Bio.SCOP.Des module

Handle the SCOP DEScription file.

The file format is described in the scop “release notes.”:http://scop.berkeley.edu/release-notes-1.55.html The latest DES file can be found “elsewhere at SCOP.”:http://scop.mrc-lmb.cam.ac.uk/scop/parse/

“Release 1.55”:http://scop.berkeley.edu/parse/des.cla.scop.txt_1.55 (July 2001)

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

Bases: object

Holds information for one node in the SCOP hierarchy.

Attributes:

  • sunid - SCOP unique identifiers

  • nodetype - One of ‘cl’ (class), ‘cf’ (fold), ‘sf’ (superfamily), ‘fa’ (family), ‘dm’ (protein), ‘sp’ (species), ‘px’ (domain). Additional node types may be added.

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

  • name - The SCOP ID (sid) for domains (e.g. d1anu1), currently empty for other node types

  • description - e.g. “All beta proteins”,”Fibronectin type III”,

__init__(self, line=None)

Initialize the class.

__str__(self)

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

Bio.SCOP.Des.parse(handle)

Iterate over a DES file as a Des record for each line.

Arguments:

  • handle - file-like object