org.biojava.nbio.structure.ecod

Interface EcodDatabase

All Known Implementing Classes:

EcodInstallation

public interface EcodDatabase

General API for interacting with ECOD.

Author:

Spencer Bliven

Method Summary

Methods

Modifier and Type	Method and Description
List<EcodDomain>	filterByHierarchy(String hierarchy) Get a list of domains within a particular level of the hierarchy
List<EcodDomain>	getAllDomains() Get all ECOD domains
EcodDomain	getDomainsById(String ecodId) Get a particular ECOD domain by the domain ID (e.g.
List<EcodDomain>	getDomainsForPdb(String pdbId) Get a list of all ECOD domains for a particular PDB ID
String	getVersion() Return the release version.

Method Detail

getVersion

String getVersion()
                  throws IOException

Return the release version.

Returns:

version

Throws:

IOException

getDomainsById

EcodDomain getDomainsById(String ecodId)
                          throws IOException

Get a particular ECOD domain by the domain ID (e.g. "e4hhbA1")

Parameters:

ecodId -

Returns:

Throws:

IOException

getDomainsForPdb

List<EcodDomain> getDomainsForPdb(String pdbId)
                                  throws IOException

Get a list of all ECOD domains for a particular PDB ID

Parameters:

pdbId -

Returns:

the list of domains, or null if no matching domains were found

Throws:

IOException

filterByHierarchy

List<EcodDomain> filterByHierarchy(String hierarchy)
                                   throws IOException

Get a list of domains within a particular level of the hierarchy

Parameters:

hierarchy - A dot-separated list giving the X-group, H-group, and/or T-group (e.g. "1.1" for all members of the RIFT-related H-group)

Returns:

Throws:

IOException

getAllDomains

List<EcodDomain> getAllDomains()
                               throws IOException

Get all ECOD domains

Returns:

Throws:

IOException