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| bulge_loop | Get bulge loops in a RNA secondary structure |
| compare | compare |
| ct2dot | ct2dot |
| hairpin_loop | hairpin_loop |
| internal_loop | Get Internal Loop |
| multi_branch_loop | multi_branch_loop |
| plot_bulge | plot_bulge |
| plot_hairpin | plot_hairpin |
| plot_internal_loop | plot_internal_loop |
| plot_multi_branch_loop | plot_multi_branch_loop |
| plot_stem | plot_stem |
| stem | stem |