A Python 3 library for building, manipulating, optimizing and designing molecules.
Clone or download
Pull request Compare This branch is even with lukasturcani:master.
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
docs
stk
tests
.gitignore
.nojekyll
license
readme.rst
requirements.txt
setup.py

readme.rst

Author: Lukas Turcani
docs/source/figures/stk.png

Requires Python 3.6.

This code was developed while doing my PhD in the Jelfs group, http://www.jelfs-group.org/.

Overview

stk is a Python library for building, manipulating, analyzing and automatic design of molecules, including a genetic algorithm. For more information, the documentation can be found at https://lukasturcani.github.io/stk/docs/build/html.

Installation

There are two ways to install stk. The first is easier, using pip. The second involves downloading the source code form GitHub. Using GitHub is the best way to get the most up-to-date code.

In both cases rdkit needs to be installed, see installing rdkit.

pip

In the terminal run

pip install stk

GitHub

Installation is simple and has two parts. First, installing stk, second, installing any libraries it requires.

installing stk

  1. Download stk from GitHub by clicking on the green "Clone or download" button and then on "Download ZIP".
  2. Extract the downloaded zip file.
  3. Using the terminal, go into the extracted directory and run:
python setup.py install
  1. stk should be installed, you can delete the downloaded and extracted folders.

installing dependencies

Apart from rdkit all dependcies of stk are listed in requirements.txt. rdkit cannot be installed via pip so it is listed separately.

rdkit

See installing rdkit.

others

All other requirements can be installed with pip.

pip install -r requirements.txt

installing rdkit

The simplest way to get rdkit is to use the Anaconda distribution of Python, which can be found on https://www.anaconda.com/download/. It comes with a lot of scientific libraries already installed and the conda package manager.

After installing Anaconda run

conda install -c rdkit rdkit

If you do not want to use Anaconda, the best place to look for advice on installing rdkit is https://github.com/rdkit/rdkit.

Publications

about stk

using stk