public class PDBBioUnitDataProvider extends java.lang.Object implements BioUnitDataProvider
Constructor and Description |
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PDBBioUnitDataProvider() |
Modifier and Type | Method and Description |
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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
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AtomCache |
getAtomCache() |
java.util.List<BiologicalAssemblyTransformation> |
getBioUnitTransformationList(java.lang.String pdbId,
int biolAssemblyNr)
get the data for a particular assembly, counting starts at 1...
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int |
getNrBiolAssemblies(java.lang.String pdbId)
Returns the number of available biological assemblies.
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boolean |
hasBiolAssembly(java.lang.String pdbId)
Does the PDB ID have biological assembly information?
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PDBHeader |
loadPDB(java.lang.String pdbId) |
void |
setAsymUnit(Structure s) |
void |
setAtomCache(AtomCache cache)
Set an AtomCache to use when fetching asymmetric units.
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public PDBHeader loadPDB(java.lang.String pdbId)
public Structure getAsymUnit(java.lang.String pdbId)
BioUnitDataProvider
getAsymUnit
in interface BioUnitDataProvider
public void setAsymUnit(Structure s)
setAsymUnit
in interface BioUnitDataProvider
public java.util.List<BiologicalAssemblyTransformation> getBioUnitTransformationList(java.lang.String pdbId, int biolAssemblyNr)
BioUnitDataProvider
getBioUnitTransformationList
in interface BioUnitDataProvider
pdbId
- the PDB ID. E.g. 1STPbiolAssemblyNr
- the number of the assembly, the first one is nr 1. 0 refers to the asym unitpublic int getNrBiolAssemblies(java.lang.String pdbId)
BioUnitDataProvider
getNrBiolAssemblies
in interface BioUnitDataProvider
pdbId
- the PDB ID. E.g. 1STPpublic boolean hasBiolAssembly(java.lang.String pdbId)
BioUnitDataProvider
hasBiolAssembly
in interface BioUnitDataProvider
pdbId
- the PDB ID. E.g. 1STPpublic void setAtomCache(AtomCache cache)
BioUnitDataProvider
setAtomCache
in interface BioUnitDataProvider
public AtomCache getAtomCache()
getAtomCache
in interface BioUnitDataProvider