Biopandas Versions Save

Working with molecular structures in pandas DataFrames

v0.5.1dev

8 months ago

v0.5.0dev

8 months ago

What's Changed

New Contributors

Full Changelog: https://github.com/BioPandas/biopandas/compare/v0.4.1...v0.5.0dev

What's Changed

New Contributors

Full Changelog: https://github.com/BioPandas/biopandas/compare/v0.4.1...v0.5.0dev

v0.4.1

1 year ago

Remove walrus operator for Python 3.7 compatibility.

v0.4.0

1 year ago
New Features

  • Adds support for extracting structures from PDB files containing multiple models. See the documentation for details. (via Arian Jamasb, PR #101).

  • Adds support for fetching mmCIF (PandasMmcif().fetch_mmcif(uniprot_id='Q5VSL9', source='alphafold2-v2')) and PDB structures (e.g., PandasPdb().fetch_pdb(uniprot_id='Q5VSL9', source="alphafold2-v2")) (via Arian Jamasb, PR #102).

Changes
  • Instead of raising a warning when no ATOM entries are loaded, raise the warning only when neither ATOM nor HETAM entries are loaded.
Bug Fixes
  • None

v0.3.0

2 years ago

0.3.0 (04-06-2022)

Downloads
New Features
  • Adds support for parsing mmCIF protein structure files (via Arian Jamasb, PR #94)
Changes
Bug Fixes
  • Fixes a bug where coordinates with more than 4 digits before the decimal point caused a column shift when saving a PDB file. (via PR #90)
  • Fixes a bug where the invert parameter in get_carbon was selecting the wrong case. (via Arian Jamasb PR #96)

v0.2.9

2 years ago

0.2.9 (08-30-2021)

Downloads
New Features
Changes
  • Now also allow .ent and .ent.gz file endings for PDB files. (via PR 82
  • Added Python 3.8 and 3.9 to setup.py in order to support these versions via conda-forge. (via PR 87
Bug Fixes

v0.2.8

3 years ago

0.2.8 (03-30-2021)

New Features
  • A PandasPdb.read_pdb_from_list method was added analogous to the existing PandasMol2.read_mol2_from_list (via PR 72 by dominiquesydow)
Changes
  • ValueError raising and improved file format error messages for read_pdb and read_mol2 functionality. (via PR 73 by dominiquesydow)
Bug Fixes

None

v0.2.7

3 years ago
New Features
Changes
Bug Fixes
  • Fix Manifest file to include license file in the PyPI tar.gz file so that BioPandas can be packaged by conda-forge.

v0.2.6

3 years ago
New Features
Changes
  • Uses more modern https queries for the RCSB server via the fetch_pdb function.
  • Updates the documentation (incl. a code of conduct)
Bug Fixes

v0.2.5

3 years ago
New Features
Changes
Bug Fixes
  • The PandasPdb.amino3to1 method now also considers insertion codes when converting the amino acid codes; before, inserted amino acides were skipped.