org.biojava.bio.structure.quaternary

Class BiologicalAssemblyBuilder

java.lang.Object

org.biojava.bio.structure.quaternary.BiologicalAssemblyBuilder

public class BiologicalAssemblyBuilder
extends java.lang.Object

Reconstructs the quaternary structure of a protein from an asymmetric unit

Author:

Peter Rose, Andreas Prlic

Constructor Summary

Constructors

Constructor and Description
BiologicalAssemblyBuilder()

Method Summary

Methods

Modifier and Type	Method and Description
java.util.ArrayList<ModelTransformationMatrix>	getBioUnitTransformationList(PdbxStructAssembly psa, java.util.List<PdbxStructAssemblyGen> psags, java.util.List<PdbxStructOperList> operators) Returns a list of transformation matrices for the generation of a macromolecular assembly for the specified assembly Id.
Structure	rebuildQuaternaryStructure(Structure asymUnit, java.util.List<ModelTransformationMatrix> transformations)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BiologicalAssemblyBuilder

public BiologicalAssemblyBuilder()

Method Detail

rebuildQuaternaryStructure

public Structure rebuildQuaternaryStructure(Structure asymUnit,
                                   java.util.List<ModelTransformationMatrix> transformations)

getBioUnitTransformationList

public java.util.ArrayList<ModelTransformationMatrix> getBioUnitTransformationList(PdbxStructAssembly psa,
                                                                          java.util.List<PdbxStructAssemblyGen> psags,
                                                                          java.util.List<PdbxStructOperList> operators)

Returns a list of transformation matrices for the generation of a macromolecular assembly for the specified assembly Id.

Parameters:

assemblyId - Id of the macromolecular assembly to be generated

Returns:

list of transformation matrices to generate macromolecular assembly