Global alifold (const char **strings, char *structure)

Usage of this function is discouraged! Use vrna_alifold(), or vrna_mfe() instead!

Global alimake_pair_table (const char *structure)

Use vrna_pt_ali_get() instead!

Global alipbacktrack (double *prob)

Use vrna_pbacktrack() instead!

Global alipf_circ_fold (const char **sequences, char *structure, vrna_ep_t **pl)

Use vrna_pf() instead

Global alipf_fold (const char **sequences, char *structure, vrna_ep_t **pl)

Use vrna_pf() instead

Global alipf_fold_par (const char **sequences, char *structure, vrna_ep_t **pl, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained, int is_circular)

Use vrna_pf() instead

Global aliPS_color_aln (const char *structure, const char *filename, const char *seqs[], const char *names[])

Use vrna_file_PS_aln() instead!

File aln_util.h

Use ViennaRNA/utils/alignments.h instead

Global assign_plist_from_db (vrna_ep_t **pl, const char *struc, float pr)

Use vrna_plist() instead

Global assign_plist_from_pr (vrna_ep_t **pl, FLT_OR_DBL *probs, int length, double cutoff)

Use vrna_plist_from_probs() instead!

Global b2C (const char *structure)

See vrna_db_to_tree_string() and VRNA_STRUCTURE_TREE_SHAPIRO_SHORT for a replacement

Global b2HIT (const char *structure)

See vrna_db_to_tree_string() and VRNA_STRUCTURE_TREE_HIT for a replacement

Global b2Shapiro (const char *structure)

See vrna_db_to_tree_string() and VRNA_STRUCTURE_TREE_SHAPIRO_WEIGHT for a replacement

Global base_pair

Do not use this variable anymore!

Global bondT

Use vrna_bp_stack_t instead!

Global bp_distance (const char *str1, const char *str2)

Use vrna_bp_distance instead

Global bppm_symbol (const float *x)

Use vrna_bpp_symbol() instead!

Global bppm_to_structure (char *structure, FLT_OR_DBL *pr, unsigned int length)

Use vrna_db_from_probs() instead!

Global centroid (int length, double *dist)

This function is deprecated and should not be used anymore as it is not threadsafe!

File char_stream.h

Use ViennaRNA/datastructures/char_stream.h instead

Global circalifold (const char **strings, char *structure)

Usage of this function is discouraged! Use vrna_alicircfold(), and vrna_mfe() instead!

Global circfold (const char *sequence, char *structure)

Use vrna_circfold(), or vrna_mfe() instead!

Global co_pf_fold (char *sequence, char *structure)

{Use vrna_pf_dimer() instead!}

Global co_pf_fold_par (char *sequence, char *structure, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained)

Use vrna_pf_dimer() instead!

Global cofold (const char *sequence, char *structure)

use vrna_mfe_dimer() instead

Global cofold_par (const char *string, char *structure, vrna_param_t *parameters, int is_constrained)

use vrna_mfe_dimer() instead

Global compute_BPdifferences (short *pt1, short *pt2, unsigned int turn)

Use vrna_refBPdist_matrix() instead

Global compute_probabilities (double FAB, double FEA, double FEB, vrna_ep_t *prAB, vrna_ep_t *prA, vrna_ep_t *prB, int Alength)

{ Use vrna_pf_dimer_probs() instead!}

Global constrain_ptypes (const char *constraint, unsigned int length, char *ptype, int *BP, int min_loop_size, unsigned int idx_type)

Do not use this function anymore! Structure constraints are now handled through vrna_hc_t and related functions.

File constraints.h

Use ViennaRNA/constraints/basic.h instead

File constraints_hard.h

Use ViennaRNA/constraints/hard.h instead

File constraints_ligand.h

Use ViennaRNA/constraints/ligand.h instead

File constraints_SHAPE.h

Use ViennaRNA/constraints/SHAPE.h instead

File constraints_soft.h

Use ViennaRNA/constraints/soft.h instead

File convert_epars.h

Use ViennaRNA/params/convert.h instead

Global copy_pair_table (const short *pt)

Use vrna_ptable_copy() instead

Global cpair

Use vrna_cpair_t instead!

Global cv_fact

See vrna_md_t.cv_fact, and vrna_mfe() to avoid using global variables

File data_structures.h

Use ViennaRNA/datastructures/basic.h instead

Global destroy_TwoDfold_variables (TwoDfold_vars *our_variables)

Use the new API that relies on vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(), vrna_mfe_TwoD(), and vrna_fold_compound_free() instead!

Global destroy_TwoDpfold_variables (TwoDpfold_vars *vars)

Use the new API that relies on vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(), vrna_pf_TwoD(), and vrna_fold_compound_free() instead!

Global E_Stem (int type, int si1, int sj1, int extLoop, vrna_param_t *P)

Please use one of the functions vrna_E_ext_stem() and E_MLstem() instead! Use the former for cases where extLoop != 0 and the latter otherwise.

File energy_const.h

Use ViennaRNA/params/constants.h instead

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!

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!

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!

Global energy_of_circ_structure (const char *string, const char *structure, int verbosity_level)

Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!

Global energy_of_move (const char *string, const char *structure, int m1, int m2)

Use vrna_eval_move() instead!

Global energy_of_move_pt (short *pt, short *s, short *s1, int m1, int m2)

Use vrna_eval_move_pt() instead!

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!

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!

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!

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!

Global energy_of_structure (const char *string, const char *structure, int verbosity_level)

Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!

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!

File energy_par.h

Use ViennaRNA/params/default.h instead

Global exp_E_ExtLoop (int type, int si1, int sj1, vrna_exp_param_t *P)

Use vrna_exp_E_ext_stem() instead!

Global expHairpinEnergy (int u, int type, short si1, short sj1, const char *string)

Use exp_E_Hairpin() from loop_energies.h instead

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

Global export_ali_bppm (void)

Usage of this function is discouraged! The new vrna_fold_compound_t 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_pf(), or any of the old API calls for consensus structure partition function folding.

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_mfe() and vrna_fold_compound_t for the usage of the new API!

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_mfe() and vrna_fold_compound_t for the usage of the new API!

Global export_co_bppm (void)

This function is deprecated and will be removed soon! The base pair probability array is available through the vrna_fold_compound_t data structure, and its associated vrna_mx_pf_t member.

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 vrna_fold_compound_t. Thus, this function will only work in conjunction with a prior call to the deprecated functions cofold() or cofold_par()

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()

Global export_fold_arrays (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p)

See vrna_mfe() and vrna_fold_compound_t for the usage of the new API!

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_mfe() and vrna_fold_compound_t for the usage of the new API!

File exterior_loops.h

Use ViennaRNA/loops/external.h instead

File file_formats.h

Use ViennaRNA/io/file_formats.h instead

File file_formats_msa.h

Use ViennaRNA/io/file_formats_msa.h instead

File file_utils.h

Use ViennaRNA/io/utils.h instead

Global filecopy (FILE *from, FILE *to)

Use vrna_file_copy() instead!

Global find_saddle (const char *seq, const char *s1, const char *s2, int width)

Use vrna_path_findpath_saddle() instead!

File findpath.h

Use ViennaRNA/landscape/findpath.h instead

Global fold (const char *sequence, char *structure)

use vrna_fold(), or vrna_mfe() instead!

Global fold_par (const char *sequence, char *structure, vrna_param_t *parameters, int is_constrained, int is_circular)

use vrna_mfe() instead!

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_t is handled by vrna_fold_compound_free()

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!

Global free_arrays (void)

See vrna_fold(), vrna_circfold(), or vrna_mfe() and vrna_fold_compound_t for the usage of the new API!

Global free_co_arrays (void)

This function will only free memory allocated by a prior call of cofold() or cofold_par(). See vrna_mfe_dimer() for how to use the new API

Global free_co_pf_arrays (void)

This function will be removed for the new API soon! See vrna_pf_dimer(), vrna_fold_compound(), and vrna_fold_compound_free() for an alternative

Global free_path (vrna_path_t *path)

Use vrna_path_free() instead!

Global free_pf_arrays (void)

See vrna_fold_compound_t and its related functions for how to free memory occupied by the dynamic programming matrices

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, short **pscore)

It is discouraged to use this function! The new vrna_fold_compound_t allows direct access to all necessary consensus structure prediction related variables!

Global get_boltzmann_factor_copy (vrna_exp_param_t *parameters)

Use vrna_exp_params_copy() instead!

Global get_boltzmann_factors (double temperature, double betaScale, vrna_md_t md, double pf_scale)

Use vrna_exp_params() instead!

Global get_boltzmann_factors_ali (unsigned int n_seq, double temperature, double betaScale, vrna_md_t md, double pf_scale)

Use vrna_exp_params_comparative() instead!

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!

Global get_centroid_struct_pl (int length, double *dist, vrna_ep_t *pl)

This function was renamed to vrna_centroid_from_plist()

Global get_centroid_struct_pr (int length, double *dist, FLT_OR_DBL *pr)

This function was renamed to vrna_centroid_from_probs()

Global get_concentrations (double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc)

{ Use vrna_pf_dimer_concentrations() instead!}

Global get_line (FILE *fp)

Use vrna_read_line() as a substitute!

Global get_monomere_mfes (float *e1, float *e2)

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

Global get_mpi (char *Alseq[], int n_seq, int length, int *mini)

Use vrna_aln_mpi() as a replacement

Global get_path (const char *seq, const char *s1, const char *s2, int width)

Use vrna_path_findpath() instead!

Global get_plist (vrna_ep_t *pl, int length, double cut_off)

{ This function is deprecated and will be removed soon!} use assign_plist_from_pr() instead!

Global get_scaled_alipf_parameters (unsigned int n_seq)

Use vrna_exp_params_comparative() instead!

Global get_scaled_parameters (double temperature, vrna_md_t md)

Use vrna_params() instead!

Global get_scaled_pf_parameters (void)

Use vrna_exp_params() instead!

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_t and the corresponding functions vrna_fold_compound_TwoD(), vrna_mfe_TwoD(), and vrna_fold_compound_free() instead!

Global get_TwoDpfold_variables (const char *seq, const char *structure1, char *structure2, int circ)

Use the new API that relies on vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(), vrna_pf_TwoD(), and vrna_fold_compound_free() instead!

File hairpin_loops.h

Use ViennaRNA/loops/hairpin.h instead

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!}

Global hamming (const char *s1, const char *s2)

Use vrna_hamming_distance() instead!

Global hamming_bound (const char *s1, const char *s2, int n)

Use vrna_hamming_distance_bound() instead!

Global iindx

Do not use this variable anymore!

Global init_co_pf_fold (int length)

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

Global init_pf_fold (int length)

This function is obsolete and will be removed soon!

Global init_rand (void)

Use vrna_init_rand() instead!

Global initialize_cofold (int length)

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

Global initialize_fold (int length)

See vrna_mfe() and vrna_fold_compound_t for the usage of the new API!

Global int_urn (int from, int to)

Use vrna_int_urn() instead!

File interior_loops.h

Use ViennaRNA/loops/internal.h instead

Global Lfold (const char *string, const char *structure, int maxdist)

Use vrna_mfe_window() instead!

Global Lfoldz (const char *string, const char *structure, int maxdist, int zsc, double min_z)

Use vrna_mfe_window_zscore() instead!

File loop_energies.h

Use ViennaRNA/loops/all.h instead

Global loop_energy (short *ptable, short *s, short *s1, int i)

Use vrna_eval_loop_pt() instead!

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!}

Global Make_bp_profile (int length)

This function is deprecated and will be removed soon! See Make_bp_profile_bppm() for a replacement

Global make_pair_table (const char *structure)

Use vrna_ptable() instead

Global make_pair_table_snoop (const char *structure)

Use vrna_pt_snoop_get() instead!

Global make_referenceBP_array (short *reference_pt, unsigned int turn)

Use vrna_refBPcnt_matrix() instead

Global MEA (plist *p, char *structure, double gamma)

Use vrna_MEA() or vrna_MEA_from_plist() instead!

Global mean_bp_dist (int length)

This function is not threadsafe and should not be used anymore. Use mean_bp_distance() instead!

Global mean_bp_distance (int length)

Use vrna_mean_bp_distance() or vrna_mean_bp_distance_pr() instead!

Global mean_bp_distance_pr (int length, FLT_OR_DBL *pr)

Use vrna_mean_bp_distance() or vrna_mean_bp_distance_pr() instead!

File multibranch_loops.h

Use ViennaRNA/loops/multibranch.h instead

File naview.h

Use ViennaRNA/plotting/naview.h instead

Global naview_xy_coordinates (short *pair_table, float *X, float *Y)

Consider using vrna_plot_coords_naview_pt() instead!

Global nc_fact

See vrna_md_t.nc_fact, and vrna_mfe() to avoid using global variables

File neighbor.h

Use ViennaRNA/landscape/neighbor.h instead

Global nrerror (const char message[])

Use vrna_message_error() instead!

Global pack_structure (const char *struc)

Use vrna_db_pack() as a replacement

Global PAIR

Use vrna_basepair_t instead!

Global pair_info

Use vrna_pinfo_t instead!

File params.h

Use ViennaRNA/params/basic.h instead

Global paramT

Use vrna_param_t instead!

Global parenthesis_structure (char *structure, vrna_bp_stack_t *bp, int length)

use vrna_parenthesis_structure() instead

Global parenthesis_zuker (char *structure, vrna_bp_stack_t *bp, int length)

use vrna_parenthesis_zuker instead

Global path_t

Use vrna_path_t instead!

Global pbacktrack_circ (char *sequence)

Use vrna_pbacktrack() instead.

Global pf_circ_fold (const char *sequence, char *structure)

Use vrna_pf() instead!

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() instead

Global pf_paramT

Use vrna_exp_param_t instead!

Global plist

Use vrna_ep_t or vrna_elem_prob_s instead!

File plot_aln.h

Use ViennaRNA/plotting/alignments.h instead

File plot_layouts.h

Use ViennaRNA/plotting/layouts.h instead

File plot_structure.h

Use ViennaRNA/plotting/structures.h instead

File plot_utils.h

Use ViennaRNA/plotting/utils.h instead

Global pr

Do not use this variable anymore!

Global print_tty_constraint (unsigned int option)

Use vrna_message_constraints() instead!

Global print_tty_constraint_full (void)

Use vrna_message_constraint_options_all() instead!

Global print_tty_input_seq (void)

Use vrna_message_input_seq_simple() instead!

Global print_tty_input_seq_str (const char *s)

Use vrna_message_input_seq() instead!

Global PS_color_aln (const char *structure, const char *filename, const char *seqs[], const char *names[])

Use vrna_file_PS_aln() instead!

File PS_dot.h

Use ViennaRNA/plotting/probabilities.h instead

Global PS_dot_plot (char *string, char *file)

This function is deprecated and will be removed soon! Use PS_dot_plot_list() instead!

Global PS_rna_plot (char *string, char *structure, char *file)

Use vrna_file_PS_rnaplot() instead!

Global PS_rna_plot_a (char *string, char *structure, char *file, char *pre, char *post)

Use vrna_file_PS_rnaplot_a() instead!

Global PS_rna_plot_a_gquad (char *string, char *structure, char *ssfile, char *pre, char *post)

Use vrna_file_PS_rnaplot_a() instead!

Global random_string (int l, const char symbols[])

Use vrna_random_string() instead!

File read_epars.h

Use ViennaRNA/params/io.h instead

Global read_parameter_file (const char fname[])

Use vrna_params_load() instead!

Global read_record (char **header, char **sequence, char ***rest, unsigned int options)

This function is deprecated! Use vrna_file_fasta_read_record() as a replacment.

Global scale_parameters (void)

Use vrna_params() instead!

Global sect

Use vrna_sect_t instead!

Global set_model_details (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!

Global simple_circplot_coordinates (short *pair_table, float *x, float *y)

Consider switching to vrna_plot_coords_circular_pt() instead!

Global simple_xy_coordinates (short *pair_table, float *X, float *Y)

Consider switching to vrna_plot_coords_simple_pt() instead!

Global SOLUTION

Use vrna_subopt_solution_t instead!

Global space (unsigned size)

Use vrna_alloc() instead!

Global st_back

set the uniq_ML flag in vrna_md_t before passing it to vrna_fold_compound().

Global stackProb (double cutoff)

Use vrna_stack_prob() instead!

Global str_DNA2RNA (char *sequence)

Use vrna_seq_toRNA() instead!

Global str_uppercase (char *sequence)

Use vrna_seq_toupper() instead!

File stream_output.h

Use ViennaRNA/datastructures/stream_output.h instead

File string_utils.h

Use ViennaRNA/utils/strings.h instead

File structure_utils.h

Use ViennaRNA/utils/structures.h instead

File svm_utils.h

Use ViennaRNA/utils/svm.h instead

Global temperature

Use vrna_md_defaults_temperature(), and vrna_md_defaults_temperature_get() to change, and read the global default temperature settings

Global time_stamp (void)

Use vrna_time_stamp() instead!

Global TwoDfold_backtrack_f5 (unsigned int j, int k, int l, TwoDfold_vars *vars)

Use the new API that relies on vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(), vrna_mfe_TwoD(), vrna_backtrack5_TwoD(), and vrna_fold_compound_free() instead!

Global TwoDfold_vars

This data structure will be removed from the library soon! Use vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(), vrna_mfe_TwoD(), and vrna_fold_compound_free() instead!

Global TwoDfoldList (TwoDfold_vars *vars, int distance1, int distance2)

Use the new API that relies on vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(), vrna_mfe_TwoD(), and vrna_fold_compound_free() instead!

Global TwoDpfold_pbacktrack (TwoDpfold_vars *vars, int d1, int d2)

Use the new API that relies on vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(), vrna_pf_TwoD(), vrna_pbacktrack_TwoD(), and vrna_fold_compound_free() instead!

Global TwoDpfold_pbacktrack5 (TwoDpfold_vars *vars, int d1, int d2, unsigned int length)

Use the new API that relies on vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(), vrna_pf_TwoD(), vrna_pbacktrack5_TwoD(), and vrna_fold_compound_free() instead!

Class TwoDpfold_vars

This data structure will be removed from the library soon! Use vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(), vrna_pf_TwoD(), and vrna_fold_compound_free() instead!

Global TwoDpfoldList (TwoDpfold_vars *vars, int maxDistance1, int maxDistance2)

Use the new API that relies on vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(), vrna_pf_TwoD(), and vrna_fold_compound_free() instead!

Global unpack_structure (const char *packed)

Use vrna_db_unpack() as a replacement

Global update_alifold_params (void)

Usage of this function is discouraged! The new API uses vrna_fold_compound_t 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_t.

Global update_co_pf_params (int length)