biopandas version: 0.2.5

PandasPdb

PandasPdb()

Object for working with Protein Databank structure files.

Attributes

Methods


amino3to1(record='ATOM', residue_col='residue_name', fillna='?')

Creates 1-letter amino acid codes from DataFrame

Non-canonical amino-acids are converted as follows:
ASH (protonated ASP) => D
CYX (disulfide-bonded CYS) => C
GLH (protonated GLU) => E
HID/HIE/HIP (different protonation states of HIS) = H
HYP (hydroxyproline) => P
MSE (selenomethionine) => M

Parameters

Returns


distance(xyz=(0.0, 0.0, 0.0), records=('ATOM', 'HETATM'))

Computes Euclidean distance between atoms and a 3D point.

Parameters

Returns


distance_df(df, xyz=(0.0, 0.0, 0.0))

Computes Euclidean distance between atoms and a 3D point.

Parameters

Returns


fetch_pdb(pdb_code)

Fetches PDB file contents from the Protein Databank at rcsb.org.

Parameters

Returns

self


get(s, df=None, invert=False, records=('ATOM', 'HETATM'))

Filter PDB DataFrames by properties

Parameters

Returns


impute_element(records=('ATOM', 'HETATM'), inplace=False)

Impute element_symbol from atom_name section.

Parameters

Returns

DataFrame


parse_sse()

Parse secondary structure elements


read_pdb(path)

Read PDB files (unzipped or gzipped) from local drive

Attributes

Returns

self


rmsd(df1, df2, s=None, invert=False)

Compute the Root Mean Square Deviation between molecules.

Parameters

Returns


to_pdb(path, records=None, gz=False, append_newline=True)

Write record DataFrames to a PDB file or gzipped PDB file.

Parameters

Properties


df

Acccess dictionary of pandas DataFrames for PDB record sections.