java.lang.Object
- org.biojava.nbio.structure.quaternary.io.PDBBioUnitDataProvider

All Implemented Interfaces:

BioUnitDataProvider
```
public class PDBBioUnitDataProvider
extends java.lang.Object
implements BioUnitDataProvider
```
A BioUnitDataProvider that extracts the necessary info from PDB files

Author:

Andreas Prlic

Constructor Summary

Constructors
Constructor Description

PDBBioUnitDataProvider()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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()`
`java.util.List<BiologicalAssemblyTransformation>`	`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)`
`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(java.lang.String pdbId)
```
  - 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<BiologicalAssemblyTransformation> 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)
```
    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

Class PDBBioUnitDataProvider

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

PDBBioUnitDataProvider

Method Detail

loadPDB

getAsymUnit

setAsymUnit

getBioUnitTransformationList

getNrBiolAssemblies

hasBiolAssembly

setAtomCache

getAtomCache