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Recent Releases of BioPandas

BioPandas - 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

Scientific Software - Peer-reviewed - Python
Published by a-r-j over 1 year ago

BioPandas - Version 0.5.1dev

Scientific Software - Peer-reviewed - Python
Published by a-r-j over 2 years ago

BioPandas - Version 0.5.0dev

What's Changed

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

New Contributors

  • @goniochromatic made their first contribution in https://github.com/BioPandas/biopandas/pull/116
  • @anton-bushuiev made their first contribution in https://github.com/BioPandas/biopandas/pull/128
  • @nunziati made their first contribution in https://github.com/BioPandas/biopandas/pull/131
  • @zehraacarsarica made their first contribution in https://github.com/BioPandas/biopandas/pull/134
  • @AH-Merii made their first contribution in https://github.com/BioPandas/biopandas/pull/135

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

What's Changed

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

New Contributors

  • @goniochromatic made their first contribution in https://github.com/BioPandas/biopandas/pull/116
  • @anton-bushuiev made their first contribution in https://github.com/BioPandas/biopandas/pull/128
  • @nunziati made their first contribution in https://github.com/BioPandas/biopandas/pull/131
  • @zehraacarsarica made their first contribution in https://github.com/BioPandas/biopandas/pull/134
  • @AH-Merii made their first contribution in https://github.com/BioPandas/biopandas/pull/135

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

Scientific Software - Peer-reviewed - Python
Published by a-r-j over 2 years ago

BioPandas - Version 0.4.1

Remove walrus operator for Python 3.7 compatibility.

Scientific Software - Peer-reviewed - Python
Published by rasbt almost 4 years ago

BioPandas - 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

Scientific Software - Peer-reviewed - Python
Published by rasbt almost 4 years ago

BioPandas - 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)

Scientific Software - Peer-reviewed - Python
Published by rasbt almost 4 years ago

BioPandas - 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
  • -

Scientific Software - Peer-reviewed - Python
Published by rasbt over 4 years ago

BioPandas - 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

Scientific Software - Peer-reviewed - Python
Published by rasbt almost 5 years ago

BioPandas - 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.

Scientific Software - Peer-reviewed - Python
Published by rasbt over 5 years ago

BioPandas - 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
  • -

Scientific Software - Peer-reviewed - Python
Published by rasbt over 5 years ago

BioPandas - Version 0.2.5

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.

Scientific Software - Peer-reviewed - Python
Published by rasbt over 5 years ago

BioPandas - v0.2.4

New Features
  • -
Changes
  • Minor adjustments to support to address deprecation warnings in pandas >= 23.0
Bug Fixes
  • -

Scientific Software - Peer-reviewed - Python
Published by rasbt about 7 years ago

BioPandas - v0.2.3

New Features
  • N/A
Changes
  • PandasMol2.distance_df was added as a static method that allows distance computations based for external data frames with its behavior otherwise similar to PandasMol2.distance.
  • PandasPdb.distance_df was added as a static method that allows distance computations based for external data frames with its behavior otherwise similar to PandasPdb.distance.
  • PandasPdb.distance now supports multiple record sections to be considered (e.g., records=('ATOM', 'HETATM') to include both protein and ligand in a query. Now also defaults to records=('ATOM', 'HETATM') for concistency with the impute method.
  • PandasPdb.get(...) now supports external data frames and lets the user specify the record section to be considered (e.g., records=('ATOM', 'HETATM') to include both protein and ligand in a query. Now also defaults to records=('ATOM', 'HETATM') for concistency with the impute method.
  • The section parameter of PandasPdb.impute_element(...) was renamed to records for API consistency.
Bug Fixes
  • N/A

Scientific Software - Peer-reviewed - Python
Published by rasbt almost 8 years ago

BioPandas - v0.2.2 (06-07-2017)

New Features
  • -
Changes
  • Raises a meaningful error message if attempting to overwrite the df attributes of PandasMol2 and PandasPdb directly.
  • Added PandasPdb.pdb_path and PandasMol2.mol2_path attributes that store the location of the data file last read.
Bug Fixes
  • The rmsd methods of PandasMol2 and PandasPdb don't return a NaN anymore if the array indices of to structures are different.

Scientific Software - Peer-reviewed - Python
Published by rasbt over 8 years ago

BioPandas - v0.2.1 (2017-05-11)

0.2.1 (2017-05-11)

Downloads
New Features
  • -
Changes
  • The amino3to1 method of biopandas.pdb.PandasPDB objects now returns a pandas DataFrame instead of a pandas Series object. The returned data frame has two columns, 'chain_id' and 'residue_name', where the former contains the chain ID of the amino acid and the latter contains the 1-letter amino acid code, respectively.
  • Significant speed improvements of the distance method of both PandasPdb and PandasMol2 (now about 300 percent faster than previously).
Bug Fixes
  • The amino3to1 method of biopandas.pdb.PandasPDB objects now handles multi-chain proteins correctly.
  • The amino3to1 method of biopandas.pdb.PandasPDB objects now also works as expected if the 'ATOM' entry DataFrame contains disordered DataFrame indices or duplicate DataFrame index values.

Scientific Software - Peer-reviewed - Python
Published by rasbt almost 9 years ago

BioPandas - v0.2.0 (2017-04-02)

Downloads
New Features
  • Added an amino3to1 method to PandasPdb data frames to convert 3-amino acid letter codes to 1-letter codes.
  • Added a distance method to PandasPdb data frames to compute the Euclidean distance between atoms and a reference point.
  • Added the PandasMol2 class for working with Tripos MOL2 files in pandas DataFrames.
Changes
  • PandasPDB was renamed to PandasPdb.
  • Raises a warning if PandasPdb is written to PDB and ATOM and HETAM section contains unexpected columns; these columns will now be skipped.
Bug Fixes
  • -

Scientific Software - Peer-reviewed - Python
Published by rasbt almost 9 years ago

BioPandas - v0.1.5

0.1.5

  • Included test data in the PyPI package; add install_requires for pandas
  • Added an impute_element method to PandasPDB objects to infer the Element Symbol from the Atom Name column
  • Added two new selection types for PandasPDB ATOM and HETATM coordinate sections: 'heavy' and 'carbon'
  • The 'hydrogen' atom selection in PandasPDB methods is now based on the element type instead of the atom name
  • By default, the RMSD is now computed on all atoms unless a specific selection is defined

Scientific Software - Peer-reviewed - Python
Published by rasbt over 9 years ago

BioPandas - v0.1.4

0.1.4 (2015-11-24)

  • Needed to bump the version number due to a bug in the PyPI setup.py script
  • Support for the old pandas sorting syntax (DataFrame.sort vs DataFrame.sort_values) incl. DeprecationWarning

0.1.3 (2015-11-23)

  • Exception handling in tests if PDB goes down (which just happened)
  • Added a separate ANISOU engine to handle those records correctly

0.1.2 (2015-11-23)

  • First Release

Scientific Software - Peer-reviewed - Python
Published by rasbt over 9 years ago