Class MmCifBiolAssemblyProvider
- java.lang.Object
-
- org.biojava.nbio.structure.quaternary.io.MmCifBiolAssemblyProvider
-
- All Implemented Interfaces:
BioUnitDataProvider
public class MmCifBiolAssemblyProvider extends java.lang.Object implements BioUnitDataProvider
-
-
Constructor Summary
Constructors Constructor Description MmCifBiolAssemblyProvider()
-
Method Summary
All Methods Instance Methods Concrete 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()
Structure
getBiolAssembly(java.lang.String pdbId, int biolAssemblyNr)
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 s)
void
setAtomCache(AtomCache cache)
Set an AtomCache to use when fetching asymmetric units.
-
-
-
Method Detail
-
getAsymUnit
public Structure getAsymUnit(java.lang.String pdbId)
Description copied from interface:BioUnitDataProvider
load the asym unit, but set the info how to re-create the bio unit in the PdbHeader object- Specified by:
getAsymUnit
in interfaceBioUnitDataProvider
- Returns:
-
setAsymUnit
public void setAsymUnit(Structure s)
- Specified by:
setAsymUnit
in interfaceBioUnitDataProvider
-
getBioUnitTransformationList
public java.util.List<BiologicalAssemblyTransformation> getBioUnitTransformationList(java.lang.String pdbId, int biolAssemblyNr)
Description copied from interface:BioUnitDataProvider
get the data for a particular assembly, counting starts at 1...- Specified by:
getBioUnitTransformationList
in interfaceBioUnitDataProvider
- 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.
-
getNrBiolAssemblies
public int getNrBiolAssemblies(java.lang.String pdbId)
Description copied from interface:BioUnitDataProvider
Returns the number of available biological assemblies.- Specified by:
getNrBiolAssemblies
in interfaceBioUnitDataProvider
- Parameters:
pdbId
- the PDB ID. E.g. 1STP- Returns:
- nr of available assemblies.
-
hasBiolAssembly
public boolean hasBiolAssembly(java.lang.String pdbId)
Description copied from interface:BioUnitDataProvider
Does the PDB ID have biological assembly information?- Specified by:
hasBiolAssembly
in interfaceBioUnitDataProvider
- Parameters:
pdbId
- the PDB ID. E.g. 1STP- Returns:
- boolean flag
-
getBiolAssembly
public Structure getBiolAssembly(java.lang.String pdbId, int biolAssemblyNr) throws java.io.IOException, StructureException
- Throws:
java.io.IOException
StructureException
-
setAtomCache
public void setAtomCache(AtomCache cache)
Description copied from interface:BioUnitDataProvider
Set an AtomCache to use when fetching asymmetric units. If null, a new cache will be created with default parameters.- Specified by:
setAtomCache
in interfaceBioUnitDataProvider
-
getAtomCache
public AtomCache getAtomCache()
- Specified by:
getAtomCache
in interfaceBioUnitDataProvider
- Returns:
- The current cache, or null if no cache has been initialized
-
-