org.rcsb.mmtf.dataholders

Class BioAssemblyTransformation

java.lang.Object

org.rcsb.mmtf.dataholders.BioAssemblyTransformation

All Implemented Interfaces:

Serializable

public class BioAssemblyTransformation
extends Object
implements Serializable

The transformation needed for generation of biological assemblies from the contents of a PDB/mmCIF file. It contains both the actual transformation (rotation+translation) and the chain identifier to which it should be applied.

Author:

Anthony Bradley

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
BioAssemblyTransformation()

Method Summary

Modifier and Type	Method and Description
int[]	getChainIndexList() Gets the indices of the chains this bioassembly refers to.
double[]	getMatrix() Gets the 4x4 matrix transformation specifying a rotation and a translation.
void	setChainIndexList(int[] inputChainId) Sets the chain id.
void	setMatrix(double[] transformation) Sets the 4x4 matrix transformation specifying a rotation and a translation.

Methods inherited from class java.lang.Object

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

Constructor Detail

BioAssemblyTransformation

public BioAssemblyTransformation()

Method Detail

getMatrix

public double[] getMatrix()

Gets the 4x4 matrix transformation specifying a rotation and a translation. Stored linearly in row major order.

Returns:

the transformation

setMatrix

public void setMatrix(double[] transformation)

Sets the 4x4 matrix transformation specifying a rotation and a translation. Stored linearly in row major order.

Parameters:

transformation - the new transformation

getChainIndexList

public int[] getChainIndexList()

Gets the indices of the chains this bioassembly refers to.

Returns:

a list of integers indicating the indices (zero indexed) of the chains this bioassembly refers to.

setChainIndexList

public void setChainIndexList(int[] inputChainId)

Sets the chain id.

Parameters:

inputChainId - a list of integers indicating the indices (zero indexed) of the chains this bioassembly refers to.