Package org.biojava.nbio.structure.scop

Parsers and API for SCOP, Structural Classification of Proteins.

See: Description

Interface Summary

Interface	Description
LocalScopDatabase	Classes which implement ScopDatabase in a way which allows them to serve queries without accessing the internet should implement this interface instead.
ScopDatabase	General API how to interact with SCOP

Class Summary

Class	Description
Astral	Provides programmatic access to ASTRAL representative sets.
BerkeleyScopInstallation	SCOPe: The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley (http://scop.berkeley.edu/).
CachedRemoteScopInstallation	An extension of the RemoteScopInstallation that caches some of the data locally.
RemoteScopInstallation	A class that fetches information about SCOP from a remote data-source.
ScopDescription	Contains data from dir.des.scop.txt_1.75 e.g SunID Cat Class Name Description ----- --- ----- ---- ----------- 26154 px b.47.1.2 d1nrs.1 1nrs L:,H: 125030 px b.47.1.2 d1zgia1 1zgi A:1A-245
ScopDomain	Container for the information for a domain.
ScopFactory	Controls the global ScopDatabase being used.
ScopInstallation	This class provides access to the SCOP protein structure classification.
ScopMirror	Helper class to store paths to the four SCOP files The string "%s" is replaced with the version number.
ScopNode

Enum Summary

Enum	Description
Astral.AstralSet	An ASTRAL sequence-identity cutoff with an identifier such as: 1.75A_95 Also contains a URL pointing to a FASTA file containing the representatives.
ScopCategory	The various categories provided by SCOP.

Exception Summary

Exception	Description
ScopIOException	Indicates that an I/O error occurred with SCOP lazy initialization.

Package org.biojava.nbio.structure.scop Description

Parsers and API for SCOP, Structural Classification of Proteins. See DemoSCOP.java for an example.