BioPandas / BioPandas/biopandas

Add/Parse Information about Secondary Structure Elements

Open
#40 0 comments 0 reactions 0 assignees View on GitHub
enhancement
Dominant language
Python
Stars
756
Forks
119
Avg merge
23h 8m
Merged PRs (30d)
2

Description

Add a new dataframe object as `PandasPdb.df['SSE']`, which contains secondary structure element information. This pandas `DataFrame` would have the same number of rows as the coordinate section DataFrame (`'ATOM'`) and columns "helix" and "sheet" with type "bool."

For ease of use, the SSE dataframe could share the dataframe indices with the `PandasPdb.df['ATOM']` section. It may only get tricky if one ('ATOM' or 'SSE') gets updated & reindex and not the other.

Thus, alternatively, SSE information could be added directly to the 'ATOM' DataFrame, for instance as `bool` columns `'helix'` and `'sheet'`.

In any case, I would suggest to make this feature optional; for instance, by calling a function "`parse_sse`" that uses the information provided in the `.pdb_text`.

Contributor guide

Open the contributing guide

Research direction

Locate the PDB parsing entry point and the construction of df['ATOM']; review how pdb_text records are represented. Use the proposed parse_sse entry point to resolve whether SSE is a separate df['SSE'] or columns on ATOM, preserving boolean helix/sheet values and index behavior. Done means secondary-structure information is available through the chosen API and remains consistent with the coordinate data.

Written by the indexing model from the issue text.

Assessment

Tech stack
pandas, python
Domain
bioinformatics, data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
32/100

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