org.biojava.nbio.structure.quaternary.io

Class PDBBioUnitDataProvider

java.lang.Object

org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider

All Implemented Interfaces:

BioUnitDataProvider

public class PDBBioUnitDataProvider
extends Object
implements BioUnitDataProvider

A BioUnitDataProvider that extracts the necessary info from PDB files

Author:

Andreas Prlic

Constructor Summary

Constructors

Constructor and Description
PDBBioUnitDataProvider()

Method Summary

Modifier and Type	Method and Description
Structure	getAsymUnit(String pdbId) load the asym unit, but set the info how to re-create the bio unit in the PdbHeader object
AtomCache	getAtomCache()
List<BiologicalAssemblyTransformation>	getBioUnitTransformationList(String pdbId, int biolAssemblyNr) get the data for a particular assembly, counting starts at 1...
int	getNrBiolAssemblies(String pdbId) Returns the number of available biological assemblies.
boolean	hasBiolAssembly(String pdbId) Does the PDB ID have biological assembly information?
PDBHeader	loadPDB(String pdbId)
void	setAsymUnit(Structure s)
void	setAtomCache(AtomCache cache) Set an AtomCache to use when fetching asymmetric units.

Methods inherited from class java.lang.Object

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

Constructor Detail

PDBBioUnitDataProvider

public PDBBioUnitDataProvider()

Method Detail

loadPDB

public PDBHeader loadPDB(String pdbId)

getAsymUnit

public Structure getAsymUnit(String pdbId)

Description copied from interface: BioUnitDataProvider

load the asym unit, but set the info how to re-create the bio unit in the PdbHeader object

Specified by:

getAsymUnit in interface BioUnitDataProvider

Returns:

setAsymUnit

public void setAsymUnit(Structure s)

Specified by:

setAsymUnit in interface BioUnitDataProvider

getBioUnitTransformationList

public List<BiologicalAssemblyTransformation> getBioUnitTransformationList(String pdbId,
                                                                           int biolAssemblyNr)

Description copied from interface: BioUnitDataProvider

get the data for a particular assembly, counting starts at 1...

Specified by:

getBioUnitTransformationList in interface BioUnitDataProvider

Parameters:

pdbId - the PDB ID. E.g. 1STP

biolAssemblyNr - the number of the assembly, the first one is nr 1. 0 refers to the asym unit

Returns:

list of transformations.

getNrBiolAssemblies

public int getNrBiolAssemblies(String pdbId)

Description copied from interface: BioUnitDataProvider

Returns the number of available biological assemblies.

Specified by:

getNrBiolAssemblies in interface BioUnitDataProvider

Parameters:

pdbId - the PDB ID. E.g. 1STP

Returns:

nr of available assemblies.

hasBiolAssembly

public boolean hasBiolAssembly(String pdbId)

Description copied from interface: BioUnitDataProvider

Does the PDB ID have biological assembly information?

Specified by:

hasBiolAssembly in interface BioUnitDataProvider

Parameters:

pdbId - the PDB ID. E.g. 1STP

Returns:

boolean flag

setAtomCache

public void setAtomCache(AtomCache cache)

Description copied from interface: BioUnitDataProvider

Set an AtomCache to use when fetching asymmetric units. If null, a new cache will be created with default parameters.

Specified by:

setAtomCache in interface BioUnitDataProvider

getAtomCache

public AtomCache getAtomCache()

Specified by:

getAtomCache in interface BioUnitDataProvider

Returns:

The current cache, or null if no cache has been initialized