Uses of Class
org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation
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Packages that use BiologicalAssemblyTransformation Package Description org.biojava.nbio.structure.quaternary -
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Uses of BiologicalAssemblyTransformation in org.biojava.nbio.structure.quaternary
Methods in org.biojava.nbio.structure.quaternary that return BiologicalAssemblyTransformation Modifier and Type Method 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 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 ofBiologicalAssemblyTransformation
s needed to generate the biological assembly.Methods in org.biojava.nbio.structure.quaternary with parameters of type BiologicalAssemblyTransformation Modifier and Type Method Description static BiologicalAssemblyTransformation
BiologicalAssemblyTransformation. combine(BiologicalAssemblyTransformation matrix1, BiologicalAssemblyTransformation matrix2)
Returns the combination (product) of two biological assembly transformations.int
BiologicalAssemblyTransformation. compareTo(BiologicalAssemblyTransformation other)
Method parameters in org.biojava.nbio.structure.quaternary with type arguments of type BiologicalAssemblyTransformation Modifier and Type Method 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, boolean useAsymIds, boolean multiModel)
Builds a Structure object containing the quaternary structure built from given asymUnit and transformations, by adding symmetry partners as new models.void
BioAssemblyInfo. setTransforms(List<BiologicalAssemblyTransformation> transforms)
Constructors in org.biojava.nbio.structure.quaternary with parameters of type BiologicalAssemblyTransformation Constructor Description BiologicalAssemblyTransformation(BiologicalAssemblyTransformation src)
Copy Constructor
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