org.biojava.nbio.structure.rcsb

Class PdbIdLists

java.lang.Object

org.biojava.nbio.structure.rcsb.PdbIdLists

public class PdbIdLists
extends Object

Utility classes for retrieving lists of PDB IDs.

Since:

4.2.0

Author:

Andreas Prlic

Field Summary

Fields

Modifier and Type	Field and Description
static String	SERVICELOCATION

Constructor Summary

Constructors

Constructor and Description
PdbIdLists()

Method Summary

Modifier and Type	Method and Description
static InputStream	doPOST(URL url, String data) do a POST to a URL and return the response stream for further processing elsewhere.
static Set<String>	getAllViruses() Get the PDB IDs of all virus structures in the current PDB
static Set<String>	getCurrentPDBIds() get the list of current PDB IDs
static Set<String>	getGagPolyproteins() get all PDB IDs of gag-polyproteins
static Set<String>	getNMRStructures() get list of all current NMR structures
static Set<String>	getNucleotides()
static Set<String>	getRibosomes()
static Set<String>	getTransmembraneProteins() get all Transmembrane proteins
static void	main(String[] args)
static Set<String>	postQuery(String xml) post am XML query (PDB XML query format) to the RESTful RCSB web service

Methods inherited from class java.lang.Object

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

Field Detail

SERVICELOCATION

public static final String SERVICELOCATION

See Also:

Constant Field Values

Constructor Detail

PdbIdLists

public PdbIdLists()

Method Detail

getCurrentPDBIds

public static Set<String> getCurrentPDBIds()
                                    throws IOException

get the list of current PDB IDs

Returns:

list of current PDB IDs

Throws:

IOException

getAllViruses

public static Set<String> getAllViruses()
                                 throws IOException

Get the PDB IDs of all virus structures in the current PDB

Returns:

list of all virus structures

Throws:

IOException

getNMRStructures

public static Set<String> getNMRStructures()
                                    throws IOException

get list of all current NMR structures

Returns:

list of NMR structures

Throws:

IOException

getGagPolyproteins

public static Set<String> getGagPolyproteins()
                                      throws IOException

get all PDB IDs of gag-polyproteins

Returns:

list of PDB IDs

Throws:

IOException

getTransmembraneProteins

public static Set<String> getTransmembraneProteins()
                                            throws IOException

get all Transmembrane proteins

Returns:

list of PDB IDs

Throws:

IOException

getNucleotides

public static Set<String> getNucleotides()
                                  throws IOException

Throws:

IOException

getRibosomes

public static Set<String> getRibosomes()
                                throws IOException

Throws:

IOException

postQuery

public static Set<String> postQuery(String xml)
                             throws IOException

post am XML query (PDB XML query format) to the RESTful RCSB web service

Parameters:

xml -

Returns:

a list of PDB ids.

Throws:

IOException

doPOST

public static InputStream doPOST(URL url,
                                 String data)
                          throws IOException

do a POST to a URL and return the response stream for further processing elsewhere.

Parameters:

url -

Returns:

Throws:

IOException

main

public static void main(String[] args)