BioPandas / BioPandas/biopandas
Add/Parse Information about Secondary Structure Elements
- 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
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