This package provides a set of tools for modeling protein knots, lassos and other.
Project description
# Topoly
Protein knots and lassos search tools from the INTERDISCIPLINARY LABORATORY of BIOLOGICAL SYSTEMS MODELLING, University of Warsaw, Warsaw, Poland
This package provides a set of executable programs as well as a shared library with a Python 3 wrapper.
knotnet
homflylink
surfacesmytraj
ncuclinks
lmpoly
gln
## Requirements 1. Python 3 (3.5 or later) 2. NumPy 3. Matplotlib
## Installation as python PIP package
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/
Please note that after the installation it is necessary to add the folder that contains libraries
## Installation as DEB, RPM, ZIP
Topoly is also distributed as a DEB, RPM and ZIP package.
DEB and RPM packages install the package to /usr, so binaries should be found in /usr/bin, libraries in /usr/lib and the documentation in /usr/share/doc
If you choose to install Topoly from a ZIP package please make sure that the libraries from the lib subfolder are placed in a folder that is listed in the LD_LIBRARY_PATH.
The Python wrappers are built as module extensions and therefore they require that the lib subfolder should be added to your PYTHONPATH variable.
## Testing
To verify that the topoly is correctly installed please run the runtests.sh script located in share/doc/topoly/test. (/usr/share/doc/topoly/test if installed from RPM or DEB)
## Using Topoly
Please have a look at the tests in share/doc/topoly/test to see usage examples. or have a look at our test project:
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