org.biojava.nbio.structure.domain

Class PDBDomainProvider

java.lang.Object

org.biojava.nbio.structure.domain.PDBDomainProvider

All Implemented Interfaces:

DomainProvider

public class PDBDomainProvider
extends Object
implements DomainProvider

Class to fetch domains through the RCSB's REST API.

Author:

Spencer Bliven

Field Summary

Fields

Modifier and Type	Field and Description
static String	DEFAULT_PDB_API_URL
static String	DEFAULT_PDB_HOST

Constructor Summary

Constructors

Constructor and Description
PDBDomainProvider()
PDBDomainProvider(String base, int cutoff)

Method Summary

Methods

Modifier and Type	Method and Description
SortedSet<String>	getDomainNames(String name) Gets a list of domain representatives for a given PDB ID.
SortedSet<String>	getRepresentativeDomains() Gets a list of all domain representatives
static void	main(String[] args)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_PDB_HOST

public static final String DEFAULT_PDB_HOST

See Also:

Constant Field Values

DEFAULT_PDB_API_URL

public static final String DEFAULT_PDB_API_URL

See Also:

Constant Field Values

Constructor Detail

PDBDomainProvider

public PDBDomainProvider()

PDBDomainProvider

public PDBDomainProvider(String base,
                 int cutoff)

Parameters:

base -

cutoff -

Method Detail

getDomainNames

public SortedSet<String> getDomainNames(String name)

Gets a list of domain representatives for a given PDB ID.

Specified by:

getDomainNames in interface DomainProvider

Parameters:

name - a structure identifier

Returns:

A list of domain names

getRepresentativeDomains

public SortedSet<String> getRepresentativeDomains()

Gets a list of all domain representatives

Specified by:

getRepresentativeDomains in interface DomainProvider

Returns:

A full list of all representative domains recognized by this provider

main

public static void main(String[] args)