RNAlib-2.1.8

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- a
- b
- c
- d
- e
- f
- g
- h
- i
- l
- m
- n
- p
- r
- s
- t
- u
- w
- x
- z

### - a -

- add_root() : RNAstruct.h
- alifold() : alifold.h
- aliLfold() : Lfold.h
- alimake_pair_table() : utils.h
- alipbacktrack() : alifold.h
- alipf_circ_fold() : alifold.h
- alipf_fold() : alifold.h
- alipf_fold_par() : alifold.h
- aliPS_color_aln() : PS_dot.h
- alloc_sequence_arrays() : alifold.h
- assign_plist_from_db() : fold.h
- assign_plist_from_pr() : part_func.h

### - b -

- b2C() : RNAstruct.h
- b2HIT() : RNAstruct.h
- b2Shapiro() : RNAstruct.h
- backtrack_GQuad_IntLoop() : gquad.h
- backtrack_GQuad_IntLoop_L() : gquad.h
- bppm_symbol() : part_func.h
- bppm_to_structure() : part_func.h

### - c -

- centroid() : part_func.h
- circalifold() : alifold.h
- circfold() : fold.h
- co_pf_fold() : part_func_co.h
- co_pf_fold_par() : part_func_co.h
- cofold() : cofold.h
- cofold_par() : cofold.h
- compute_probabilities() : part_func_co.h
- constrain_ptypes() : utils.h
- convert_parameter_file() : convert_epars.h
- copy_pair_table() : utils.h

### - d -

- destroy_TwoDfold_variables() : 2Dfold.h
- destroy_TwoDpfold_variables() : 2Dpfold.h

### - e -

- E_Hairpin() : loop_energies.h
- E_IntLoop() : loop_energies.h
- E_Stem() : loop_energies.h
- encode_ali_sequence() : alifold.h
- energy_of_alistruct() : alifold.h
- energy_of_circ_struct() : fold.h
- energy_of_circ_struct_par() : fold.h
- energy_of_circ_structure() : fold.h
- energy_of_move() : fold.h
- energy_of_move_pt() : fold.h
- energy_of_struct() : fold.h
- energy_of_struct_par() : fold.h
- energy_of_struct_pt() : fold.h
- energy_of_struct_pt_par() : fold.h
- energy_of_structure() : fold.h
- energy_of_structure_pt() : fold.h
- exp_E_Hairpin() : loop_energies.h
- exp_E_IntLoop() : loop_energies.h
- exp_E_Stem() : loop_energies.h
- expand_Full() : RNAstruct.h
- expand_Shapiro() : RNAstruct.h
- expHairpinEnergy() : part_func.h
- expLoopEnergy() : part_func.h
- export_ali_bppm() : alifold.h
- export_bppm() : part_func.h
- export_co_bppm() : part_func_co.h
- export_cofold_arrays() : cofold.h
- export_cofold_arrays_gq() : cofold.h

### - f -

- find_saddle() : findpath.h
- fold() : fold.h
- fold_par() : fold.h
- free_alifold_arrays() : alifold.h
- free_arrays() : fold.h
- free_co_arrays() : cofold.h
- free_co_pf_arrays() : part_func_co.h
- free_interact() : part_func_up.h
- free_path() : findpath.h
- free_pf_arrays() : part_func.h
- free_profile() : profiledist.h
- free_pu_contrib_struct() : part_func_up.h
- free_sequence_arrays() : alifold.h
- free_tree() : treedist.h

### - g -

- get_alipf_arrays() : alifold.h
- get_boltzmann_factor_copy() : params.h
- get_boltzmann_factors() : params.h
- get_boltzmann_factors_ali() : params.h
- get_centroid_struct_pl() : part_func.h
- get_centroid_struct_pr() : part_func.h
- get_concentrations() : part_func_co.h
- get_gquad_matrix() : gquad.h
- get_iindx() : utils.h
- get_indx() : utils.h
- get_input_line() : utils.h
- get_line() : utils.h
- get_monomere_mfes() : cofold.h
- get_mpi() : alifold.h
- get_path() : findpath.h
- get_pf_arrays() : part_func.h
- get_plist() : part_func_co.h
- get_scaled_alipf_parameters() : params.h
- get_scaled_parameters() : params.h
- get_scaled_pf_parameters() : params.h
- get_subseq_F() : part_func.h
- get_TwoDfold_variables() : 2Dfold.h
- get_TwoDpfold_variables() : 2Dpfold.h
- get_TwoDpfold_variables_from_MFE() : 2Dpfold.h
- gmlRNA() : PS_dot.h

### - h -

- HairpinE() : fold.h
- hamming() : utils.h
- hamming_bound() : utils.h

### - i -

- init_co_pf_fold() : part_func_co.h
- init_pf_fold() : part_func.h
- init_pf_foldLP() : LPfold.h
- init_rand() : utils.h
- initialize_cofold() : cofold.h
- initialize_fold() : fold.h
- int_urn() : utils.h
- inverse_fold() : inverse.h
- inverse_pf_fold() : inverse.h

### - l -

- Lfold() : Lfold.h
- Lfoldz() : Lfold.h
- loop_energy() : fold.h
- LoopEnergy() : fold.h

### - m -

- Make_bp_profile() : profiledist.h
- Make_bp_profile_bppm() : profiledist.h
- make_loop_index_pt() : utils.h
- make_pair_table() : utils.h
- make_pair_table_snoop() : utils.h
- Make_swString() : stringdist.h
- make_tree() : treedist.h
- MEA() : MEA.h
- mean_bp_dist() : part_func.h
- mean_bp_distance() : part_func.h
- mean_bp_distance_pr() : part_func.h

### - n -

- nrerror() : utils.h

### - p -

- pack_structure() : utils.h
- parenthesis_structure() : fold.h
- parenthesis_zuker() : fold.h
- parse_gquad() : gquad.h
- parse_structure() : RNAstruct.h
- pbacktrack() : part_func.h
- pbacktrack_circ() : part_func.h
- pf_circ_fold() : part_func.h
- pf_fold() : part_func.h
- pf_fold_par() : part_func.h
- pf_interact() : part_func_up.h
- pf_unstru() : part_func_up.h
- pfl_fold() : LPfold.h
- pfl_fold_par() : LPfold.h
- print_bppm() : profiledist.h
- print_tree() : treedist.h
- print_tty_constraint() : utils.h
- print_tty_constraint_full() : utils.h
- print_tty_input_seq() : utils.h
- print_tty_input_seq_str() : utils.h
- profile_edit_distance() : profiledist.h
- PS_dot_plot() : PS_dot.h
- PS_dot_plot_list() : PS_dot.h
- PS_rna_plot() : PS_dot.h
- PS_rna_plot_a() : PS_dot.h
- putoutpU_prob() : LPfold.h
- putoutpU_prob_bin() : LPfold.h

### - r -

- random_string() : utils.h
- read_parameter_file() : read_epars.h
- read_record() : utils.h
- readribosum() : alifold.h

### - s -

- scale_parameters() : params.h
- set_model_details() : fold_vars.h
- simple_circplot_coordinates() : plot_layouts.h
- simple_xy_coordinates() : plot_layouts.h
- space() : utils.h
- ssv_rna_plot() : PS_dot.h
- str_DNA2RNA() : utils.h
- str_uppercase() : utils.h
- string_edit_distance() : stringdist.h
- subopt() : subopt.h
- subopt_circ() : subopt.h
- subopt_par() : subopt.h
- svg_rna_plot() : PS_dot.h

### - t -

- time_stamp() : utils.h
- tree_edit_distance() : treedist.h
- TwoDfold_backtrack_f5() : 2Dfold.h
- TwoDfoldList() : 2Dfold.h
- TwoDpfold_pbacktrack() : 2Dpfold.h
- TwoDpfold_pbacktrack5() : 2Dpfold.h
- TwoDpfoldList() : 2Dpfold.h

### - u -

- unexpand_aligned_F() : RNAstruct.h
- unexpand_Full() : RNAstruct.h
- unpack_structure() : utils.h
- unweight() : RNAstruct.h
- update_alifold_params() : alifold.h
- update_co_pf_params() : part_func_co.h
- update_co_pf_params_par() : part_func_co.h
- update_cofold_params() : cofold.h
- update_fold_params() : fold.h
- update_pf_params() : part_func.h
- update_pf_params_par() : part_func.h
- update_pf_paramsLP() : LPfold.h
- urn() : utils.h

### - w -

- warn_user() : utils.h
- write_parameter_file() : read_epars.h

### - x -

- xrealloc() : utils.h
- xrna_plot() : PS_dot.h

### - z -

- zukersubopt() : cofold.h
- zukersubopt_par() : cofold.h