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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

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/

Project details


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Files for topoly, version 0.9.13
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Filename, size topoly-0.9.13-cp35-cp35m-manylinux2010_x86_64.whl (5.7 MB) File type Wheel Python version cp35 Upload date Hashes View
Filename, size topoly-0.9.13-cp36-cp36m-macosx_10_9_intel.whl (3.0 MB) File type Wheel Python version cp36 Upload date Hashes View
Filename, size topoly-0.9.13-cp36-cp36m-manylinux2010_x86_64.whl (5.7 MB) File type Wheel Python version cp36 Upload date Hashes View
Filename, size topoly-0.9.13-cp37-cp37m-macosx_10_9_intel.whl (3.0 MB) File type Wheel Python version cp37 Upload date Hashes View
Filename, size topoly-0.9.13-cp37-cp37m-manylinux2010_x86_64.whl (5.7 MB) File type Wheel Python version cp37 Upload date Hashes View
Filename, size topoly-0.9.13-cp38-cp38-macosx_10_9_intel.whl (3.0 MB) File type Wheel Python version cp38 Upload date Hashes View
Filename, size topoly-0.9.13-cp38-cp38-manylinux2010_x86_64.whl (6.0 MB) File type Wheel Python version cp38 Upload date Hashes View
Filename, size topoly-0.9.13-cp39-cp39-macosx_10_9_intel.whl (3.0 MB) File type Wheel Python version cp39 Upload date Hashes View
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