- 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_plist_t **pl)
- Use vrna_pf() instead
- Global alipf_fold (const char **sequences, char *structure, vrna_plist_t **pl)
- Use vrna_pf() instead
- Global alipf_fold_par (const char **sequences, char *structure, vrna_plist_t **pl, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained, int is_circular)
- Use vrna_pf() instead
- Global assign_plist_from_db (vrna_plist_t **pl, const char *struc, float pr)
- Use vrna_plist() instead
- Global assign_plist_from_pr (vrna_plist_t **pl, FLT_OR_DBL *probs, int length, double cutoff)
- Use vrna_plist_from_probs() instead!
- 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!
- 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_plist_t *prAB, vrna_plist_t *prA, vrna_plist_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.
- 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
- 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 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!
- 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!
- Global filecopy (FILE *from, FILE *to)
- Use vrna_file_copy() 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_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_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_plist_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_plist (vrna_plist_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!
- 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!
- Global Lfold (const char *string, char *structure, int maxdist)
- Use vrna_mfe_window() instead!
- Global Lfoldz (const char *string, char *structure, int maxdist, int zsc, double min_z)
- Use vrna_mfe_window_zscore() 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 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!
- Global nc_fact
- See vrna_md_t.nc_fact, and vrna_mfe() to avoid using global variables
- 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!
- 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_plist_t 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_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!
- 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 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!
- 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)
- 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!
- 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!
- 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 warn_user (const char message[])
- Use vrna_message_warning() instead!
- Global xrealloc (void *p, unsigned size)
- Use vrna_realloc() instead!
- Global zukersubopt (const char *string)
- use vrna_zukersubopt() instead
- Global zukersubopt_par (const char *string, vrna_param_t *parameters)
- use vrna_zukersubopt() instead