Adding 200m structures to biopandas

[a-r-j]

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Small update to support AF2 v3.

Very high structure:code ratio in this PR 😁

[pep8speaks]

Hello @a-r-j! Thanks for updating this PR.

• In the file biopandas/mmcif/pandas_mmcif.py:

Line 83:54: W291 trailing whitespace Line 84:89: E501 line too long (102 > 88 characters) Line 119:17: E128 continuation line under-indented for visual indent Line 119:89: E501 line too long (96 > 88 characters)

• In the file biopandas/mmcif/tests/test_read_mmcif.py:

Line 148:13: W503 line break before binary operator Line 163:13: W503 line break before binary operator

• In the file biopandas/pdb/pandas_pdb.py:

Line 131:54: W291 trailing whitespace Line 132:89: E501 line too long (109 > 88 characters) Line 168:17: E128 continuation line under-indented for visual indent Line 168:89: E501 line too long (99 > 88 characters)

• In the file biopandas/pdb/tests/test_read_pdb.py:

Line 154:13: W503 line break before binary operator Line 172:13: W503 line break before binary operator

Comment last updated at 2022-08-06 04:25:25 UTC

[rasbt]

Thanks a lot for the update!

[a-r-j]

It looks like tests are failing due to metadata changes in the local AF2 pdb/mmcif files. I'll fix this up.

[rasbt]

Thanks! So it looks like they also updated the previous alphafold-v2 structures? If that's just the meta-data, theoretically we could also just check for Atom entries. Otherwise, I am not sure whether we would have to update the check every few months or so 😅

[a-r-j]

It looks like it was just metadata. They just changed the date in the PDB file. In the mmCIF there were more changes but coords are unaffected. I added another block to test for the latest release but updated the old test to make sure everything works nicely with retrieving structures from previous releases too.

[rasbt]

Awesome, thanks!