pdbx get_sequence return dict of seq#611
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padix-key merged 10 commits intobiotite-dev:masterfrom Jun 28, 2024
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'get_sequence' in the module 'biotite.structure.io.pdb' to return a dictionary mapping chain_id to the sequence
with entity_poly.pdbx_strand_id as keys. Updated test_pdx.py test_get_sequence to reflect returning a dict instead of a list
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For reference: This is the continuation of #600 |
padix-key
approved these changes
Jun 25, 2024
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Looks good to me. I will keep this PR open until patch version 0.41.2 was released (due to #605), which should arrive in the upcoming days. |
padix-key
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Jun 28, 2024
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Excellent! Thank you for your patience. I learned a lot despite this being such a small change. |
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Accidentally deleted my last pull request on this topic.
Purpose:
Modified biotite.structure.io.pdbx.get_sequence to return a dictionary of sequences instead of a list. This change provides a more intuitive way to access sequences by their chain identifiers.
Details:
Old Behavior: Returned a list of sequences.
New Behavior: Returns a dictionary where keys are derived from entity_poly.pdbx_strand_id (often equivalent to chain_id and atom_site.auth_asym_id in most cases). Dictionary values are the corresponding sequences.
Example Usage:
Rationale:
The change in return type improves the usability of the function by allowing direct access to sequences using chain identifiers, which is a common use case.
Impact:
This change is non-backwards compatible. Code that relies on the previous list-based return type will need to be updated.
Tests and examples have been updated to reflect this change in return type.