Bio.SCOP.Cla module

Handle the SCOP CLAssification file, which describes SCOP domains.

The file format is described in the scop “release notes.”:http://scop.mrc-lmb.cam.ac.uk/scop/release-notes.html The latest CLA file can be found “elsewhere at SCOP.”:http://scop.mrc-lmb.cam.ac.uk/scop/parse/

“Release 1.73”: http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.73 (July 2008)

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

Bases: object

Holds information for one SCOP domain.

Attributes:

  • 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.

__str__(self)

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

Bio.SCOP.Cla.parse(handle)

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

Arguments:

  • 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.

Arguments:

  • filename - The file to index

__getitem__(self, key)

Return an item from the indexed file.