This repo contains code for extracting the molecules in https://data.hpc.imperial.ac.uk/resolve/?doi=4618 into an AtomLite database.
Why?
Because the original format of the published data is an out-of-date format, namely an stk JSON dump.
How?
The easiest thing to do is
pip install cage-json-extractorNow 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
tar xf cages.tar.gz
cage_json_extractor cages/amine2aldehyde3.json cage_prediction.db amine2aldehyde3.dbNow if we want to extract all the shape persistent 4+6 cages we can run
extract_cages amine2aldehyde3.db FourPlusSix --output_directory extracted_cagesThis 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.
Enjoy! (and sorry I deprecated the .json files)
=)
1 maintainer
Metadata
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Release files for cage-json-extractor 1.0.0
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| cage_json_extractor-1.0.0-py3-none-any.whl | Python 3 | none | any | Details for cage_json_extractor-1.0.0-py3-none-any.whl |
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