RNAlib-2.2.0-RC2
Deprecated List
globalScope> Global alifold (const char **strings, char *structure)
Usage of this function is discouraged! Use vrna_ali_fold() instead
See also
vrna_ali_fold()
globalScope> Global alimake_pair_table (const char *structure)
Use vrna_pt_ali_get() instead!
globalScope> Global alipbacktrack (double *prob)
Use vrna_ali_pbacktrack() instead!
globalScope> Global alipf_circ_fold (const char **sequences, char *structure, plist **pl)
Use vrna_ali_pf_fold() instead
globalScope> Global alipf_fold (const char **sequences, char *structure, plist **pl)
Use vrna_ali_pf_fold() instead
globalScope> Global alipf_fold_par (const char **sequences, char *structure, plist **pl, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained, int is_circular)
Use vrna_ali_pf_fold() instead
globalScope> Global assign_plist_from_db (plist **pl, const char *struc, float pr)
Use vrna_pl_get() instead
globalScope> Global assign_plist_from_pr (plist **pl, FLT_OR_DBL *probs, int length, double cutoff)
Use vrna_pl_get_from_pr() instead!
globalScope> Global base_pair
Do not use this variable anymore!
globalScope> Global bp_distance (const char *str1, const char *str2)
Use vrna_bp_distance instead
Parameters
str1First structure in dot-bracket notation
str2Second structure in dot-bracket notation
Returns
The base pair distance between str1 and str2
globalScope> Global bppm_symbol (const float *x)
Use vrna_bpp_symbol() instead!
globalScope> Global bppm_to_structure (char *structure, FLT_OR_DBL *pr, unsigned int length)
Use vrna_db_get_from_pr() instead!
globalScope> Global centroid (int length, double *dist)
This function is deprecated and should not be used anymore as it is not threadsafe!
See also
get_centroid_struct_pl(), get_centroid_struct_pr()
globalScope> Global circalifold (const char **strings, char *structure)
Usage of this function is discouraged! Use vrna_ali_fold() instead
See also
vrna_ali_fold()
globalScope> Global circfold (const char *sequence, char *structure)
Use vrna_fold() instead!
globalScope> Global co_pf_fold (char *sequence, char *structure)
{Use vrna_co_pf_fold() instead!}
globalScope> Global cofold (const char *sequence, char *structure)
use vrna_cofold() instead
globalScope> Global cofold_par (const char *string, char *structure, vrna_param_t *parameters, int is_constrained)
use vrna_cofold() instead
globalScope> Global compute_BPdifferences (short *pt1, short *pt2, unsigned int turn)
Use vrna_refBPdist_matrix() instead
globalScope> Global compute_probabilities (double FAB, double FEA, double FEB, struct plist *prAB, struct plist *prA, struct plist *prB, int Alength)
{ Use vrna_co_pf_dimer_probs() instead!}
globalScope> Global copy_pair_table (const short *pt)
Use vrna_pt_copy() instead
globalScope> Global cv_fact
See vrna_md_t.cv_fact, and vrna_ali_fold() to avoid using global variables
globalScope> Global destroy_TwoDfold_variables (TwoDfold_vars *our_variables)
Use the new API that relies on vrna_fold_compound and the corresponding functions vrna_get_fold_copound_2D(), vrna_TwoD_fold(), and vrna_free_fold_compound() instead!
globalScope> Global destroy_TwoDpfold_variables (TwoDpfold_vars *vars)
Use the new API that relies on vrna_fold_compound and the corresponding functions vrna_get_fold_copound_2D(), vrna_TwoD_pf_fold(), and vrna_free_fold_compound() instead!
globalScope> Global energy_of_alistruct (const char **sequences, const char *structure, int n_seq, float *energy)
Usage of this function is discouraged! Use vrna_eval_structure(), and vrna_eval_covar_structure() instead!
globalScope> Global energy_of_circ_struct (const char *string, const char *structure)
This function is deprecated and should not be used in future programs Use energy_of_circ_structure() instead!
globalScope> Global energy_of_circ_struct_par (const char *string, const char *structure, vrna_param_t *parameters, int verbosity_level)
Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!
globalScope> Global energy_of_circ_structure (const char *string, const char *structure, int verbosity_level)
Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!
globalScope> Global energy_of_move (const char *string, const char *structure, int m1, int m2)
Use vrna_eval_move() instead!
globalScope> Global energy_of_move_pt (short *pt, short *s, short *s1, int m1, int m2)
Use vrna_eval_move_pt() instead!
globalScope> Global energy_of_struct (const char *string, const char *structure)
This function is deprecated and should not be used in future programs! Use energy_of_structure() instead!
globalScope> Global energy_of_struct_par (const char *string, const char *structure, vrna_param_t *parameters, int verbosity_level)
Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!
globalScope> Global energy_of_struct_pt (const char *string, short *ptable, short *s, short *s1)
This function is deprecated and should not be used in future programs! Use energy_of_structure_pt() instead!
globalScope> Global energy_of_struct_pt_par (const char *string, short *ptable, short *s, short *s1, vrna_param_t *parameters, int verbosity_level)
Use vrna_eval_structure_pt() or vrna_eval_structure_pt_verbose() instead!
globalScope> Global energy_of_structure (const char *string, const char *structure, int verbosity_level)
Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!
globalScope> Global energy_of_structure_pt (const char *string, short *ptable, short *s, short *s1, int verbosity_level)
Use vrna_eval_structure_pt() or vrna_eval_structure_pt_verbose() instead!
globalScope> Global expHairpinEnergy (int u, int type, short si1, short sj1, const char *string)
Use exp_E_Hairpin() from loop_energies.h instead
globalScope> Global expLoopEnergy (int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)
Use exp_E_IntLoop() from loop_energies.h instead
globalScope> Global export_ali_bppm (void)
Usage of this function is discouraged! The new vrna_fold_compound allows direct access to the folding matrices, including the pair probabilities! The pair probability array returned here reflects the one of the latest call to vrna_ali_pf_fold(), or any of the old API calls for consensus structure partition function folding.
globalScope> Global export_circfold_arrays (int *Fc_p, int *FcH_p, int *FcI_p, int *FcM_p, int **fM2_p, int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p)
See vrna_fold() and vrna_fold_compound for the usage of the new API!
globalScope> Global export_circfold_arrays_par (int *Fc_p, int *FcH_p, int *FcI_p, int *FcM_p, int **fM2_p, int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p, vrna_param_t **P_p)
See vrna_fold() and vrna_fold_compound for the usage of the new API!
globalScope> Global export_cofold_arrays (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **indx_p, char **ptype_p)
folding matrices now reside within the fold compound. Thus, this function will only work in conjunction with a prior call to cofold() or cofold_par()
globalScope> Global export_cofold_arrays_gq (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **ggg_p, int **indx_p, char **ptype_p)
folding matrices now reside within the fold compound. Thus, this function will only work in conjunction with a prior call to cofold() or cofold_par()
globalScope> Global export_fold_arrays (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p)
See vrna_fold() and vrna_fold_compound for the usage of the new API!
globalScope> Global export_fold_arrays_par (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p, vrna_param_t **P_p)
See vrna_fold() and vrna_fold_compound for the usage of the new API!
globalScope> Global filecopy (FILE *from, FILE *to)
Use vrna_file_copy() instead!
globalScope> Global fold (const char *sequence, char *structure)
use vrna_fold() instead
globalScope> Global fold_par (const char *sequence, char *structure, vrna_param_t *parameters, int is_constrained, int is_circular)
use vrna_fold() instead
globalScope> Global free_alifold_arrays (void)
Usage of this function is discouraged! It only affects memory being free'd that was allocated by an old API function before. Release of memory occupied by the newly introduced vrna_fold_compound is handled by vrna_vrna_free_fold_compound()
globalScope> Global free_alipf_arrays (void)
Usage of this function is discouraged! This function only free's memory allocated by old API function calls. Memory allocated by any of the new API calls (starting with vrna_) will be not affected!
globalScope> Global free_arrays (void)
See vrna_fold() and vrna_fold_compound for the usage of the new API!
globalScope> Global free_co_arrays (void)
This function will only free memory allocated by a prior call of cofold() or cofold_par(). See vrna_cofold() for how to use the new API
globalScope> Global free_pf_arrays (void)
See vrna_fold_compound and its related functions for how to free memory occupied by the dynamic programming matrices
globalScope> Global get_alipf_arrays (short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, FLT_OR_DBL **qb_p, FLT_OR_DBL **qm_p, FLT_OR_DBL **q1k_p, FLT_OR_DBL **qln_p, int **pscore)
It is discouraged to use this function! The new vrna_fold_compound allows direct access to all necessary consensus structure prediction related variables!
globalScope> Global get_boltzmann_factor_copy (vrna_exp_param_t *parameters)
Use vrna_exp_params_copy() instead!
globalScope> Global get_boltzmann_factors (double temperature, double betaScale, vrna_md_t md, double pf_scale)
Use vrna_exp_params_get() instead!
globalScope> Global get_boltzmann_factors_ali (unsigned int n_seq, double temperature, double betaScale, vrna_md_t md, double pf_scale)
Use vrna_exp_params_ali_get() instead!
globalScope> Global get_centroid_struct_gquad_pr (int length, double *dist)
This function is deprecated and should not be used anymore as it is not threadsafe!
See also
vrna_get_centroid_struct(), vrna_get_centroid_struct_pr(), vrna_get_centroid_struct_pl()
globalScope> Global get_centroid_struct_pl (int length, double *dist, plist *pl)
This function was renamed to vrna_get_centroid_struct_pl()
globalScope> Global get_centroid_struct_pr (int length, double *dist, FLT_OR_DBL *pr)
This function was renamed to vrna_get_centroid_struct_pr()
globalScope> Global get_concentrations (double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc)
{ Use vrna_co_pf_get_concentrations() instead!}
globalScope> Global get_mpi (char *Alseq[], int n_seq, int length, int *mini)
Use vrna_ali_get_mpi() as a replacement
globalScope> Global get_plist (struct plist *pl, int length, double cut_off)
{ This function is deprecated and will be removed soon!} use assign_plist_from_pr() instead!
globalScope> Global get_scaled_alipf_parameters (unsigned int n_seq)
Use vrna_exp_params_ali_get() instead!
globalScope> Global get_scaled_parameters (double temperature, vrna_md_t md)
Use vrna_params_get() instead!
globalScope> Global get_scaled_pf_parameters (void)
Use vrna_exp_params_get() instead!
globalScope> Global get_TwoDfold_variables (const char *seq, const char *structure1, const char *structure2, int circ)
Use the new API that relies on vrna_fold_compound and the corresponding functions vrna_get_fold_copound_2D(), vrna_TwoD_fold(), and vrna_free_fold_compound() instead!
globalScope> Global get_TwoDpfold_variables (const char *seq, const char *structure1, char *structure2, int circ)
Use the new API that relies on vrna_fold_compound and the corresponding functions vrna_get_fold_copound_2D(), vrna_TwoD_pf_fold(), and vrna_free_fold_compound() instead!
globalScope> Global HairpinE (int size, int type, int si1, int sj1, const char *string)
{This function is deprecated and will be removed soon. Use E_Hairpin() instead!}
globalScope> Global hamming (const char *s1, const char *s2)
Use vrna_hamming_distance() instead!
globalScope> Global hamming_bound (const char *s1, const char *s2, int n)
Use vrna_hamming_distance_bound() instead!
globalScope> Global iindx
Do not use this variable anymore!
globalScope> Global init_co_pf_fold (int length)
{ This function is deprecated and will be removed soon!}
globalScope> Global init_pf_fold (int length)
This function is obsolete and will be removed soon!
globalScope> Global init_rand (void)
Use vrna_init_rand() instead!
globalScope> Global initialize_cofold (int length)
{This function is obsolete and will be removed soon!}
globalScope> Global initialize_fold (int length)

{This function is deprecated and will be removed soon!}

See vrna_fold() and vrna_fold_compound for the usage of the new API!

globalScope> Global int_urn (int from, int to)
Use vrna_int_urn() instead!
globalScope> Global loop_energy (short *ptable, short *s, short *s1, int i)
Use vrna_eval_loop_pt() instead!
globalScope> Global LoopEnergy (int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1)
{This function is deprecated and will be removed soon. Use E_IntLoop() instead!}
globalScope> Global Make_bp_profile (int length)
This function is deprecated and will be removed soon! See Make_bp_profile_bppm() for a replacement
globalScope> Global make_pair_table (const char *structure)
Use vrna_pt_get() instead
globalScope> Global make_pair_table_snoop (const char *structure)
Use vrna_pt_snoop_get() instead!
globalScope> Global make_referenceBP_array (short *reference_pt, unsigned int turn)
Use vrna_refBPcnt_matrix() instead
globalScope> Global mean_bp_dist (int length)
This function is not threadsafe and should not be used anymore. Use mean_bp_distance() instead!
globalScope> Global mean_bp_distance (int length)
Use vrna_mean_bp_distance() or vrna_mean_bp_distance_pr() instead!
See also
vrna_mean_bp_distance(), vrna_mean_bp_distance_pr()
globalScope> Global mean_bp_distance_pr (int length, FLT_OR_DBL *pr)
Use vrna_mean_bp_distance() or vrna_mean_bp_distance_pr() instead!
globalScope> Global nc_fact
See #vrna_md_t.nc_fact, and vrna_ali_fold() to avoid using global variables
globalScope> Global nrerror (const char message[])
Use vrna_message_error() instead!
globalScope> Global pack_structure (const char *struc)
Use vrna_db_pack() as a replacement
Parameters
strucThe secondary structure in dot-bracket notation
Returns
The binary encoded structure
globalScope> Global parenthesis_structure (char *structure, bondT *bp, int length)
use vrna_parenthesis_structure() instead
globalScope> Global parenthesis_zuker (char *structure, bondT *bp, int length)
use vrna_parenthesis_zuker instead
globalScope> Global pbacktrack_circ (char *sequence)
Use vrna_pbacktrack() instead.
globalScope> Global pf_circ_fold (const char *sequence, char *structure)
Use vrna_pf_fold() instead!
Parameters
[in]sequenceThe RNA sequence input
[in,out]structureA pointer to a char array where a base pair probability information can be stored in a pseudo-dot-bracket notation (may be NULL, too)
Returns
The Gibbs free energy of the ensemble ( $G = -RT \cdot \log(Q) $) in kcal/mol
globalScope> Global pf_fold_par (const char *sequence, char *structure, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained, int is_circular)
Use vrna_pf_fold() instead
globalScope> Global pr
Do not use this variable anymore!
globalScope> Global print_tty_input_seq (void)
Use vrna_message_input_seq_simple() instead!
globalScope> Global print_tty_input_seq_str (const char *s)
Use vrna_message_input_seq() instead!
globalScope> Global PS_dot_plot (char *string, char *file)
This function is deprecated and will be removed soon! Use PS_dot_plot_list() instead!
globalScope> Global random_string (int l, const char symbols[])
Use vrna_random_string() instead!
globalScope> Global read_record (char **header, char **sequence, char ***rest, unsigned int options)
This function is deprecated! Use vrna_read_fasta_record() as a replacment.
globalScope> Global scale_parameters (void)
Use vrna_params_get() instead!
globalScope> Global space (unsigned size)
Use vrna_alloc() instead!
globalScope> Global str_DNA2RNA (char *sequence)
Use vrna_seq_toRNA() instead!
globalScope> Global str_uppercase (char *sequence)
Use vrna_seq_toupper() instead!
globalScope> Global time_stamp (void)
Use vrna_time_stamp() instead!
globalScope> Global TwoDfold_backtrack_f5 (unsigned int j, int k, int l, TwoDfold_vars *vars)
Use the new API that relies on vrna_fold_compound and the corresponding functions vrna_get_fold_copound_2D(), vrna_TwoD_fold(), vrna_TwoD_backtrack5(), and vrna_free_fold_compound() instead!
Class TwoDfold_vars
This data structure will be removed from the library soon! Use vrna_fold_compound and the corresponding functions vrna_get_fold_copound_2D(), vrna_TwoD_fold(), and vrna_free_fold_compound() instead!
globalScope> Global TwoDfoldList (TwoDfold_vars *vars, int distance1, int distance2)
Use the new API that relies on vrna_fold_compound and the corresponding functions vrna_get_fold_copound_2D(), vrna_TwoD_fold(), and vrna_free_fold_compound() instead!
globalScope> Global TwoDpfold_pbacktrack (TwoDpfold_vars *vars, int d1, int d2)
Use the new API that relies on vrna_fold_compound and the corresponding functions vrna_get_fold_copound_2D(), vrna_TwoD_pf_fold(), vrna_TwoD_pbacktrack(), and vrna_free_fold_compound() instead!
globalScope> Global TwoDpfold_pbacktrack5 (TwoDpfold_vars *vars, int d1, int d2, unsigned int length)
Use the new API that relies on vrna_fold_compound and the corresponding functions vrna_get_fold_copound_2D(), vrna_TwoD_pf_fold(), vrna_TwoD_pbacktrack5(), and vrna_free_fold_compound() instead!
Class TwoDpfold_vars
This data structure will be removed from the library soon! Use vrna_fold_compound and the corresponding functions vrna_get_fold_copound_2D(), vrna_TwoD_pf_fold(), and vrna_free_fold_compound() instead!
globalScope> Global TwoDpfoldList (TwoDpfold_vars *vars, int maxDistance1, int maxDistance2)
Use the new API that relies on vrna_fold_compound and the corresponding functions vrna_get_fold_copound_2D(), vrna_TwoD_pf_fold(), and vrna_free_fold_compound() instead!
globalScope> Global unpack_structure (const char *packed)
Use vrna_db_unpack() as a replacement
Parameters
packedThe binary encoded packed secondary structure
Returns
The unpacked secondary structure in dot-bracket notation
globalScope> Global update_alifold_params (void)
Usage of this function is discouraged! The new API uses vrna_fold_compound to lump all folding related necessities together, including the energy parameters. Use vrna_update_fold_params() to update the energy parameters within a vrna_fold_compound.
globalScope> Global update_fold_params (void)
use vrna_update_fold_params() instead
globalScope> Global update_fold_params_par (vrna_param_t *parameters)
use vrna_update_fold_params() instead
globalScope> Global update_pf_params (int length)

Use vrna_update_pf_params() instead

globalScope> Global update_pf_params_par (int length, vrna_exp_param_t *parameters)

Use vrna_update_pf_params() instead

globalScope> Global urn (void)
Use vrna_urn() instead!
Global vrna_exp_param_t::id
This attribute will be removed in version 3
Global vrna_fold_compound::ptype_pf_compat
This attribute will vanish in the future! It's meant for backward compatibility only!
Warning
Only available if
type==VRNA_VC_TYPE_SINGLE 
globalScope> Global vrna_md_set_globals (vrna_md_t *md)
This function will vanish as soon as backward compatibility of RNAlib is dropped (expected in version 3). Use vrna_md_set_default() instead!
globalScope> Global warn_user (const char message[])
Use vrna_message_warning() instead!
globalScope> Global xrealloc (void *p, unsigned size)
Use vrna_realloc() instead!
globalScope> Global zukersubopt (const char *string)
use vrna_zukersubopt() instead
globalScope> Global zukersubopt_par (const char *string, vrna_param_t *parameters)
use vrna_zukersubopt() instead