corebio.resource.scop.DesRecord

Package corebio :: Package resource :: Module scop :: Class DesRecord

Type DesRecord

object --+
         |
        DesRecord

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/

The DES file consisnt of one DES record per line. Each record 
holds information for one node in the SCOP hierarchy, and consist
of 5 tab deliminated fields,
sunid, node type, sccs, node name, node description.

For example ::

21953   px      b.1.2.1 d1dan.1 1dan T:,U:91-106
48724   cl      b       -       All beta proteins
48725   cf      b.1     -       Immunoglobulin-like beta-sandwich
49265   sf      b.1.2   -       Fibronectin type III
49266   fa      b.1.2.1 -       Fibronectin type III


- 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",

Method Summary
	`__init__(self, record)`
	`__str__(self)`
	`records(des_file)` Iterates over a DES file, generating DesRecords... (Static method)
Inherited from object
	`__delattr__(...)` x.__delattr__('name') <==> del x.name...
	`__getattribute__(...)` x.__getattribute__('name') <==> x.name...
	`__hash__(x)` x.__hash__() <==> hash(x)...
	`__new__(T, S, ...)` T.__new__(S, ...) -> a new object with type S, a subtype of T...
	`__reduce__(...)` helper for pickle...
	`__reduce_ex__(...)` helper for pickle...
	`__repr__(x)` x.__repr__() <==> repr(x)...
	`__setattr__(...)` x.__setattr__('name', value) <==> x.name = value...

Static Method Details

records(des_file)

Iterates over a DES file, generating DesRecords

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