topoly 0.4.0

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

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