Working with molecular structures in pandas DataFrames
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.section parameter of PandasPdb.impute_element(...) was renamed to records for API consistency.df attributes of PandasMol2 and PandasPdb directly.PandasPdb.pdb_path and PandasMol2.mol2_path attributes that store the location of the data file last read.rmsd methods of PandasMol2 and PandasPdb don't return a NaN anymore if the array indices of to structures are different.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.distance method of both PandasPdb and PandasMol2 (now about 300 percent faster than previously).amino3to1 method of biopandas.pdb.PandasPDB objects now handles multi-chain proteins correctly.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.amino3to1 method to PandasPdb data frames to convert 3-amino acid letter codes to 1-letter codes.distance method to PandasPdb data frames to compute the Euclidean distance between atoms and a reference point.PandasMol2 class for working with Tripos MOL2 files in pandas DataFrames.PandasPDB was renamed to PandasPdb.PandasPdb is written to PDB and ATOM and HETAM section contains unexpected columns; these columns will now be skipped.impute_element method to PandasPDB objects to infer the Element Symbol from the Atom Name columnPandasPDB ATOM and HETATM coordinate sections: 'heavy' and 'carbon'
'hydrogen' atom selection in PandasPDB methods is now based on the element type instead of the atom nameDataFrame.sort vs DataFrame.sort_values) incl. DeprecationWarning