Mmtf

[a-r-j]

Description

Adds support for reading MMTF files. MMTF is cool because:

1. it's lightweight (can fit the whole pdb in 7gb on disk(!!!))
2. it's fast!

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. The MMTF is available with:

from rich import inspect
from biopandas.mmtf import PandasMmtf

p = PandasMmtf().fetch_mmtf("3eiy")

inspect(p.mmtf)

I've also exposed some primitive functions for users who want the df, biopandas utils be damned.

from biopandas.mmtf import fetch_mmtf, parse_mmtf

fetch_mmtf("4hhb")
parse_mmtf("tests/data/3eiy.mmtf")

Speed

Related issues or pull requests

N/A

Pull Request Checklist

• Added a note about the modification or contribution to the ./docs/sources/CHANGELOG.md file (if applicable)
• Added appropriate unit test functions in the ./biopandas/*/tests directories (if applicable)
• Modify documentation in the corresponding Jupyter Notebook under biopandas/docs/sources/ (if applicable)
• Ran 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)
• Checked for style issues by running flake8 ./biopandas

[rasbt]

Wow this is cool stuff. I actually also really like the idea of having fetch_* and parse_* functions!

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[a-r-j]

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.

[rasbt]

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.
(If you are interested, we should maybe move biopandas into it's own org biopandas/biopandas so that you can become a maintainer as well)

[a-r-j]

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. (If you are interested, we should maybe move biopandas into it's own org biopandas/biopandas so that you can become a maintainer as well)

I'd be very happy to become a maintainer 🥳