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 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 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_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. |
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 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! |
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_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_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_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! |
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_ep_t or vrna_elem_prob_s 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 |