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-0.9.5-cp38-cp38m-manylinux2010_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 285ac62806e5c6f99016c57694654dbde981bca7ad70bb701b7a5d2919162e19 |
|
MD5 | 1dcc01359518c65309ff9e61313b7e52 |
|
BLAKE2b-256 | d3615f904e0bcdba3716272857d504d148ce2cc388cd743414b0262a4e5fa160 |
Hashes for topoly-0.9.5-cp38-cp38m-macosx_10_9_intel.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8128f31807d77017d9773d0b22af82898bafd49a5c4e50c15e82e6fa2755feb0 |
|
MD5 | e965c2fc7d9d651f7b53ce93d042ae2d |
|
BLAKE2b-256 | 2d21f768eabc0413d024f44b4d0e99c50492f059c4c9543a48e005146a318991 |
Hashes for topoly-0.9.5-cp37-cp37m-manylinux2010_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | c9c3c9ed2111e49172ab50e640e40a1a89aa0ccb2e82f2e4a2f1414d6dfb3782 |
|
MD5 | 89dd5edf499b0d7ede1ef25bfe7bc524 |
|
BLAKE2b-256 | fd4c3583bb041f5471870e4a7f86beb102a6ee46a871994ff31fc7671d58fd3f |
Hashes for topoly-0.9.5-cp37-cp37m-macosx_10_9_intel.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 7e5b60ece021c22400e16f5f6c5321c6b281c692df462611884cb19107052ac7 |
|
MD5 | 0d3a99d7b452da2541ed5e5b06728a26 |
|
BLAKE2b-256 | 364171b837e113c0cf3d8b17a11f087685c311b0bc0eb89137dca482ed0a21cc |
Hashes for topoly-0.9.5-cp36-cp36m-manylinux2010_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | e54753878c3207f1d464b6c44de53385ddb63edc9bcc37f1b2b79731e32c98c8 |
|
MD5 | 8fd18b995b5895b4377aeb85e0f1082b |
|
BLAKE2b-256 | 7015ff0843ec34be9b4465a448d0eefc070782c3280c616910e036c893d5b2d2 |
Hashes for topoly-0.9.5-cp36-cp36m-macosx_10_9_intel.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 759bd7f93556af8059d8a22e4b26e68c759523f7e2d0ad1012d002d9645071f3 |
|
MD5 | 079d66331aa1241892cf162db28a82bd |
|
BLAKE2b-256 | b8242f2522e9b673fd1b103e1f2be2e3067d0c5c9fabb040d104bdc696450ddd |
Hashes for topoly-0.9.5-cp35-cp35m-manylinux2010_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 0af95102d3c6d5c56f8198cc0f777cddc5eab273edc277dd8d035c1d6fcf4148 |
|
MD5 | dc641dec44929565b3fa502d92e4c736 |
|
BLAKE2b-256 | fd0a25219225390d53a4f34219a2b244f09699f04e93d9e0c1e96e7db0426b30 |
Hashes for topoly-0.9.5-cp35-cp35m-macosx_10_9_intel.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 3c05ab827242dcfd73714857f3c25947c413327ed28764fb6da32984e5ad92a7 |
|
MD5 | afdd377ea0e47c928776455a4b2e0f74 |
|
BLAKE2b-256 | 063f6a7018895088243712750f60c0a6c5eea43123a70ed8a7efc3e05d48d8b2 |