org.biojava.bio.structure.quaternary.io
Class FileBasedPDBBioUnitDataProvider

java.lang.Object
  org.biojava.bio.structure.quaternary.io.FileBasedPDBBioUnitDataProvider

All Implemented Interfaces:

BioUnitDataProvider

public class FileBasedPDBBioUnitDataProvider
extends java.lang.Object
implements BioUnitDataProvider

A biounit provider that loads the biol assembly from thepublic PDB file, rather than re-creating it on the fly out of the default PDB file for the asym unit

Author:

Andreas Prlic

Constructor Summary

FileBasedPDBBioUnitDataProvider()

Method Summary

Structure	getAsymUnit(java.lang.String pdbId) load the asym unit, but set the info how to re-create the bio unit in the PdbHeader object
AtomCache	getAtomCache()
Structure	getBioUnit(java.lang.String pdbId, int bioUnit)
java.util.List<ModelTransformationMatrix>	getBioUnitTransformationList(java.lang.String pdbId, int biolAssemblyNr) get the data for a particular assembly, counting starts at 1...
int	getNrBiolAssemblies(java.lang.String pdbId) Returns the number of available biological assemblies.
boolean	hasBiolAssembly(java.lang.String pdbId) Does the PDB ID have biological assembly information?
PDBHeader	loadPDB(java.lang.String pdbId, int bioUnit)
void	setAsymUnit(Structure s)
void	setAtomCache(AtomCache cache)

Methods inherited from class java.lang.Object

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

Constructor Detail

FileBasedPDBBioUnitDataProvider

public FileBasedPDBBioUnitDataProvider()

Method Detail

getBioUnit

public Structure getBioUnit(java.lang.String pdbId,
                            int bioUnit)
                     throws java.io.IOException

Throws:

java.io.IOException

loadPDB

public PDBHeader loadPDB(java.lang.String pdbId,
                         int bioUnit)

getAsymUnit

public Structure getAsymUnit(java.lang.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 java.util.List<ModelTransformationMatrix> getBioUnitTransformationList(java.lang.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(java.lang.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(java.lang.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)

Specified by:

setAtomCache in interface BioUnitDataProvider

getAtomCache

public AtomCache getAtomCache()

Specified by:

getAtomCache in interface BioUnitDataProvider