Trees | Indices | Help |
---|
|
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. * "SCOP":http://scop.mrc-lmb.cam.ac.uk/scop/ * "Introduction":http://scop.mrc-lmb.cam.ac.uk/scop/intro.html * "SCOP parsable files":http://scop.mrc-lmb.cam.ac.uk/scop/parse/ 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.
|
|||
|
|
|||
Scop The entire SCOP hierarchy. |
|||
Node A node in the Scop hierarchy |
|||
Domain A SCOP domain. |
|||
Astral Abstraction of the ASTRAL database, which has sequences for all the SCOP domains, as well as clusterings by percent id or evalue. |
|
|||
|
|||
|
|||
|
|
|||
nodeCodeDict =
|
|||
_nodetype_to_code =
|
|||
nodeCodeOrder =
|
|||
astralBibIds =
|
|||
astralEvs =
|
|||
astralEv_to_file =
|
|||
astralEv_to_sql =
|
|||
_domain_re = re.compile(r'>
|
|
Order SCOP concise classification strings (sccs). a.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. |
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} |
|
nodeCodeDict
|
_nodetype_to_code
|
astralEvs
|
astralEv_to_file
|
astralEv_to_sql
|
_domain_re
|
Trees | Indices | Help |
---|
Generated by Epydoc 3.0.1 on Thu Feb 7 11:50:20 2008 | http://epydoc.sourceforge.net |