Version 0.5.1

0.5.1 (01/08/2024)

• Fix: improves support for writing PDBs with OTHERS records to stream. PR #149. Addresses issue #141.
• Feature: added method to PandasMmcif that allow to select by model ids. PR #145
• Dev: switched testing framework entirely to pytest. Drops nose dependency due to version conflicts with Python 3.12 (nose) and 3.8 (nose) PR #146
• Dev: adds GitHub actions-based CI. PR #149.
• Avoid inclusion of test scripts and test data in the PyPI release of the Biopandas library. PR #148. Addresses issue #147

Version 0.5.1dev

v0.5.1dev

bump version string

Version 0.5.0dev

What's Changed

• Adding 200m structures to biopandas by @a-r-j in #105
• Add mmCIF -> PDB conversion by @a-r-j in #107
• Mmtf by @a-r-j in #111
• update url by @rasbt in #115
• Fix to pdb stream by @goniochromatic in #116
• feature: MMTF Parser Improvements + MMTF Export by @a-r-j in #119
• Add PandasPdb.gyradius by @goniochromatic in #118
• update af2 versions to latest by @a-r-j in #121
• Add GH action for autorelease on tag #120 by @a-r-j in #122
• Add MMTF gzip reading support by @a-r-j in #123
• Add support for pathlib by @anton-bushuiev in #128
• explicit copy dataframe in pandas_pdb.py to avoid warnings by @nunziati in #131
• b_factor one white space format fix by @zehraacarsarica in #134
• Implement add_remark for PandasPdb by @anton-bushuiev in #129
• Mmtf gzip by @a-r-j in #126
• Add automated tests and release v0.5.0-dev by @AH-Merii in #135

New Contributors

• @goniochromatic made their first contribution in #116
• @anton-bushuiev made their first contribution in #128
• @nunziati made their first contribution in #131
• @zehraacarsarica made their first contribution in #134
• @AH-Merii made their first contribution in #135

Full Changelog: v0.4.1...v0.5.0dev

What's Changed

• Adding 200m structures to biopandas by @a-r-j in #105
• Add mmCIF -> PDB conversion by @a-r-j in #107
• Mmtf by @a-r-j in #111
• update url by @rasbt in #115
• Fix to pdb stream by @goniochromatic in #116
• feature: MMTF Parser Improvements + MMTF Export by @a-r-j in #119
• Add PandasPdb.gyradius by @goniochromatic in #118
• update af2 versions to latest by @a-r-j in #121
• Add GH action for autorelease on tag #120 by @a-r-j in #122
• Add MMTF gzip reading support by @a-r-j in #123
• Add support for pathlib by @anton-bushuiev in #128
• explicit copy dataframe in pandas_pdb.py to avoid warnings by @nunziati in #131
• b_factor one white space format fix by @zehraacarsarica in #134
• Implement add_remark for PandasPdb by @anton-bushuiev in #129
• Mmtf gzip by @a-r-j in #126
• Add automated tests and release v0.5.0-dev by @AH-Merii in #135

New Contributors

• @goniochromatic made their first contribution in #116
• @anton-bushuiev made their first contribution in #128
• @nunziati made their first contribution in #131
• @zehraacarsarica made their first contribution in #134
• @AH-Merii made their first contribution in #135

Full Changelog: v0.4.1...v0.5.0dev

Version 0.4.1

Remove walrus operator for Python 3.7 compatibility.

Version 0.4.0

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

Version 0.3.0

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)

Version 0.2.9

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

Version 0.2.8

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

Version 0.2.7

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.

Version 0.2.6

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