Package org.biojava.nbio.structure.scop

Interface ScopDatabase

All Known Subinterfaces:

LocalScopDatabase

All Known Implementing Classes:

BerkeleyScopInstallation, ScopInstallation

public interface ScopDatabase

General API how to interact with SCOP

Since:

3.0.2

Author:

Andreas Prlic

See Also:

LocalScopDatabase

Method Summary

Modifier and Type	Method	Description
List<ScopDescription>	filterByClassificationId(String query)	Get all scop descriptions that start with a classification ID, e.g. b.1.18
List<ScopDescription>	filterByDescription(String query)	Get all scop descriptions that start with a certain name. e.g.
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.
List<String>	getComments(int sunid)	Get comments about a SCOP domain by its sunid
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.
void	setScopVersion(String version)	Sets the scop version used.

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 classification 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

setScopVersion

void setScopVersion(String version)

Sets the scop version used.

Parameters:

version -

Throws:

UnsupportedOperationException - If the version cannot be changed

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

getComments

List<String> getComments(int sunid)

Get comments about a SCOP domain by its sunid

Parameters:

sunid -

Returns: