org.biojava.nbio.structure.cath

Interface CathDatabase

All Known Implementing Classes:

CathInstallation

public interface CathDatabase

General API for interacting with CATH.

Author:

Daniel Asarnow

Method Summary

Methods

Modifier and Type	Method and Description
List<CathDomain>	filterByCathCode(String query) Return list of CATH descriptions whose CATH codes (e.g.
List<CathDomain>	filterByDescription(String query) Return list of CATH descriptions whose descriptions (name field) starts with the query.
List<CathDomain>	filterByNodeName(String query) Return list of CATH domains whose node name (e.g.
List<CathDomain>	getByCategory(CathCategory category) Return list of CATH descriptions for node representatives at a CATH category (e.g.
CathNode	getCathNode(String nodeId) Return the CathNode for a node ID.
String	getCathVersion() Return the CATH release version.
CathDomain	getDescriptionByCathId(String cathId) Return CATH description for CATH domain ID.
CathDomain	getDescriptionByNodeId(String nodeId) Return CATH description for node representative by node ID.
CathDomain	getDomainByCathId(String cathId) Return CATH domain for CATH domain ID.
List<CathDomain>	getDomainsByNodeId(String nodeId) Return all CATH domains for a particular CATH node.
List<CathDomain>	getDomainsForPdb(String pdbId) Return all CATH domains for a PDB ID.
List<CathFragment>	getFragmentsByPdbId(String pdbId)
List<CathNode>	getTree(CathDomain domain) Return the CATH sub-tree for a particular domain.

Method Detail

getCathVersion

String getCathVersion()

Return the CATH release version.

Returns:

CATH version

getCathNode

CathNode getCathNode(String nodeId)

Return the CathNode for a node ID.

Parameters:

nodeId -

Returns:

CATH node

getByCategory

List<CathDomain> getByCategory(CathCategory category)

Return list of CATH descriptions for node representatives at a CATH category (e.g. "T").

Parameters:

category -

Returns:

CATH descriptions

filterByCathCode

List<CathDomain> filterByCathCode(String query)

Return list of CATH descriptions whose CATH codes (e.g. 1.4.6.10) start with the query. This is currently redundant with getDescriptionsByNodeId.

Parameters:

query -

Returns:

CATH descriptions

getTree

List<CathNode> getTree(CathDomain domain)

Return the CATH sub-tree for a particular domain.

Parameters:

domain -

Returns:

CATH sub-tree

filterByNodeName

List<CathDomain> filterByNodeName(String query)

Return list of CATH domains whose node name (e.g. Orthogonal Bundle) starts with the query.

Parameters:

query -

Returns:

CATH domains

filterByDescription

List<CathDomain> filterByDescription(String query)

Return list of CATH descriptions whose descriptions (name field) starts with the query.

Parameters:

query -

Returns:

CATH descriptions

getDescriptionByNodeId

CathDomain getDescriptionByNodeId(String nodeId)

Return CATH description for node representative by node ID.

Parameters:

nodeId -

Returns:

CATH description

getDomainsForPdb

List<CathDomain> getDomainsForPdb(String pdbId)

Return all CATH domains for a PDB ID.

Parameters:

pdbId -

Returns:

CATH domains

getDomainByCathId

CathDomain getDomainByCathId(String cathId)

Return CATH domain for CATH domain ID.

Parameters:

cathId -

Returns:

CATH domain

getDescriptionByCathId

CathDomain getDescriptionByCathId(String cathId)

Return CATH description for CATH domain ID.

Parameters:

cathId -

Returns:

getDomainsByNodeId

List<CathDomain> getDomainsByNodeId(String nodeId)

Return all CATH domains for a particular CATH node.

Parameters:

nodeId -

Returns:

getFragmentsByPdbId

List<CathFragment> getFragmentsByPdbId(String pdbId)