org.biojava.nbio.structure.domain

Interface PDPProvider

All Known Implementing Classes:

RemotePDPProvider

public interface PDPProvider

Decomposes a structure into representative PDP domains. Implementations will probably want to also implement DomainProvider, which provides a very similar set of methods for general structure domain decomposition.

Since:

3.0.2

Author:

Andreas Prlic

Method Summary

Methods

Modifier and Type	Method and Description
Structure	getDomain(String pdpDomainName, AtomCache cache) Get the structure for a particular PDP domain
PDPDomain	getPDPDomain(String pdpDomainName) Get a StructureIdentifier representing the specified PDP domain.
SortedSet<String>	getPDPDomainNamesForPDB(String pdbId) Get a list of all PDP domains for a given PDB entry

Method Detail

getPDPDomainNamesForPDB

SortedSet<String> getPDPDomainNamesForPDB(String pdbId)
                                          throws IOException

Get a list of all PDP domains for a given PDB entry

Parameters:

pdbId - PDB ID

Returns:

Set of domain names, e.g. "PDP:4HHBAa"

Throws:

IOException

getDomain

Structure getDomain(String pdpDomainName,
                  AtomCache cache)
                    throws IOException,
                           StructureException

Get the structure for a particular PDP domain

Parameters:

pdpDomainName - PDP identifier, e.g. "PDP:4HHBAa"

cache - AtomCache, responsible for fetching and storing the coordinates

Returns:

Structure representing the PDP domain

Throws:

IOException - For IO errors, e.g. when parsing PDP information

StructureException - For errors creating the structure

getPDPDomain

PDPDomain getPDPDomain(String pdpDomainName)
                       throws IOException

Get a StructureIdentifier representing the specified PDP domain.

Parameters:

pdpDomainName - PDP domain name

Returns:

a PDPDomain representing this domain name

Throws:

IOException