public class FileBasedPDBBioUnitDataProvider extends java.lang.Object implements BioUnitDataProvider
Constructor and Description |
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FileBasedPDBBioUnitDataProvider() |
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() |
Structure |
getBioUnit(java.lang.String pdbId,
int bioUnit) |
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,
int bioUnit) |
void |
setAsymUnit(Structure s) |
void |
setAtomCache(AtomCache cache) |
public Structure getBioUnit(java.lang.String pdbId, int bioUnit) throws java.io.IOException
java.io.IOException
public PDBHeader loadPDB(java.lang.String pdbId, int bioUnit)
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)
setAtomCache
in interface BioUnitDataProvider
public AtomCache getAtomCache()
getAtomCache
in interface BioUnitDataProvider