MmCifPDBBiolAssemblyProvider

java.lang.Object
- org.biojava.nbio.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

Constructors
Constructor Description

MmCifPDBBiolAssemblyProvider()

Constructors
Constructor	Description
`MmCifPDBBiolAssemblyProvider()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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)
```

Class MmCifPDBBiolAssemblyProvider

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

MmCifPDBBiolAssemblyProvider

Method Detail

setPdbId

getPdbId

getPdbxStructAssemblies

getPdbxStructAssemblyGens

getPdbxStructOperList

getNrBiolAssemblies

hasBiolAssembly

getPdbxStructAssembly

getPdbxStructAssemblyGen

getAsymUnit

setAsymUnit

getAtomCache

setAtomCache