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Update biopandas usage: Read pdb from list of strings #48

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dominiquesydow opened this issue Oct 21, 2020 · 1 comment
Open

Update biopandas usage: Read pdb from list of strings #48

dominiquesydow opened this issue Oct 21, 2020 · 1 comment
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module-io Concerns opencadd.io module

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@dominiquesydow
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Code improvement in opencadd.io.dataframe:

Avoid to use the private PandasPdb method _construct_df.

opencadd/opencadd/io/dataframe.py

Line 128 in 912d4e9

pdb_dict = ppdb._construct_df(pdb_text.splitlines(True))

If possible in the future, use e.g.

ppdb = PandasPdb()
ppdb.read_pdb_from_list()  # New feature?

See feature request:
BioPandas/biopandas#70
@dominiquesydow
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Wait for biopandas 0.3.0 release:

  • Use new PandasPdb.read_pdb_from_list method
  • Adapt to new file format error handling in read_pdb and read_mol2

(see biopandas CHANGELOG)

@dominiquesydow dominiquesydow added the module-io Concerns opencadd.io module label Jun 30, 2021
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