issues Search Results · repo:BioPandas/biopandas language:Python
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inBioPandas/biopandas (press backspace or delete to remove)Describe the bug
Currently reading or writing PDB data with atomic charges that follow the PDB v3.3 format is not possible.
The PDB format specifies the notation for charge explicitly via: Columns 79 ...
gate-tec
- Opened on Mar 13
- #151
I have identified an issue with the Biopandas Python library where test scripts and test data are being packaged with
the main library and included in the PyPI release. This practice is not recommended ...
Irlirion
- Opened on Jul 20, 2024
- #147
!-- If this is your first Issue submitted to the BioPandas Issue Tracker, please review the code of conduct, which is available at http://rasbt.github.io/biopandas/CODE_OF_CONDUCT/.
Describe the workflow ...
gezmi
- 1
- Opened on Apr 29, 2024
- #142
Describe the bug
When trying to export pdb data with ATOM and OTHERS entries using .to_pdb_stream I always get a
pandas.errors.IntCastingNaNError (cf. Steps/Code to Reproduce). As I need to maintain the ...
gate-tec
- 1
- Opened on Mar 4, 2024
- #141
!-- If this is your first Issue submitted to the BioPandas Issue Tracker, please review the code of conduct, which is available at http://rasbt.github.io/biopandas/CODE_OF_CONDUCT/.
Describe the workflow ...
a-r-j
- 6
- Opened on Aug 29, 2023
- #139
!-- If this is your first Issue submitted to the BioPandas Issue Tracker, please review the code of conduct, which is available at http://rasbt.github.io/biopandas/Code-of-Conduct/.
!-- Before submitting ...
RafiBrent
- 2
- Opened on Jul 28, 2023
- #136
!-- If this is your first Issue submitted to the BioPandas Issue Tracker, please review the code of conduct, which is available at http://rasbt.github.io/biopandas/Code-of-Conduct/.
!-- Before submitting ...
zehrasarica
- Opened on Jul 15, 2023
- #133
I have a very basic question. I often load pdb files as ppdb objects and then convert to pandas df to manipulate them:
ppdb = PandasPdb().read_pdb(input_pdb) chainA_df = ppdb.df[ ATOM ][ppdb.df[ ATOM ...
SkwisgaarSkwigelf
- 2
- Opened on Jul 13, 2023
- #132
Describe the bug
When reading in PDB content via read_pdb_from_list(), the text itself does not contain newlines where they should be,
thus making any future commands like pdb_lines = ppdb.pdb_text.split( ...
uros-sipetic
- Opened on Jun 29, 2023
- #130
These tests raise a warning with the latest version of Pandas:
https://github.com/BioPandas/biopandas/blob/11362ec459d9c9c265d2f2416223569e9cf4fc93/biopandas/pdb/tests/test_multiple_models.py
The specific ...
tommycarstensen
- Opened on Apr 25, 2023
- #127

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