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

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

All Implemented Interfaces:

RawBioUnitDataProvider

public class MmCifPDBBiolAssemblyProvider
extends java.lang.Object
implements RawBioUnitDataProvider

A provider for information about biological units for PDB files that is based on reading local MMcif files.

Author:

Andreas Prlic

Constructor Summary

MmCifPDBBiolAssemblyProvider()

Method Summary

Structure	getAsymUnit() get the asym unit for this PDB ID
AtomCache	getAtomCache()
int	getNrBiolAssemblies() Returns the number of available biological assemblies.
java.lang.String	getPdbId()
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
boolean	hasBiolAssembly() Does the PDB ID have biological assembly information?
void	setAsymUnit(Structure s)
void	setAtomCache(AtomCache cache)
void	setPdbId(java.lang.String pdbId) Tell the provider for which PDB ID the quaternary structure should be returned.

Methods inherited from class java.lang.Object

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

Constructor Detail

MmCifPDBBiolAssemblyProvider

public MmCifPDBBiolAssemblyProvider()

Method Detail

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

getPdbId

public java.lang.String getPdbId()

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:

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:

getAsymUnit

public Structure getAsymUnit()

get the asym unit for this PDB ID

Returns:

setAsymUnit

public void setAsymUnit(Structure s)

getAtomCache

public AtomCache getAtomCache()

setAtomCache

public void setAtomCache(AtomCache cache)