pyFuRNAce

Contents:

  • About pyFuRNAce
    • Web Application
      • Modules
    • Python API
    • Citation
    • License
    • Acknowledgements
  • Install and run
  • Python API Reference
    • What’s the idea?
    • Design Core Objects
      • Strand
        • Strand
        • StrandsBlock
      • Motif
      • Origami
      • Sequence
      • Basepair
      • Common Variables
        • Useful collections
        • Translators for strings characters
      • Common functions
        • AmbiguosStructure
        • MotifStructureError
        • base_pair_difference()
        • base_pair_distance()
        • complement()
        • dot_bracket_to_pair_map()
        • dot_bracket_to_stacks()
        • dot_bracket_to_tree()
        • folding_barriers()
        • gc_content()
        • hamming_distance()
        • mutate_nucleotide()
        • pair_map_to_dot_bracket()
        • pair_nucleotide()
        • reverse_complement()
        • rotate_dot_bracket()
        • tree_to_dot_bracket()
    • Motifs
      • Stem
        • Stem
      • Dovetail
        • Dovetail
      • Loops
        • Loop
        • TetraLoop
      • Kissing loops
        • BranchedDimer
        • BranchedKissingLoop
        • KissingDimer
        • KissingDimer120
        • KissingLoop
        • KissingLoop120
        • KissingLoop180
      • Aptamers
        • Aptamer
        • Biotin()
        • Broccoli()
        • Ispinach()
        • L7Ae()
        • MS2()
        • MalachiteGreen()
        • MalachiteGreenShort()
        • Mango()
        • OrangeBroccoli()
        • PIP3()
        • PIP3_mut1()
        • PIP3_mut3()
        • PIP3_mut5()
        • PP7()
        • Pepper()
        • RedBroccoli()
        • Streptavidin()
        • TAR_TAT()
        • Thrombin_exosite1()
        • Thrombin_exosite2()
        • create_aptamer()
    • Utilities
      • Motif Utilities
        • Utils
        • single_strand()
        • start_end_stem()
        • stem_cap_link()
        • vertical_double_link()
        • vertical_link()
      • Origami Utilities
        • convert_angles_to_dt()
        • ipython_clickable_txt()
        • ipython_display_3d()
        • ipython_display_txt()
        • log_norm()
        • simple_origami()
        • template_2_helix()
        • template_3_arms_droplet()
        • template_4_arms_droplet()
        • template_pentagon_tile()
        • template_rectangle_10H_3X()
        • template_rna_filament()
        • template_rna_filament_ispinach()
    • Sequence Generation
      • generate_road()
      • parallel_road()
    • Prepare
      • Primers
        • annealing_temp()
        • auto_design_primers()
        • calculate_gc()
        • check_dimer()
        • make_tm_calculator()
      • Oxdna simulation setup
        • oxdna_simulations()
  • Limitations & Workarounds
    • PyFuRNAce folding barrier estimation
    • Revolvr
    • ViennaRNA
    • oxDNA Analysis Tools
    • References
  • Tutorials
    • Graphical User Interface Examples
      • Including a custom aptamer
        • 1) Import the tRNA-aptamer sequence
        • 2) Isolate the aptamer motif
        • 3) Optional: Add 3D structure
        • 4) Python code
      • Custom motif: origami with single-stranded region
        • 1) Create an origami with two stems
        • 2) Custom motif creation
        • 3) Complete the structure
        • 4) Equivalent Code
      • Adding an overhang at the 5’ or 3’ end
        • 1) Create an origami
        • 2) Add a line and a connection
        • 3) Create and add the single-stranded motif
        • 4) Connect the single-stranded motif
    • Python Scripting Examples
      • Two helices with FLAPs (and optimization)
      • RNA filament
      • Folding barrier optimization
        • Full optimisation
    • Jupyter Notebooks
      • RNA droplets
        • Droplet A with Malachite Green aptamer
        • Droplet B with Broccoli aptamer
      • RNA filaments assembly tutorial
        • Create a basic RNA structure
        • Adjust the ends to make a tile
        • Repeat the tiles to make a filament section
        • Repeat the sections to make a filament
        • Generete the sequence for a tile
      • A collection of origami from ROAD
        • 3H-2DT
        • 3H-3DT
        • 3H-4DT
pyFuRNAce
  • Overview: module code

All modules for which code is available

  • pyfurnace.design.core.basepair
  • pyfurnace.design.core.motif
  • pyfurnace.design.core.origami
  • pyfurnace.design.core.sequence
  • pyfurnace.design.core.strand
  • pyfurnace.design.core.symbols
  • pyfurnace.design.motifs.aptamers
  • pyfurnace.design.motifs.dovetail
  • pyfurnace.design.motifs.kissing_loops
  • pyfurnace.design.motifs.loops
  • pyfurnace.design.motifs.stem
  • pyfurnace.design.utils.motif_lib
  • pyfurnace.design.utils.origami_lib
  • pyfurnace.generate.road
  • pyfurnace.prepare.oxdna_sim
  • pyfurnace.prepare.utils

© Copyright 2025, Luca Monari.

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