joshkamm / stko

A collection of molecular optimisers and property calculators for use with stk.

Author:	Steven Bennett, Andrew Tarzia, Lukas Turcani
Documentation:	https://stko-docs.readthedocs.io

Contains molecular optimizers and property calculators for use with stk, https://github.com/lukasturcani/stk.

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.

Installation

To get stko, you can install it with pip:

$ pip install stko

Make sure you also install rdkit, which is a dependency:

$ conda install -c conda-forge rdkit

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 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 I gratefully acknowledge.

stko's Issues

Transferring torsions from building blocks

ConstructedMoleculeTorsioned should have a way to automatically set its torsions to those which correspond to the torsions of its constituent building blocks.

def transfer_torsions(self, building_block_map):
    """
    building_block_map is a map from each building block of this molecule
    to a ConstructedMoleculeTorsioned which contains its torsions
    """

Additionally, ConstructedMoleculeTorsioned will need a way to explicitly set the torsions of a base building block:

def set_torsions(self, torsions):
    'sets the torsions'