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SCOP: Structural Classification of Proteins.
The SCOP database aims to provide a manually constructed classification of
all know protein structures into a hierarchy, the main levels of which
are family, superfamily and fold.
The Scop object in this module represents the entire SCOP classification. It
can be built from the three SCOP parsable files, modified is so desired, and
converted back to the same file formats. A single SCOP domain (represented
by the Domain class) can be obtained from Scop using the domain's SCOP
identifier (sid).
- nodeCodeDict
- A mapping between known 2 letter node codes and a longer
description. The known node types are
cl (class), cf
(fold), sf (superfamily), fa (family), dm (domain),
sp (species), px (domain). Additional node types may
be added in the future.
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Imported modules
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import Cla
import Des
import Hie
from Residues import *
from types import *
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Functions
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cmp_sccs
parse_domain
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cmp_sccs
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cmp_sccs ( sccs1, sccs2 )
Order SCOP concise classification strings (sccs).
4.5.1 < a.4.5.11 < b.1.1.1
A sccs (e.g. a.4.5.11) compactly represents a domain's classification.
The letter represents the class, and the numbers are the fold,
superfamily, and family, respectively.
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parse_domain
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parse_domain ( str )
Convert an ASTRAL header string into a Scop domain.
An ASTRAL (http://astral.stanford.edu/) header contains a concise
description of a SCOP domain. A very similar format is used when a
Domain object is converted into a string. The Domain returned by this
method contains most of the SCOP information, but it will not be located
within the SCOP hierarchy (i.e. The parent node will be None). The
description is composed of the SCOP protein and species descriptions.
- A typical ASTRAL header looks like
- >d1tpt_1 a.46.2.1 (1-70) Thymidine phosphorylase {Escherichia coli}
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Classes
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| Domain |
A SCOP domain. A leaf node in the Scop hierarchy.
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| Node |
A node in the Scop hierarchy
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| Scop |
The entire SCOP hierarchy.
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