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

java.util.List<ScopDescription>	filterByClassificationId(java.lang.String query) Get all scop descriptions that start with a classifcation ID, e.g.
java.util.List<ScopDescription>	filterByDescription(java.lang.String query) Get all scop descriptions that start with a certain name.
java.util.List<ScopDomain>	filterByDomainName(java.lang.String query) search through SCOP and filter based on domain name
java.util.List<ScopDescription>	getByCategory(ScopCategory category) Get all records of a particular classification.
ScopDomain	getDomainByScopID(java.lang.String scopId) get a ScopDomain by its SCOP ID (warning, they are not stable between releases!)
java.util.List<ScopDomain>	getDomainsForPDB(java.lang.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.
java.util.List<ScopDomain>	getScopDomainsBySunid(java.lang.Integer sunid) Get a SCOP domain by its sunid
ScopNode	getScopNode(int sunid) Access a particular ScopNode.
java.lang.String	getScopVersion() Returns the SCOP version
java.util.List<ScopNode>	getTree(ScopDomain domain) get the SCOP sub-tree for a particular domain.

Method Detail

getByCategory

java.util.List<ScopDescription> getByCategory(ScopCategory category)

Get all records of a particular classification.

Parameters:

category - e.g. "superfamily"

Returns:

all records of this type

filterByClassificationId

java.util.List<ScopDescription> filterByClassificationId(java.lang.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

java.util.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

java.util.List<ScopDomain> filterByDomainName(java.lang.String query)

search through SCOP and filter based on domain name

Parameters:

query - a (part) of a name

Returns:

list of matchin ScopDomains

filterByDescription

java.util.List<ScopDescription> filterByDescription(java.lang.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

java.util.List<ScopDomain> getDomainsForPDB(java.lang.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(java.lang.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

java.lang.String getScopVersion()

Returns the SCOP version

Returns:

version of SCOP

getScopDomainsBySunid

java.util.List<ScopDomain> getScopDomainsBySunid(java.lang.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