org.biojava.bio.structure.quaternary.io
Interface RawBioUnitDataProvider

All Known Implementing Classes:

MmCifPDBBiolAssemblyProvider, RemoteRawBioUnitDataProvider

public interface RawBioUnitDataProvider

Defines the methods that have to be implemented by a class that provides the data that is necessary to recreate the correct biological assembly of a protein. This is very close to the way PDB is representing biological assemblies. For the outside it is probably easier to use the other way of accessing the data as defined in BioUnitDataProvider

Since:

3.0.5

Author:

Andreas Prlic

Method Summary

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
boolean	hasBiolAssembly() Does the PDB ID have biological assembly information?
void	setPdbId(java.lang.String pdbId) Tell the provider for which PDB ID the quaternary structure should be returned.

Method Detail

setPdbId

void setPdbId(java.lang.String pdbId)

Tell the provider for which PDB ID the quaternary structure should be returned.

Parameters:

pdbId -

getPdbxStructAssemblies

java.util.List<PdbxStructAssembly> getPdbxStructAssemblies()

Data access method for list describing all assemblies

Returns:

getPdbxStructAssemblyGens

java.util.List<PdbxStructAssemblyGen> getPdbxStructAssemblyGens()

Data access method for list describing all assemblies

Returns:

getPdbxStructOperList

java.util.List<PdbxStructOperList> getPdbxStructOperList()

Get all the possible operators

Returns:

getNrBiolAssemblies

int getNrBiolAssemblies()

Returns the number of available biological assemblies.

Returns:

hasBiolAssembly

boolean hasBiolAssembly()

Does the PDB ID have biological assembly information?

Returns:

boolean flag

getPdbxStructAssembly

PdbxStructAssembly getPdbxStructAssembly(int biolAssemblyNr)

get the data for a particular pdbxStructAssembly. We start counting at 0.

Parameters:

biolAssemblyNr -

Returns:

getPdbxStructAssemblyGen

java.util.List<PdbxStructAssemblyGen> getPdbxStructAssemblyGen(int biolAssemblyNr)

get the data for a particular pdbxStructAssemblyGen. We start counting at 0.

Parameters:

biolAssemblyNr -

Returns: