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CoreBio

Package corebio :: Package resource :: Module scop :: Class Scop
[frames | no frames]

Type Scop

object --+
         |
        Scop


The entire SCOP hierarchy.

root             -- The root node of the hierarchy 
domains          -- A list of all domains
nodes_by_sid     -- A dictionary of nodes indexed by SCOP identifier 
                    (e.g. 'd1hbia_')
domains_by_sunid -- A dictionary of domains indexed by SCOP uniquie
                    identifiers (e.g. 14996)
Method Summary
  __init__(self)
An empty Scop object.
  parse(cls, dir_path, version)
Build the SCOP hierarchy from the SCOP parsable files. (Class method)
  parse_files(cls, cla_file, des_file, hie_file)
Build the SCOP hierarchy from the SCOP parsable files. (Class method)
  write_cla(self, stream)
Build a CLA SCOP parsable file from this object...
  write_des(self, stream)
Build a DES SCOP parsable file from this object...
  write_hie(self, stream)
Build an HIE SCOP parsable file from this object...
    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...
  __str__(x)
x.__str__() <==> str(x)...

Instance Method Details

__init__(self)
(Constructor) 

An empty Scop object.

See also Scop.parse() and Scop.parse_files()
Overrides:
__builtin__.object.__init__

write_cla(self, stream) 

Build a CLA SCOP parsable file from this object

write_des(self, stream) 

Build a DES SCOP parsable file from this object

write_hie(self, stream) 

Build an HIE SCOP parsable file from this object

Class Method Details

parse(cls, dir_path, version) 

Build the SCOP hierarchy from the SCOP parsable files.
    
 - dir_path -- A directory that contains the SCOP files
 - version  -- The SCOP version (as a string)
 
The SCOP files are named dir.XXX.scop.txt_VERSION, where XXX
is 'cla', 'des' or 'hie'.

parse_files(cls, cla_file, des_file, hie_file) 

Build the SCOP hierarchy from the SCOP parsable files.

- cla_file -- the CLA clasification file
- des_file -- the DES description file
- hie_file -- the HIE hierarchy file

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