ProTopo is a lightweight Python package for drawing 2D protein topology diagrams — including α-helices, β-strands, linkers, N/C-terminals, and customizable markers.
It helps visualize and annotate simplified protein secondary structure layouts for publications, teaching, or design explanation.
GitHub repo | Issue page | Author
- Simple, declarative interface (
add_alpha,add_beta,add_linker) - Tracks residue indices and directions automatically
- Custom triangle/marker support (for cuts, domains, etc.)
- Outputs high-quality vector graphics via Matplotlib
- Built-in EGFP topology example
pip install protopo
# or if developing locally
poetry installfrom protopo import ProTopo
pt = ProTopo()
pt.add_n_term()
pt.add_alpha(1, 10, label="H1", to="→")
pt.add_linker(10, 13, to="↓→", steps=(0.5, 0.5))
pt.add_beta(13, 22, label="S1", to="→")
pt.add_triangles([15])
pt.add_c_term()
pt.show()
# pt.save("demo.pdf") # save fig
# pt.close() # release memory
This renders the schematic topology diagram of Enhanced GFP, following literature-reported secondary structure layout.
from protopo.demo import draw_egfp
egfp = draw_egfp()
egfp.add_triangles(idx=[6, 211])
egfp.show()
# egfp.save("egfp.svg")
# egfp.close() # release memorythen you will see
poetry run pytestMIT License © Huanan Herman Zhao
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