Bio.SCOP.Cla module

Handle the SCOP CLAssification file, which describes SCOP domains.

The file format is described in the scop “release notes.”: The latest CLA file can be found “elsewhere at SCOP.”:

“Release 1.73”: (July 2008)

class Bio.SCOP.Cla.Record(line=None)

Bases: object

Holds information for one SCOP domain.

  • sid - SCOP identifier. e.g. d1danl2

  • residues - The domain definition as a Residues object

  • sccs - SCOP concise classification strings. e.g. b.1.2.1

  • sunid - SCOP unique identifier for this domain

  • hierarchy - A dictionary, keys are nodetype, values are sunid, describing the location of this domain in the SCOP hierarchy. See the Scop module for a description of nodetypes. This used to be a list of (key,value) tuples in older versions of Biopython (see Bug 3109).

__init__(self, line=None)

Initialize the class.


Represent the SCOP classification record as a tab-separated string.


Iterate over a CLA file as Cla records for each line.

  • handle - file-like object.

class Bio.SCOP.Cla.Index(filename)

Bases: dict

A CLA file indexed by SCOP identifiers for rapid random access.

__init__(self, filename)

Create CLA index.

  • filename - The file to index

__getitem__(self, key)

Return an item from the indexed file.