Welcome to Topoly

Topoly is a Python package that collects programs useful for polymer topology analysis. We wanted to make it simple in use, but powerful at the same time.

We provide twofold tutorial for our package. In the first part all functions are briefly presented with explanation of idea how do they work. The second part is topoly_tutorial package with examples of Topoly package usage.

What you can do with Topoly?

  • Find knots, links, lassos, theta-curves, handcuffs and their type.

  • Calculate knot/link invariants:

    • Polynomials: Alexander, Jones, Conway, HOMFLY, Yamada, Kauffman, BLM/Ho,

    • Brackets: Kauffman, APS,

    • Other: writhe, Gaussian linking number.

  • Find minimal surface of a loop.

  • Simplify polymer structure preserving its topology.

  • Generate random polygon structures: walks, loops, lassos, handcuffs.

  • Generate knot map (like in KnotProt).

  • Calculate sum (U) and product (#) of knots.

  • Visualize structures.

Page contents

Indices and tables



All questions and remarks should be addressed to Joanna Sułkowska (jsulkowska AT cent.uw.edu.pl)