org.biojava.nbio.structure.quaternary.io

Interface BioUnitDataProvider

All Known Implementing Classes:

MmCifBiolAssemblyProvider, PDBBioUnitDataProvider, RemoteBioUnitDataProvider

public interface BioUnitDataProvider

Provides access to the data that is needed in order to rebuild the correct biological assembly of a protein. This is probably the simpler approach of accessing the necessary information. There is a second access layer, which is closer to the way the PDB is representing the files, it is defined by the interface RawBioUnitDataProvider.

Author:

Andreas Prlic

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?
void	setAsymUnit(Structure asymUnit)
void	setAtomCache(AtomCache cache) Set an AtomCache to use when fetching asymmetric units.

Method Detail

getBioUnitTransformationList

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

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

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

int getNrBiolAssemblies(String pdbId)

Returns the number of available biological assemblies.

Parameters:

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

Returns:

nr of available assemblies.

hasBiolAssembly

boolean hasBiolAssembly(String pdbId)

Does the PDB ID have biological assembly information?

Parameters:

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

Returns:

boolean flag

getAsymUnit

Structure getAsymUnit(String pdbId)

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

Parameters:

pdbId -

Returns:

setAsymUnit

void setAsymUnit(Structure asymUnit)

setAtomCache

void setAtomCache(AtomCache cache)

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

Parameters:

cache -

getAtomCache

AtomCache getAtomCache()

Returns:

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