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

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

Method Detail

getVersion

java.lang.String getVersion()
                     throws java.io.IOException

Return the release version.

Returns:

version

Throws:

java.io.IOException

getDomainsById

EcodDomain getDomainsById(java.lang.String ecodId)
                   throws java.io.IOException

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

Parameters:

ecodId -

Returns:

Throws:

java.io.IOException

getDomainsForPdb

java.util.List<EcodDomain> getDomainsForPdb(java.lang.String pdbId)
                                     throws java.io.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:

java.io.IOException

filterByHierarchy

java.util.List<EcodDomain> filterByHierarchy(java.lang.String hierarchy)
                                      throws java.io.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:

java.io.IOException

getAllDomains

java.util.List<EcodDomain> getAllDomains()
                                  throws java.io.IOException

Get all ECOD domains

Returns:

Throws:

java.io.IOException