biopandas

biopandas copied to clipboard

Following up on the comment by @wojdyr in #52 > by the way, having atoms in two separate frames is rather not a good idea. > At first glance it...

rasbt

I am cross-posting a discussion from the mailing list with regard to multi-PDB files containing MODEL & ENDMDL tags, which are currently not handled by BioPandas. However, it should definitely...

rasbt

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...

rasbt

Improve RMSD function to take molecular symmetry into consideration?

1

Just wondering what the algorithm is behind the RMSD calculation.

ravila4

rasbt

The `rgyr` staticmethod should be implemented similar to the [rmsd](https://github.com/rasbt/biopandas/blob/master/biopandas/pdb/pandas_pdb.py#L118) staticmethod in `PandasPDB`

rasbt

This should be implemented like the [`biopandas.pdb.PandasPDB.rmsd`](https://github.com/rasbt/biopandas/blob/master/biopandas/pdb/pandas_pdb.py#L118) static method.

rasbt

rasbt

Add mmCIF -> PDB conversion

11

Fixes #97 ### Description I started adding the conversion method proposed by @mrauha. I ran into an issue writing the test: ```python from pandas.testing import assert_frame_equal def test_mmcif_pdb_conversion(): pdb =PandasPdb().fetch_pdb("3EIY")...

a-r-j

Biopandas PDB output formatting leads to a ton of segments when reading with MDAnalysis: reason and my quick fix

1

Hi all, was a bit baffled opening biopandas PDB output with MDAnalysis. Instead of some dozen segments, I got thousands. Here's why & my hacky fix: Biopandas outputs the rows...

mrauha