https://github.com/lukasturcani/cage_json_extractor

https://github.com/lukasturcani/cage_json_extractor

Last synced: about 1 month ago
JSON representation

• Host: GitHub
• URL: https://github.com/lukasturcani/cage_json_extractor
• Owner: lukasturcani
• Created: 2023-07-19T14:32:11.000Z (over 1 year ago)
• Default Branch: master
• Last Pushed: 2023-07-20T08:17:02.000Z (over 1 year ago)
• Last Synced: 2024-05-01T15:31:43.634Z (8 months ago)
• Language: Python
• Size: 32.2 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst

Awesome Lists containing this project

README

        
This repo contains code for extracting the molecules in

https://data.hpc.imperial.ac.uk/resolve/?doi=4618

into an AtomLite_ database.

.. _AtomLite: https://atomlite.readthedocs.io

Why?

=====

Because the original format of the published data is an out-of-date format,

namely an stk_ JSON dump.

.. _stk: https://stk.readthedocs.io

How?

====

The easiest thing to do is

.. code-block:: bash

  pip install cage-json-extractor

Now you can download the files

* ``cages.tar.gz`` - https://data.hpc.imperial.ac.uk/resolve/?doi=4618&file=3&access=

* ``cage_prediction.db`` - https://data.hpc.imperial.ac.uk/resolve/?doi=4618&file=2&access=

And run

.. code-block:: bash

  tar xf cages.tar.gz

  cage_json_extractor cages/amine2aldehyde3.json cage_prediction.db amine2aldehyde3.db

Now if we want to extract all the shape persistent 4+6 cages we can run

.. code-block:: bash

  extract_cages amine2aldehyde3.db FourPlusSix --output_directory extracted_cages

This will create a folder ``extracted_cages`` which holds a sub-folder for every

shape persistent 4+6 cage in ``amine2aldehyde3.db``. In the sub-folder you will

find the ``.mol`` file of the cage and its building blocks.

The script will also output the number of collapsed, persistent and uncategorized

cages it found. You can compare that to the numbers reported in the paper_, to make

sure that the extraction and data conversion was done correctly.

.. _paper: https://pubs.acs.org/doi/10.1021/acs.chemmater.8b03572

Enjoy! (and sorry I deprecated the ``.json`` files)

=)