topoly 1.0.4

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

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

Installation

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:

$HOME/.local/

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: https://topoly.cent.uw.edu.pl

or our tutorial project: https://github.com/ilbsm/topoly_tutorial

Contact

INTERDISCIPLINARY LABORATORY of BIOLOGICAL SYSTEMS MODELLING, University of Warsaw, Warsaw, Poland

https://jsulkowska.cent.uw.edu.pl/