Interface BioUnitDataProvider
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- All Known Implementing Classes:
MmCifBiolAssemblyProvider
,PDBBioUnitDataProvider
,RemoteBioUnitDataProvider
public interface BioUnitDataProvider
Provides access to the data that is needed in order to rebuild the correct biological assembly of a protein. This is probably the simpler approach of accessing the necessary information. There is a second access layer, which is closer to the way the PDB is representing the files, it is defined by the interface RawBioUnitDataProvider.- Author:
- Andreas Prlic
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Method Summary
All Methods Instance Methods Abstract 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 objectAtomCache
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?void
setAsymUnit(Structure asymUnit)
void
setAtomCache(AtomCache cache)
Set an AtomCache to use when fetching asymmetric units.
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Method Detail
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getBioUnitTransformationList
java.util.List<BiologicalAssemblyTransformation> getBioUnitTransformationList(java.lang.String pdbId, int biolAssemblyNr)
get the data for a particular assembly, counting starts at 1...- Parameters:
pdbId
- the PDB ID. E.g. 1STPbiolAssemblyNr
- the number of the assembly, the first one is nr 1. 0 refers to the asym unit- Returns:
- list of transformations.
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getNrBiolAssemblies
int getNrBiolAssemblies(java.lang.String pdbId)
Returns the number of available biological assemblies.- Parameters:
pdbId
- the PDB ID. E.g. 1STP- Returns:
- nr of available assemblies.
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hasBiolAssembly
boolean hasBiolAssembly(java.lang.String pdbId)
Does the PDB ID have biological assembly information?- Parameters:
pdbId
- the PDB ID. E.g. 1STP- Returns:
- boolean flag
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getAsymUnit
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- Parameters:
pdbId
-- Returns:
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setAsymUnit
void setAsymUnit(Structure asymUnit)
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setAtomCache
void setAtomCache(AtomCache cache)
Set an AtomCache to use when fetching asymmetric units. If null, a new cache will be created with default parameters.- Parameters:
cache
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getAtomCache
AtomCache getAtomCache()
- Returns:
- The current cache, or null if no cache has been initialized
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