Uses of Class
org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation

Packages that use BiologicalAssemblyTransformation

Package	Description
org.biojava.nbio.structure.quaternary
org.biojava.nbio.structure.quaternary.io

Uses of BiologicalAssemblyTransformation in org.biojava.nbio.structure.quaternary

Methods in org.biojava.nbio.structure.quaternary that return BiologicalAssemblyTransformation

Modifier and Type	Method and Description
static BiologicalAssemblyTransformation	BiologicalAssemblyTransformation.combine(BiologicalAssemblyTransformation matrix1, BiologicalAssemblyTransformation matrix2) Returns the combination (product) of two biological assembly transformations.
static BiologicalAssemblyTransformation	BiologicalAssemblyTransformation.fromXML(String xml)

Methods in org.biojava.nbio.structure.quaternary that return types with arguments of type BiologicalAssemblyTransformation

Modifier and Type	Method and Description
static List<BiologicalAssemblyTransformation>	BiologicalAssemblyTransformation.fromMultiXML(String xml)
ArrayList<BiologicalAssemblyTransformation>	BiologicalAssemblyBuilder.getBioUnitTransformationList(PdbxStructAssembly psa, List<PdbxStructAssemblyGen> psags, List<PdbxStructOperList> operators) Returns a list of transformation matrices for the generation of a macromolecular assembly for the specified assembly Id.
List<BiologicalAssemblyTransformation>	BioAssemblyInfo.getTransforms() Return the list of BiologicalAssemblyTransformations needed to generate the biological assembly.

Methods in org.biojava.nbio.structure.quaternary with parameters of type BiologicalAssemblyTransformation

Modifier and Type	Method and Description
static BiologicalAssemblyTransformation	BiologicalAssemblyTransformation.combine(BiologicalAssemblyTransformation matrix1, BiologicalAssemblyTransformation matrix2) Returns the combination (product) of two biological assembly transformations.

Method parameters in org.biojava.nbio.structure.quaternary with type arguments of type BiologicalAssemblyTransformation

Modifier and Type	Method and Description
static double[][]	BioAssemblyTools.getBiologicalMoleculeBounds(Structure asymStructure, List<BiologicalAssemblyTransformation> transformations)
static double[]	BioAssemblyTools.getBiologicalMoleculeCentroid(Structure asymUnit, List<BiologicalAssemblyTransformation> transformations) Returns the centroid of the biological molecule.
static double	BioAssemblyTools.getBiologicalMoleculeMaximumExtend(Structure structure, List<BiologicalAssemblyTransformation> transformations) Returns the maximum extend of the biological molecule in the x, y, or z direction.
Structure	BiologicalAssemblyBuilder.rebuildQuaternaryStructure(Structure asymUnit, List<BiologicalAssemblyTransformation> transformations)
void	BioAssemblyInfo.setTransforms(List<BiologicalAssemblyTransformation> transforms)

Constructors in org.biojava.nbio.structure.quaternary with parameters of type BiologicalAssemblyTransformation

Constructor and Description
BiologicalAssemblyTransformation(BiologicalAssemblyTransformation src) Copy Constructor

Uses of BiologicalAssemblyTransformation in org.biojava.nbio.structure.quaternary.io

Methods in org.biojava.nbio.structure.quaternary.io that return types with arguments of type BiologicalAssemblyTransformation

Modifier and Type	Method and Description
List<BiologicalAssemblyTransformation>	MmCifBiolAssemblyProvider.getBioUnitTransformationList(String pdbId, int biolAssemblyNr)
List<BiologicalAssemblyTransformation>	PDBBioUnitDataProvider.getBioUnitTransformationList(String pdbId, int biolAssemblyNr)
List<BiologicalAssemblyTransformation>	RemoteBioUnitDataProvider.getBioUnitTransformationList(String pdbId, int biolAssemblyNr)
List<BiologicalAssemblyTransformation>	BioUnitDataProvider.getBioUnitTransformationList(String pdbId, int biolAssemblyNr) get the data for a particular assembly, counting starts at 1...