org.biojava.bio.structure.quaternary.io

Class RemoteRawBioUnitDataProvider

java.lang.Object

org.biojava.bio.structure.quaternary.io.RemoteRawBioUnitDataProvider

All Implemented Interfaces:

RawBioUnitDataProvider

public class RemoteRawBioUnitDataProvider
extends java.lang.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 and Description
static java.lang.String	DEFAULT_SERVERNAME
static java.lang.String	GET_ASSEMBLY
static java.lang.String	GET_ASSEMBLY_GENS
static java.lang.String	GET_STRUCT_OPER
static java.lang.String	NR_BIOL_APPEND

Constructor Summary

Constructors

Constructor and Description
RemoteRawBioUnitDataProvider()

Method Summary

Methods

Modifier and Type	Method and Description
int	getNrBiolAssemblies() Returns the number of available biological assemblies.
java.util.List<PdbxStructAssembly>	getPdbxStructAssemblies() Data access method for list describing all assemblies
PdbxStructAssembly	getPdbxStructAssembly(int biolAssemblyNr) get the data for a particular pdbxStructAssembly.
java.util.List<PdbxStructAssemblyGen>	getPdbxStructAssemblyGen(int biolAssemblyNr) get the data for a particular pdbxStructAssemblyGen.
java.util.List<PdbxStructAssemblyGen>	getPdbxStructAssemblyGens() Data access method for list describing all assemblies
java.util.List<PdbxStructOperList>	getPdbxStructOperList() Get all the possible operators
int	getTimeout()
boolean	hasBiolAssembly() Does the PDB ID have biological assembly information?
static void	main(java.lang.String[] args)
void	setPdbId(java.lang.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 Detail

DEFAULT_SERVERNAME

public static java.lang.String DEFAULT_SERVERNAME

NR_BIOL_APPEND

public static java.lang.String NR_BIOL_APPEND

GET_ASSEMBLY

public static java.lang.String GET_ASSEMBLY

GET_ASSEMBLY_GENS

public static java.lang.String GET_ASSEMBLY_GENS

GET_STRUCT_OPER

public static java.lang.String GET_STRUCT_OPER

Constructor Detail

RemoteRawBioUnitDataProvider

public RemoteRawBioUnitDataProvider()

Method Detail

main

public static void main(java.lang.String[] args)

getTimeout

public int getTimeout()

setTimeout

public void setTimeout(int timeout)

setPdbId

public void setPdbId(java.lang.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 java.util.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 java.util.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 java.util.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 java.util.List<PdbxStructOperList> getPdbxStructOperList()

Description copied from interface: RawBioUnitDataProvider

Get all the possible operators

Specified by:

getPdbxStructOperList in interface RawBioUnitDataProvider

Returns: