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.

v0.2.4

New Features

Changes

• Minor adjustments to support to address deprecation warnings in pandas >= 23.0

Bug Fixes

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

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.

v0.2.1 (2017-05-11)

0.2.1 (2017-05-11)

Downloads

• Source code (zip)
• Source code (tar.gz)

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.

v0.2.0 (2017-04-02)

Downloads

• Source code (zip)
• Source code (tar.gz)

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

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

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