### - a -

- aligned_line : dist_vars.h

### - b -

- backtrack_type : fold_vars.h
- base_pair : fold_vars.h

### - c -

- canonicalBPonly : fold_vars.h
- circ : fold_vars.h
- cost_matrix : dist_vars.h
- csv : fold_vars.h
- cut_point : fold.h , fold_vars.h
- cv_fact : alifold.h

### - d -

- dangles : fold_vars.h
- density_of_states : subopt.h
- do_backtrack : fold_vars.h

### - e -

- edit_backtrack : dist_vars.h
- energy_set : fold_vars.h
- eos_debug : fold.h

### - f -

- F_monomer : part_func_co.h
- final_cost : inverse.h
- fold_constrained : fold_vars.h

### - g -

- give_up : inverse.h
- gquad : fold_vars.h

### - h -

- helix_size : RNAstruct.h

### - i -

- iindx : fold_vars.h
- inv_verbose : inverse.h

### - j -

- james_rule : fold_vars.h

### - l -

- logML : fold.h , fold_vars.h
- loop_degree : RNAstruct.h
- loop_size : RNAstruct.h
- loops : RNAstruct.h

### - m -

- mirnatog : part_func_co.h

### - n -

- nc_fact : alifold.h
- no_closingGU : fold_vars.h
- noGU : fold_vars.h
- noLonelyPairs : fold_vars.h
- nonstandards : fold_vars.h

### - o -

- oldAliEn : fold_vars.h

### - p -

- pairs : RNAstruct.h
- pf_scale : fold_vars.h
- pr : fold_vars.h
- print_energy : subopt.h

### - r -

- ribo : fold_vars.h
- RibosumFile : fold_vars.h
- rna_plot_type : plot_layouts.h

### - s -

- st_back : part_func.h
- subopt_sorted : subopt.h
- symbolset : inverse.h

### - t -

- temperature : fold_vars.h
- tetra_loop : fold_vars.h

### - u -

- uniq_ML : fold.h
- unpaired : RNAstruct.h

### - x -

- xsubi : utils.h