stko

:maintainers: andrewtarzia <https://github.com/andrewtarzia/>, lukasturcani <https://github.com/lukasturcani/> :documentation: https://stko-docs.readthedocs.io :discord: https://discord.gg/zbCUzuxe2B

.. figure:: docs/source/_static/stko.png

.. image:: https://readthedocs.org/projects/stko-docs/badge/?version=latest :target: https://stko-docs.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status

Overview

stko is a Python library which allows for the optimisation and property calculation of molecules constructed using the library stk https://github.com/lukasturcani/stk. There is a Discord server for stk, which can be joined through https://discord.gg/zbCUzuxe2B.

Installation

To get stko, you can install it with pip:

.. code-block:: bash

pip install stko

Some optional dependencies are only available through conda:

.. code-block:: bash

for OpenMM and espaloma charge

note the temporary issue with rdkit versions and conda will overwrite pip

installed software

mamba install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge

for xtb

mamba install xtb

for openbabel

mamba install openbabel

for mdanalysis

mamba install mdanalysis

Examples

We are constantly trying to add examples to the examples/ directory and maintain examples in the doc strings of Calculator and Optimizer classes.

examples/basic_examples.py highlights basic optimisation with rdkit, openbabel and xtb (if you have xtb available).

How To Contribute

If you have any questions or find problems with the code, please submit an issue.

If you wish to add your own code to this repository, please send us a Pull Request. Please maintain the testing and style that is used throughout ```stko``.

How To Cite

If you use stko please cite

https://github.com/JelfsMaterialsGroup/stko

Acknowledgements

We developed this code when working in the Jelfs group, http://www.jelfs-group.org/, whose members often provide very valuable feedback, which we gratefully acknowledge.