Package org.biojava.nbio.structure

Class PDBStatus

java.lang.Object

org.biojava.nbio.structure.PDBStatus

public class PDBStatus
extends Object

Methods for getting the status of a PDB file (current, removed, unreleased) and for accessing different versions of the structure.

All methods query the RCSB Data REST API

Since:

3.0.2

Author:

Spencer Bliven, Amr ALHOSSARY, Jose Duarte

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	PDBStatus.Status	Represents a simplified 3 state status of PDB IDs.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	ALL_CURRENT_ENDPOINT
static final String	DEFAULT_RCSB_DATA_API_SERVER
static final String	STATUS_ENDPOINT
static final String	STATUS_LIST_ENDPOINT

Constructor Summary

Constructors

Constructor	Description
PDBStatus()

Method Summary

Modifier and Type	Method	Description
static String	getCurrent(String oldPdbId)	Gets the current version of a PDB ID.
static SortedSet<String>	getCurrentPDBIds()	Returns all current PDB IDs
static PDBStatus.Status	getStatus(String pdbId)	Get the status of a PDB id.
static PDBStatus.Status[]	getStatus(String[] pdbIds)	Get the status of a collection of PDB ids (in a single API query).
static void	main(String[] args)

Methods inherited from class java.lang.Object

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

Field Details

DEFAULT_RCSB_DATA_API_SERVER

public static final String DEFAULT_RCSB_DATA_API_SERVER

See Also:

• Constant Field Values

ALL_CURRENT_ENDPOINT

public static final String ALL_CURRENT_ENDPOINT

See Also:

• Constant Field Values

STATUS_ENDPOINT

public static final String STATUS_ENDPOINT

See Also:

• Constant Field Values

STATUS_LIST_ENDPOINT

public static final String STATUS_LIST_ENDPOINT

See Also:

• Constant Field Values

Constructor Details

PDBStatus

public PDBStatus()

Method Details

getStatus

public static PDBStatus.Status getStatus(String pdbId)
                                  throws IOException

Get the status of a PDB id.

Parameters:

pdbId - the id

Returns:

The status.

Throws:

IOException

getStatus

public static PDBStatus.Status[] getStatus(String[] pdbIds)
                                    throws IOException

Get the status of a collection of PDB ids (in a single API query).

Parameters:

pdbIds - the ids

Returns:

The status array

Throws:

IOException

See Also:

• getStatus(String)

getCurrent

public static String getCurrent(String oldPdbId)
                         throws IOException

Gets the current version of a PDB ID.

Parameters:

oldPdbId - the id

Returns:

The replacement for oldPdbId, or null if none are found. If entry is current then the input PDB id is returned

Throws:

IOException

getCurrentPDBIds

public static SortedSet<String> getCurrentPDBIds()
                                          throws IOException

Returns all current PDB IDs

Returns:

a list of PDB IDs

Throws:

IOException - if a problem occurs retrieving the information

main

public static void main(String[] args)
                 throws Exception

Throws:

Exception