biopandas version: 0.4.1

PandasMmcif

PandasMmcif(use_auth: bool = True)

None

Methods

amino3to1(record: str = 'ATOM', residue_col: str = 'auth_comp_id', residue_number_col: str = 'auth_seq_id', chain_col: str = 'auth_asym_id', fillna: str = '?')

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

Fetches mmCIF 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"). 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.

read_mmcif(path)

Read MMCIF files (unzipped or gzipped) from local drive

Attributes

  • path : str

    Path to the MMCIF file in .cif format or gzipped format (.cif.gz).

Returns

self

read_mmcif_from_list(mmcif_lines)

Reads mmCIF file from a list into DataFrames

Attributes

  • pdb_lines : list

    A list of lines containing the mmCIF 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

Properties

df

Acccess dictionary of pandas DataFrames for PDB record sections.