Topoly is a Python package that collects programs useful for polymer topology analysis.
Find knots, links, lassos, theta-curves, handcuffs and their type.
Calculate knot/link invariants:
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.
Apart from a Python library, this package provides a set of executable programs:
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/
Have a look at our website: https://topoly.cent.uw.edu.pl
or our tutorial project: https://github.com/ilbsm/topoly_tutorial
INTERDISCIPLINARY LABORATORY of BIOLOGICAL SYSTEMS MODELLING, University of Warsaw, Warsaw, Poland
FAQs
This package provides a set of tools for modeling protein knots, lassos and other.
We found that topoly demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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