chemphy / stk Goto Github PK

Requires Python 3.6.

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

stk is a Python library for building, manipulating, optimizing and designing molecules. For more information, the documentation can be found at https://lukasturcani.github.io/stk/docs/build/html.

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.

In the terminal run

pip install stk

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

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

4. stk should be installed, you can delete the downloaded and extracted folders.

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

See installing rdkit.

All other requirements can be installed with pip.

pip install -r requirements.txt

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.

https://chemrxiv.org/articles/STK_A_Python_Toolkit_for_Supramolecular_Assembly/6127826