java.lang.Object

org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider

All Implemented Interfaces:: RawBioUnitDataProvider

public class RemoteRawBioUnitDataProvider extends Object implements RawBioUnitDataProvider

A BioUnitDataProvider that fetches the symmetry operations via remote calls to servers from RCSB PDB

Author:: Andreas Prlic

Field Summary

Fields

Modifier and Type

Field

Description

static String

DEFAULT_SERVERNAME

static String

GET_ASSEMBLY

static String

GET_ASSEMBLY_GENS

static String

GET_STRUCT_OPER

static String

NR_BIOL_APPEND
Constructor Summary

Constructors

Constructor

Description

RemoteRawBioUnitDataProvider()
Method Summary

Modifier and Type

Method

Description

int

getNrBiolAssemblies()

Returns the number of available biological assemblies.

List<PdbxStructAssembly>

getPdbxStructAssemblies()

Data access method for list describing all assemblies

PdbxStructAssembly

getPdbxStructAssembly(int biolAssemblyNr)

get the data for a particular pdbxStructAssembly.

List<PdbxStructAssemblyGen>

getPdbxStructAssemblyGen(int biolAssemblyNr)

get the data for a particular pdbxStructAssemblyGen.

List<PdbxStructAssemblyGen>

getPdbxStructAssemblyGens()

Data access method for list describing all assemblies

List<PdbxStructOperList>

getPdbxStructOperList()

Get all the possible operators

int

getTimeout()

boolean

hasBiolAssembly()

Does the PDB ID have biological assembly information?

static void

main(String[] args)

void

setPdbId(String pdbId)

Tell the provider for which PDB ID the quaternary structure should be returned.

void

setTimeout(int timeout)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- DEFAULT_SERVERNAME
  
  public static String DEFAULT_SERVERNAME
- NR_BIOL_APPEND
  
  public static String NR_BIOL_APPEND
- GET_ASSEMBLY
  
  public static String GET_ASSEMBLY
- GET_ASSEMBLY_GENS
  
  public static String GET_ASSEMBLY_GENS
- GET_STRUCT_OPER
  
  public static String GET_STRUCT_OPER
Constructor Details
- RemoteRawBioUnitDataProvider
  
  public RemoteRawBioUnitDataProvider()
Method Details
- main
  
  public static void main(String[] args)
- getTimeout
  
  public int getTimeout()
- setTimeout
  
  public void setTimeout(int timeout)
- setPdbId
  
  public void setPdbId(String pdbId)
  
  Description copied from interface: RawBioUnitDataProvider
  
  Tell the provider for which PDB ID the quaternary structure should be returned.
  
  Specified by:
  
  setPdbId in interface RawBioUnitDataProvider
- getNrBiolAssemblies
  
  public int getNrBiolAssemblies()
  
  Description copied from interface: RawBioUnitDataProvider
  
  Returns the number of available biological assemblies.
  
  Specified by:
  
  getNrBiolAssemblies in interface RawBioUnitDataProvider
  
  Returns:
- hasBiolAssembly
  
  public boolean hasBiolAssembly()
  
  Description copied from interface: RawBioUnitDataProvider
  
  Does the PDB ID have biological assembly information?
  
  Specified by:
  
  hasBiolAssembly in interface RawBioUnitDataProvider
  
  Returns:
  
  boolean flag
- getPdbxStructAssembly
  
  public PdbxStructAssembly getPdbxStructAssembly(int biolAssemblyNr)
  
  Description copied from interface: RawBioUnitDataProvider
  
  get the data for a particular pdbxStructAssembly. We start counting at 0.
  
  Specified by:
  
  getPdbxStructAssembly in interface RawBioUnitDataProvider
  
  Returns:
- getPdbxStructAssemblyGen
  
  public List<PdbxStructAssemblyGen> getPdbxStructAssemblyGen(int biolAssemblyNr)
  
  Description copied from interface: RawBioUnitDataProvider
  
  get the data for a particular pdbxStructAssemblyGen. We start counting at 0.
  
  Specified by:
  
  getPdbxStructAssemblyGen in interface RawBioUnitDataProvider
  
  Returns:
- getPdbxStructAssemblies
  
  public List<PdbxStructAssembly> getPdbxStructAssemblies()
  
  Description copied from interface: RawBioUnitDataProvider
  
  Data access method for list describing all assemblies
  
  Specified by:
  
  getPdbxStructAssemblies in interface RawBioUnitDataProvider
  
  Returns:
- getPdbxStructAssemblyGens
  
  public List<PdbxStructAssemblyGen> getPdbxStructAssemblyGens()
  
  Description copied from interface: RawBioUnitDataProvider
  
  Data access method for list describing all assemblies
  
  Specified by:
  
  getPdbxStructAssemblyGens in interface RawBioUnitDataProvider
  
  Returns:
- getPdbxStructOperList
  
  public List<PdbxStructOperList> getPdbxStructOperList()
  
  Description copied from interface: RawBioUnitDataProvider
  
  Get all the possible operators
  
  Specified by:
  
  getPdbxStructOperList in interface RawBioUnitDataProvider
  
  Returns:

Class RemoteRawBioUnitDataProvider

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

DEFAULT_SERVERNAME

NR_BIOL_APPEND

GET_ASSEMBLY

GET_ASSEMBLY_GENS

GET_STRUCT_OPER

Constructor Details

RemoteRawBioUnitDataProvider

Method Details

main

getTimeout

setTimeout

setPdbId

getNrBiolAssemblies

hasBiolAssembly

getPdbxStructAssembly

getPdbxStructAssemblyGen

getPdbxStructAssemblies

getPdbxStructAssemblyGens

getPdbxStructOperList