topoly 0.1.7

This package provides a set of tools for modeling protein knots, lassos and other.

# 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.

1. knotnet

2. homflylink

3. surfacesmytraj

4. ncuclinks

5. lmpoly

6. gln

## Requirements 1. Python 3 (3.5 or later) 2. NumPy 3. Matplotlib 4. Boost 1.50 or later

## 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:

https://github.com/ilbsm/topoly_test