biopandas version: 0.4.1

PandasPdb

PandasPdb()

Object for working with Protein Databank structure files.

Attributes

  • df : dict

    Dictionary storing pandas DataFrames for PDB record sections. The dictionary keys are {'ATOM', 'HETATM', 'ANISOU', 'OTHERS'} where 'OTHERS' contains all entries that are not parsed as 'ATOM', 'HETATM', or 'ANISOU'.

  • pdb_text : str

    PDB file contents in raw text format.

  • pdb_path : str

    Location of the PDB file that was read in via read_pdb or URL of the page where the PDB content was fetched from if fetch_pdb was called.

  • header : str

    PDB file description.

  • code : str

    PDB code

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

  • record : str, default: 'ATOM'

    Specfies the record DataFrame.

  • residue_col : str, default: 'residue_name'

    Column in record DataFrame to look for 3-letter amino acid codes for the conversion.

  • fillna : str, default: '?'

    Placeholder string to use for unknown amino acids.

Returns

  • pandas.DataFrame : Pandas DataFrame object consisting of 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(xyz=(0.0, 0.0, 0.0), records=('ATOM', 'HETATM'))

Computes Euclidean distance between atoms and a 3D point.

Parameters

  • xyz : tuple, default: (0.00, 0.00, 0.00)

    X, Y, and Z coordinate of the reference center for the distance computation.

  • records : iterable, default: ('ATOM', 'HETATM')

    Specify which record sections to consider. For example, to consider both protein and ligand atoms, set records=('ATOM', 'HETATM'). This setting is ignored if df is not set to None. For downward compatibility, a string argument is still supported but deprecated and will be removed in future versions.

Returns

  • pandas.Series : Pandas Series object containing the Euclidean

    distance between the atoms in the record section and xyz.

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

Computes Euclidean distance between atoms and a 3D point.

Parameters

  • df : DataFrame

    DataFrame containing entries in the PandasPdb.df['ATOM'] or PandasPdb.df['HETATM'] format for the the distance computation to the xyz reference coordinates.

  • xyz : tuple, default: (0.00, 0.00, 0.00)

    X, Y, and Z coordinate of the reference center for the distance computation.

Returns

  • pandas.Series : Pandas Series object containing the Euclidean

    distance between the atoms in the record section and xyz.

fetch_pdb(pdb_code: 'Optional[str]' = None, uniprot_id: 'Optional[str]' = None, source: 'str' = 'pdb')

Fetches PDB file contents from the Protein Databank at rcsb.org or AlphaFold database at https://alphafold.ebi.ac.uk/. .

Parameters

  • pdb_code : str, optional

    A 4-letter PDB code, e.g., "3eiy" to retrieve structures from the PDB. Defaults to None.

  • uniprot_id : str, optional

    A UniProt Identifier, e.g., "Q5VSL9" to retrieve structures from the AF2 database. Defaults to None.

  • source : str

    The source to retrieve the structure from ("pdb", "alphafold2-v1" or "alphafold2-v2" (latest)). Defaults to "pdb".

Returns

self

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

Filter PDB DataFrames by properties

Parameters

  • s : str in {'main chain', 'hydrogen', 'c-alpha', 'heavy'}

    String to specify which entries to return.

  • df : pandas.DataFrame, default: None

    Optional DataFrame to perform the filter operation on. If df=None, filters on self.df['ATOM'].

  • invert : bool, default: True

    Inverts the search query. For example if s='hydrogen' and invert=True, all but hydrogen entries are returned.

  • records : iterable, default: ('ATOM', 'HETATM')

    Specify which record sections to consider. For example, to consider both protein and ligand atoms, set records=('ATOM', 'HETATM'). This setting is ignored if df is not set to None. For downward compatibility, a string argument is still supported but deprecated and will be removed in future versions.

Returns

  • df : pandas.DataFrame

    Returns a DataFrame view on the filtered entries.

get_model(model_index: 'int') -> 'PandasPdb'

Returns a new PandasPDB object with the dataframes subset to the given model index.

Parameters

  • model_index : int

    An integer representing the model index to subset to.

Returns

  • pandas_pdb.PandasPdb : A new PandasPdb object containing the

    structure subsetted to the given model.

get_model_start_end() -> 'pd.DataFrame'

Get the start and end of the models contained in the PDB file.

Extracts model start and end line indexes based
on lines labelled 'OTHERS' during parsing.

Returns

  • pandas.DataFrame : Pandas DataFrame object containing

    the start and end line indexes of the models.

get_models(model_indices: 'List[int]') -> 'PandasPdb'

Returns a new PandasPDB object with the dataframes subset to the given model index.

Parameters

  • model_index : int

    An integer representing the model index to subset to.

Returns

  • pandas_pdb.PandasPdb : A new PandasPdb object

    containing the structure subsetted to the given model.

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

Impute element_symbol from atom_name section.

Parameters

  • records : iterable, default: ('ATOM', 'HETATM')

    Coordinate sections for which the element symbols should be imputed.

  • inplace : bool, (default: False

    Performs the operation in-place if True and returns a copy of the PDB DataFrame otherwise.

Returns

DataFrame

label_models()

Adds a column ("model_id") to the underlying DataFrames containing the model number.

parse_sse()

Parse secondary structure elements

read_pdb(path)

Read PDB files (unzipped or gzipped) from local drive

Attributes

  • path : str

    Path to the PDB file in .pdb format or gzipped format (.pdb.gz).

Returns

self

read_pdb_from_list(pdb_lines)

Reads PDB file from a list into DataFrames

Attributes

  • pdb_lines : list

    A list of lines containing the pdb file contents.

Returns

self

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

Compute the Root Mean Square Deviation between molecules.

Parameters

  • df1 : pandas.DataFrame

    DataFrame with HETATM, ATOM, and/or ANISOU entries.

  • df2 : pandas.DataFrame

    Second DataFrame for RMSD computation against df1. Must have the same number of entries as df1.

  • s : {'main chain', 'hydrogen', 'c-alpha', 'heavy', 'carbon'} or None,

    default: None String to specify which entries to consider. If None, considers all atoms for comparison.

  • invert : bool, default: False

    Inverts the string query if true. For example, the setting s='hydrogen', invert=True computes the RMSD based on all but hydrogen atoms.

Returns

  • rmsd : float

    Root Mean Square Deviation between df1 and df2

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

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

Parameters

  • path : str

    A valid output path for the pdb file

  • records : iterable, default: None

    A list of PDB record sections in {'ATOM', 'HETATM', 'ANISOU', 'OTHERS'} that are to be written. Writes all lines to PDB if records=None.

  • gz : bool, default: False

    Writes a gzipped PDB file if True.

  • append_newline : bool, default: True

    Appends a new line at the end of the PDB file if True

Properties

df

Acccess dictionary of pandas DataFrames for PDB record sections.