Deprecated List

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_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/naview.h 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! (since v2.3.0)

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! (since v2.2.0)

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!

Class 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!

File units.h: Use ViennaRNA/utils/units.h 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): Use vrna_exp_params_subst() instead!

Global update_co_pf_params_par (int length, vrna_exp_param_t *parameters): Use vrna_exp_params_subst() instead!

Global update_cofold_params (void): See vrna_params_subst() for an alternative using the new API

Global update_cofold_params_par (vrna_param_t *parameters): See vrna_params_subst() for an alternative using the new API

Global update_fold_params (void): For non-default model settings use the new API with vrna_params_subst() and vrna_mfe() instead!

Global update_fold_params_par (vrna_param_t *parameters): For non-default model settings use the new API with vrna_params_subst() and vrna_mfe() instead!

Global update_pf_params (int length): Use vrna_exp_params_subst() instead

Global update_pf_params_par (int length, vrna_exp_param_t *parameters): Use vrna_exp_params_subst() instead

Global urn (void): Use vrna_urn() instead!

File utils.h

Use ViennaRNA/utils/basic.h instead

Global vrna_callback_free_auxdata (void *data): Use vrna_auxdata_free_f(void *data) instead!

Global vrna_cofold (const char *sequence, char *structure): This function is obsolete since vrna_mfe()/vrna_fold() can handle complexes multiple sequences since v2.5.0. Use vrna_mfe()/vrna_fold() for connected component MFE instead and compute MFEs of unconnected states separately.

Global VRNA_CONSTRAINT_FILE: Use 0 instead!

Global VRNA_CONSTRAINT_MULTILINE: see vrna_extract_record_rest_structure()

Global VRNA_CONSTRAINT_NO_HEADER: This mode is not supported anymore!

Global VRNA_CONSTRAINT_SOFT_MFE: This flag has no meaning anymore, since constraints are now always stored! (since v2.2.6)

Global VRNA_CONSTRAINT_SOFT_PF: Use VRNA_OPTION_PF instead!

Global vrna_exp_param_s::id: This attribute will be removed in version 3

Global vrna_extract_record_rest_constraint (char **cstruc, const char **lines, unsigned int option): Use vrna_extract_record_rest_structure() instead!

Global vrna_fc_s::pscore_pf_compat: This attribute will vanish in the future!

Global vrna_fc_s::ptype_pf_compat: This attribute will vanish in the future! It’s meant for backward compatibility only!

Global vrna_mfe_dimer (vrna_fold_compound_t *fc, char *structure): This function is obsolete since vrna_mfe() can handle complexes multiple sequences since v2.5.0. Use vrna_mfe() for connected component MFE instead and compute MFEs of unconnected states separately.

File walk.h: Use ViennaRNA/landscape/walk.h instead

Global warn_user (const char message[]): Use vrna_message_warning() instead! (since v2.3.0)

Global write_parameter_file (const char fname[]): Use vrna_params_save() instead!

Global xrealloc (void *p, unsigned size): Use vrna_realloc() instead! (since v2.2.0)

Global zukersubopt (const char *string): use vrna_zukersubopt() instead

Global zukersubopt_par (const char *string, vrna_param_t *parameters): use vrna_zukersubopt() instead