org.biojava.bio.structure.scop
Interface ScopDatabase

All Known Implementing Classes:
BerkeleyScopInstallation, CachedRemoteScopInstallation, RemoteScopInstallation, ScopInstallation

public interface ScopDatabase

General API how to interact with SCOP

Since:
3.0.2
Author:
Andreas Prlic

Method Summary
 List<ScopDescription> filterByClassificationId(String query)
          Get all scop descriptions that start with a classifcation ID, e.g.
 List<ScopDescription> filterByDescription(String query)
          Get all scop descriptions that start with a certain name.
 List<ScopDomain> filterByDomainName(String query)
          search through SCOP and filter based on domain name
 List<ScopDescription> getByCategory(ScopCategory category)
          Get all records of a particular classification.
 ScopDomain getDomainByScopID(String scopId)
          get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
 List<ScopDomain> getDomainsForPDB(String pdbId)
          Get a list of ScopDomains that have been assigned to a PDB ID
 ScopDescription getScopDescriptionBySunid(int sunid)
          Return the SCOP description for a node in the hierarchy by its "sunid" id.
 List<ScopDomain> getScopDomainsBySunid(Integer sunid)
          Get a SCOP domain by its sunid
 ScopNode getScopNode(int sunid)
          Access a particular ScopNode.
 String getScopVersion()
          Returns the SCOP version
 List<ScopNode> getTree(ScopDomain domain)
          get the SCOP sub-tree for a particular domain.
 

Method Detail

getByCategory

List<ScopDescription> getByCategory(ScopCategory category)
Get all records of a particular classification.

Parameters:
category - e.g. "superfamily"
Returns:
all records of this type

filterByClassificationId

List<ScopDescription> filterByClassificationId(String query)
Get all scop descriptions that start with a classifcation ID, e.g. b.1.18

Parameters:
query -
Returns:
list of scop descriptions

getTree

List<ScopNode> getTree(ScopDomain domain)
get the SCOP sub-tree for a particular domain.

Parameters:
domain -
Returns:
list of ScopNodes providing the path to this domain

filterByDomainName

List<ScopDomain> filterByDomainName(String query)
search through SCOP and filter based on domain name

Parameters:
query - a (part) of a name
Returns:
list of matchin ScopDomains

filterByDescription

List<ScopDescription> filterByDescription(String query)
Get all scop descriptions that start with a certain name. e.g. Globin

Parameters:
query -
Returns:
list of scop descriptions

getScopDescriptionBySunid

ScopDescription getScopDescriptionBySunid(int sunid)
Return the SCOP description for a node in the hierarchy by its "sunid" id.

Parameters:
sunid -
Returns:
a ScopDescription object

getDomainsForPDB

List<ScopDomain> getDomainsForPDB(String pdbId)
Get a list of ScopDomains that have been assigned to a PDB ID

Parameters:
pdbId - the PDB entry
Returns:
a list of ScopDomains

getDomainByScopID

ScopDomain getDomainByScopID(String scopId)
get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)

Parameters:
scopId - e.g. d2bq6a1
Returns:
a ScopDomain or null if no domain with the particular ID could be found

getScopNode

ScopNode getScopNode(int sunid)
Access a particular ScopNode. The scopNode then allows to traverse through the scop hierarchy...

Parameters:
sunid - the scop unique id
Returns:
a ScopNode that matches this sunid

getScopVersion

String getScopVersion()
Returns the SCOP version

Returns:
version of SCOP

getScopDomainsBySunid

List<ScopDomain> getScopDomainsBySunid(Integer sunid)
Get a SCOP domain by its sunid

Parameters:
sunid - the scop unique id
Returns:
a list of scop domains that match this sunid