| maintainers: | andrewtarzia, lukasturcani |
|---|---|
| documentation: | https://stko-docs.readthedocs.io |
| discord: | https://discord.gg/zbCUzuxe2B |
stko is a Python library for
performing optimizations and calculations on complex molecules built using
stk. In the case of
optimizations, a clone of stk.Molecule is returned. For
calculators, a Results class are used to calculate and extract
properties of an stk.Molecule. There is a Discord server
for stk, which can be joined through https://discord.gg/zbCUzuxe2B.
To get stko, you can install it with pip:
pip install stkoSome optional dependencies are only available through conda:
# for xtb
mamba install xtb
# for openbabel, assuming you are not using Python >= 3.13!
mamba install openbabelTo get stko and use OpenMM, we had some installation issues. The
current solution is to first, in a new environment, install the OpenMM
requirements:
mamba install -c conda-forge openff-toolkitThen install stko with pip, but with the cuda variant to take advantage
of GPU speed up (note that this is a heavy installation!).
pip install stko[cuda]We also removed the default installation of espaloma_charge that provides
the ML-based espaloma-am1bcc partial charges method. If users want this
package, create a new environment and install their dependancies (if this
fails, please check their
instructions), then install
stko:
mamba install -c conda-forge espaloma_charge openff-toolkit
pip install stko[cuda]- Install just.
- In a new virtual environment run:
just dev- Run code checks:
just checkWe 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).
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.
If you use stko please cite
https://github.com/JelfsMaterialsGroup/stko
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.