https://github.com/andrewtarzia/cage-construction-template

https://github.com/andrewtarzia/cage-construction-template

Last synced: 17 days ago
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• Host: GitHub
• URL: https://github.com/andrewtarzia/cage-construction-template
• Owner: andrewtarzia
• License: mit
• Created: 2024-12-11T10:17:48.000Z (29 days ago)
• Default Branch: main
• Last Pushed: 2024-12-18T19:58:49.000Z (21 days ago)
• Last Synced: 2024-12-18T20:36:29.086Z (21 days ago)
• Language: Python
• Size: 2.93 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

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README

        
:maintainers:

  `andrewtarzia `_

:documentation: https://cage_construct.readthedocs.io/en/latest/

Overview

========

A code base for using `stk `_ to

construct and optimise two porous cage molecules.

Thank you to Lukas Turcani for the initial template this was built on. However,

there are significant differences due to ``stk`` ecosystem incompatability with

``uv``.

Installation

============

To run the scripts or develop this code, you can clone the repo and use

`just `_ to setup the dev environment:

.. code-block:: bash

  just dev

Usage

=====

I have written this template to build two cages, one porous organic cage and

one metal-organic cage. Both constructions use ``stk`` alchemical approach.

Upon using this template, you should see the shared functions and template

processes to take advantage of.

The template is set up to use project scripts (found in ``pyproject.toml``,

``src/cage_construct/scripts``), with shared functions in

``src/cage_construct/utilities``.

The output for the template is saved in ``examples/template_output`` using

``--working_path`` on all scripts.

The test and example suite is also exemplified based on the function

``cage_construct.foo``.