skills/bioskills/bio-rna-structure-secondary-structure-prediction/scripts/rnafold_analysis.py

• fold_ensemble · function · L15-L29 — def fold_ensemble(sequence)
• positional_confidence · function · L32-L37 — def positional_confidence(sequence)
• get_bpp_matrix · function · L40-L51 — def get_bpp_matrix(sequence)
• plot_bpp_dotplot · function · L54-L70 — def plot_bpp_dotplot(sequence, output_file='bpp_dotplot.png')
• fold_with_constraints · function · L73-L80 — def fold_with_constraints(sequence, forced_unpaired=None, forced_pairs=None)
• fold_with_shape · function · L83-L92 — def fold_with_shape(sequence, reactivities, m=1.8, b=-0.6)