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:
- knotnet - find knots using the Alexander Polynomial
- homflylink
- surfacesmytraj
- ncuclinks
- lmpoly
- 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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distributions
Built Distributions
Hashes for topoly-0.9.10-cp39-cp39m-macosx_10_9_intel.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 974ce7674ecda6ff14cde7e22d1a46344e66209910ff3a5d89a5418b30f8430a |
|
MD5 | e10f2aa8b6fc42b924ad79a2964ff82e |
|
BLAKE2b-256 | 30649c4b64a8cfbea855b20cd4ade11765281fe2f480308e43171d9da3573978 |
Hashes for topoly-0.9.10-cp39-cp39-manylinux2010_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 4d1ebcb430d094eb6a7c973e01a04dbfd69c64322131fabcdfadb8a66ba104dc |
|
MD5 | 4219478d8259f88ededf84a30ba12a9c |
|
BLAKE2b-256 | 77680a41116b072222e3aa1a44dc33fdd5994c32fe36ede95736f270bf7b8347 |
Hashes for topoly-0.9.10-cp38-cp38-manylinux2010_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 1dd70d5a2a663b15a1a560a82cd23b3cf72f452d73920dd30fe54866590f28b0 |
|
MD5 | 07dd375d1c6ab9661c16128f22051a08 |
|
BLAKE2b-256 | e495f88a281fc9e292f8209c909931231ac6858de38018bcc410d200218c0a06 |
Hashes for topoly-0.9.10-cp38-cp38-macosx_10_9_intel.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 55ba368e85c992d13d1ba1113d25d4e7365d9f93d3c4619edc4ffd24c47c90b9 |
|
MD5 | b2ef26db0d3a481f43c9fc06d382265d |
|
BLAKE2b-256 | 863953b4e51135d76b6be93ea808354742c429ece429078e977d7cce36d85f69 |
Hashes for topoly-0.9.10-cp37-cp37m-manylinux2010_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | a5dd9128748b585b17701f0b4e28946b631811338d9bafd9a220b9d9658a6651 |
|
MD5 | cee84eb3207c6ee1b1de03607b32001a |
|
BLAKE2b-256 | 6126ede27955bf52802766d77484621bc3d2eae4d9f52d6825e489e99c49751f |
Hashes for topoly-0.9.10-cp37-cp37m-macosx_10_9_intel.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 2d08d8074d4517276086f5f7d4427c3a83768fddc485ae05ad123c9051b73c8b |
|
MD5 | 85d334796c9536ae0413007d2126d78a |
|
BLAKE2b-256 | 4d3ac0e58daa85f6b082b426c90f9838b37b7fbab82ae811fca7d8c8f7cb48dd |
Hashes for topoly-0.9.10-cp36-cp36m-manylinux2010_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | fa295b42db977b99ea8bcb488643d82f2426ef62e2eb3d11fba4cac54cc12057 |
|
MD5 | 142dc3f1147343d0a02b591b650c93a6 |
|
BLAKE2b-256 | 8989b3dcb5b499b79eecdcdaa0043757f9af1faa9f3b47b9ceba3f4f41b11428 |
Hashes for topoly-0.9.10-cp36-cp36m-macosx_10_9_intel.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 44be23f42fc5097f16c55a70e494241c747c2e0f592e0aa3b21a707040f07a89 |
|
MD5 | 67d19475799d3ad52ab5423d5b53e5db |
|
BLAKE2b-256 | 631baea897cfd6f51db464cd66d640944ec0fcaffd7866f2b0b636b458bebe9a |
Hashes for topoly-0.9.10-cp35-cp35m-manylinux2010_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 69533482974a51596a749ad52e9e990c73feaa8ac0c9504e64c13fd1de7d1b45 |
|
MD5 | 778ed16809a5fdaedfdf018a116277c2 |
|
BLAKE2b-256 | 7ed36db764ffe587a5aa11f962c6177b0c12ca520243f081f73b255f200e69c2 |