_md_defaults_backtrack_type()
do_backtrack this is an alias of compute_bpp
compute_bpp vrna_md_defaults_compute_bpp_get() vrna_md_defaults_compute_bpp()
max_bp_span vrna_md_defaults_max_bp_span_get() vrna_md_defaults_max_bp_span()
min_loop_size vrna_md_defaults_min_loop_size_get() vrna_md_defaults_min_loop_size()
window_size vrna_md_defaults_window_size_get() vrna_md_defaults_window_size()
oldAliEn vrna_md_defaults_oldAliEn_get() vrna_md_defaults_oldAliEn()
ribo vrna_md_defaults_ribo_get() vrna_md_defaults_ribo()
cv_fact vrna_md_defaults_cv_fact_get() vrna_md_defaults_cv_fact()
nc_fact vrna_md_defaults_nc_fact_get() vrna_md_defaults_nc_fact()
sfact vrna_md_defaults_sfact_get() vrna_md_defaults_sfact()
Global vrna_mean_bp_distance (vrna_fold_compound_t *vc)
This function is attached as method mean_bp_distance() to objects of type fold_compound
Global vrna_mfe (vrna_fold_compound_t *vc, char *structure)
This function is attached as method mfe() to objects of type fold_compound
Global vrna_mfe_dimer (vrna_fold_compound_t *vc, char *structure)
This function is attached as method mfe_dimer() to objects of type fold_compound
Global vrna_mfe_window (vrna_fold_compound_t *vc, FILE *file)
This function is attached as method mfe_window() to objects of type fold_compound
Global vrna_params_reset (vrna_fold_compound_t *vc, vrna_md_t *md_p)

This function is attached to vrna_fc_s objects as overloaded params_reset() method.

When no parameter is passed to this method, the resulting action is the same as passing NULL as second parameter to vrna_params_reset(), i.e. global default model settings are used. Passing an object of type vrna_md_s resets the fold compound according to the specifications stored within the vrna_md_s object.

Global vrna_params_subst (vrna_fold_compound_t *vc, vrna_param_t *par)
This function is attached to vrna_fc_s objects as params_subst() method.
Global vrna_pf (vrna_fold_compound_t *vc, char *structure)
This function is attached as method pf() to objects of type fold_compound
Global vrna_pf_dimer (vrna_fold_compound_t *vc, char *structure)
This function is attached as method pf_dimer() to objects of type fold_compound
Global vrna_sc_add_bp (vrna_fold_compound_t *vc, int i, int j, FLT_OR_DBL energy, unsigned int options)

This function is attached as an overloaded method sc_add_bp() to objects of type fold_compound. The method either takes arguments for a single base pair (i,j) with the corresponding energy value:

fold_compound.sc_add_bp(i, j, energy, options)

or an entire 2-dimensional matrix with dimensions n x n that stores free energy contributions for any base pair (i,j) with $ 1 \leq i < j \leq n $:

fold_compound.sc_add_bp(matrix, options)

In both variants, the options argument is optional can may be omitted.

Global vrna_sc_add_bt (vrna_fold_compound_t *vc, vrna_callback_sc_backtrack *f)
This function is attached as method sc_add_bt() to objects of type fold_compound
Global vrna_sc_add_data (vrna_fold_compound_t *vc, void *data, vrna_callback_free_auxdata *free_data)
This function is attached as method sc_add_data() to objects of type fold_compound
Global vrna_sc_add_exp_f (vrna_fold_compound_t *vc, vrna_callback_sc_exp_energy *exp_f)
This function is attached as method sc_add_exp_f() to objects of type fold_compound
Global vrna_sc_add_f (vrna_fold_compound_t *vc, vrna_callback_sc_energy *f)
This function is attached as method sc_add_f() to objects of type fold_compound
Global vrna_sc_add_hi_motif (vrna_fold_compound_t *vc, const char *seq, const char *structure, FLT_OR_DBL energy, unsigned int options)
This function is attached as method sc_add_hi_motif() to objects of type fold_compound
Global vrna_sc_add_SHAPE_deigan (vrna_fold_compound_t *vc, const double *reactivities, double m, double b, unsigned int options)
This function is attached as method sc_add_SHAPE_deigan() to objects of type fold_compound
Global vrna_sc_add_SHAPE_deigan_ali (vrna_fold_compound_t *vc, const char **shape_files, const int *shape_file_association, double m, double b, unsigned int options)
This function is attached as method sc_add_SHAPE_deigan_ali() to objects of type fold_compound
Global vrna_sc_add_SHAPE_zarringhalam (vrna_fold_compound_t *vc, const double *reactivities, double b, double default_value, const char *shape_conversion, unsigned int options)
This function is attached as method sc_add_SHAPE_zarringhalam() to objects of type fold_compound
Global vrna_sc_add_up (vrna_fold_compound_t *vc, int i, FLT_OR_DBL energy, unsigned int options)
This function is attached as an overloaded method sc_add_up() to objects of type fold_compound. The method either takes arguments for a single nucleotide $i $ with the corresponding energy value:
fold_compound.sc_add_up(i, energy, options)
or an entire vector that stores free energy contributions for each nucleotide $i $ with $ 1 \leq i \leq n $:
fold_compound.sc_add_bp(vector, options)
In both variants, the options argument is optional can may be omitted.
Global vrna_sc_init (vrna_fold_compound_t *vc)
This function is attached as method sc_init() to objects of type fold_compound
Global vrna_sc_remove (vrna_fold_compound_t *vc)
This function is attached as method sc_remove() to objects of type fold_compound
Global vrna_sc_set_bp (vrna_fold_compound_t *vc, const FLT_OR_DBL **constraints, unsigned int options)
This function is attached as method sc_set_bp() to objects of type fold_compound
Global vrna_sc_set_up (vrna_fold_compound_t *vc, const FLT_OR_DBL *constraints, unsigned int options)
This function is attached as method sc_set_up() to objects of type fold_compound
Global vrna_subopt (vrna_fold_compound_t *vc, int delta, int sorted, FILE *fp)
This function is attached as method subopt() to objects of type fold_compound
Global vrna_subopt_cb (vrna_fold_compound_t *vc, int delta, vrna_subopt_callback *cb, void *data)
This function is attached as method subopt_cb() to objects of type fold_compound
Global vrna_subopt_zuker (vrna_fold_compound_t *vc)
This function is attached as method subopt_zuker() to objects of type fold_compound
Global vrna_ud_add_motif (vrna_fold_compound_t *vc, const char *motif, double motif_en, unsigned int loop_type)
This function is attached as method ud_add_motif() to objects of type fold_compound
Global vrna_ud_remove (vrna_fold_compound_t *vc)
This function is attached as method ud_remove() to objects of type fold_compound
Global vrna_ud_set_data (vrna_fold_compound_t *vc, void *data, vrna_callback_free_auxdata *free_cb)
This function is attached as method ud_set_data() to objects of type fold_compound
Global vrna_ud_set_exp_prod_rule_cb (vrna_fold_compound_t *vc, vrna_callback_ud_exp_production *pre_cb, vrna_callback_ud_exp_energy *exp_e_cb)
This function is attached as method ud_set_exp_prod_rule_cb() to objects of type fold_compound
Global vrna_ud_set_prob_cb (vrna_fold_compound_t *vc, vrna_callback_ud_probs_add *setter, vrna_callback_ud_probs_get *getter)
This function is attached as method ud_set_prob_cb() to objects of type fold_compound
Global vrna_ud_set_prod_rule_cb (vrna_fold_compound_t *vc, vrna_callback_ud_production *pre_cb, vrna_callback_ud_energy *e_cb)
This function is attached as method ud_set_prod_rule_cb() to objects of type fold_compound