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This package provides a set of tools for modeling protein knots, lassos and other.

Project description

Topoly is a Python package that collects programs useful for polymer topology analysis.

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.

Provided executable programs

Apart from a Python library, this package provides a set of executable programs:

  1. knotnet - find knots using the Alexander Polynomial
  2. homflylink
  3. surfacesmytraj
  4. ncuclinks
  5. lmpoly
  6. gln - compute the Gaussian linking number


Make sure you have a recent version of pip. You can upgrade it by running:

pip3 install --upgrade pip

Install Topoly using the standard python package installer PIP:

pip3 install topoly

Topoly can be installed without administrative privileges in the home folder of a particular user or in a Python Virtual Environment. In that case all files (binaries, documentation, libraries and python modules) will be installed in:


or venv/ respectively.

If you choose to install Topoly with administrative privileges then everything will be installed in: /usr/local/

Using Topoly

Have a look at our website:

or our tutorial project:



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