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Mmtf #111
Mmtf #111
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Wow this is cool stuff. I actually also really like the idea of having |
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
This should be good to go now. I added a tutorial notebook but I'm not sure how the docs are built for biopandas & whether the remaining md files are autogenerated. |
Wow very cool. I haven't worked with MMTF's yet, thanks a lot for this PR. And no worries, I can take care of the docs. Probably will make a new release tonight or on the weekend. |
I'd be very happy to become a maintainer 🥳 |
Description
Adds support for reading MMTF files. MMTF is cool because:
There's also plenty of metadata in the MMTF file I'm not parsing in - it's essentially recreating a df object that behaves like
PandasPdb
. This can be done later, I suppose, but I'm opting for speed here. TheMMTF
is available with:I've also exposed some primitive functions for users who want the df, biopandas utils be damned.
Speed
Related issues or pull requests
N/A
Pull Request Checklist
./docs/sources/CHANGELOG.md
file (if applicable)./biopandas/*/tests
directories (if applicable)biopandas/docs/sources/
(if applicable)PYTHONPATH='.' pytest ./biopandas -sv
and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g.,PYTHONPATH='.' pytest ./biopandas/classifier/tests/test_stacking_cv_classifier.py -sv
)flake8 ./biopandas