org.biojava.nbio.structure.quaternary

Class BiologicalAssemblyBuilder

java.lang.Object

org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder

public class BiologicalAssemblyBuilder
extends 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

Modifier and Type	Method and Description
ArrayList<BiologicalAssemblyTransformation>	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.
Structure	rebuildQuaternaryStructure(Structure asymUnit, List<BiologicalAssemblyTransformation> 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,
                                            List<BiologicalAssemblyTransformation> transformations)

getBioUnitTransformationList

public ArrayList<BiologicalAssemblyTransformation> 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.

Parameters:

assemblyId - Id of the macromolecular assembly to be generated

Returns:

list of transformation matrices to generate macromolecular assembly