Class MmCifPDBBiolAssemblyProvider
- java.lang.Object
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- org.biojava.nbio.structure.quaternary.io.MmCifPDBBiolAssemblyProvider
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- 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
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Constructor Summary
Constructors Constructor Description MmCifPDBBiolAssemblyProvider()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Structure
getAsymUnit()
get the asym unit for this PDB IDAtomCache
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 assembliesPdbxStructAssembly
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 assembliesjava.util.List<PdbxStructOperList>
getPdbxStructOperList()
Get all the possible operatorsboolean
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.
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Method Detail
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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 interfaceRawBioUnitDataProvider
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getPdbId
public java.lang.String getPdbId()
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getPdbxStructAssemblies
public java.util.List<PdbxStructAssembly> getPdbxStructAssemblies()
Description copied from interface:RawBioUnitDataProvider
Data access method for list describing all assemblies- Specified by:
getPdbxStructAssemblies
in interfaceRawBioUnitDataProvider
- Returns:
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getPdbxStructAssemblyGens
public java.util.List<PdbxStructAssemblyGen> getPdbxStructAssemblyGens()
Description copied from interface:RawBioUnitDataProvider
Data access method for list describing all assemblies- Specified by:
getPdbxStructAssemblyGens
in interfaceRawBioUnitDataProvider
- Returns:
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getPdbxStructOperList
public java.util.List<PdbxStructOperList> getPdbxStructOperList()
Description copied from interface:RawBioUnitDataProvider
Get all the possible operators- Specified by:
getPdbxStructOperList
in interfaceRawBioUnitDataProvider
- Returns:
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getNrBiolAssemblies
public int getNrBiolAssemblies()
Description copied from interface:RawBioUnitDataProvider
Returns the number of available biological assemblies.- Specified by:
getNrBiolAssemblies
in interfaceRawBioUnitDataProvider
- Returns:
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hasBiolAssembly
public boolean hasBiolAssembly()
Description copied from interface:RawBioUnitDataProvider
Does the PDB ID have biological assembly information?- Specified by:
hasBiolAssembly
in interfaceRawBioUnitDataProvider
- Returns:
- boolean flag
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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 interfaceRawBioUnitDataProvider
- Returns:
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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 interfaceRawBioUnitDataProvider
- Returns:
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getAsymUnit
public Structure getAsymUnit()
get the asym unit for this PDB ID- Returns:
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setAsymUnit
public void setAsymUnit(Structure s)
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getAtomCache
public AtomCache getAtomCache()
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setAtomCache
public void setAtomCache(AtomCache cache)
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