org.biojava.nbio.structure.xtal

Class UnitCellBoundingBox

java.lang.Object

org.biojava.nbio.structure.xtal.UnitCellBoundingBox

public class UnitCellBoundingBox
extends Object

A class to contain the BoundingBoxes of all polymeric molecules in a full unit cell.

Author:

Jose Duarte

Constructor Summary

Constructors

Constructor and Description
UnitCellBoundingBox(int numOperatorsSg, int numPolyChainsAu)

Method Summary

Modifier and Type	Method and Description
BoundingBox	getAuBoundingBox(int cellIdx) Get the AU BoundingBox for the given cell index (cellIdx=0 would be original AU) The AU BoundingBox is the BoundingBox that bounds all chains belonging to the AU
BoundingBox	getChainBoundingBox(int cellIdx, int chainIdx) Get the chain BoundingBox for the given cell index (cellIdx=0 would be original AU) and chain index
UnitCellBoundingBox	getTranslatedBbs(javax.vecmath.Vector3d translation) Returns a new BoundingBoxes object containing the same bounds as this BoundingBoxes object translated by the given translation
void	setBbs(Structure structure, javax.vecmath.Matrix4d[] ops, boolean includeHetAtoms)

Methods inherited from class java.lang.Object

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

Constructor Detail

UnitCellBoundingBox

public UnitCellBoundingBox(int numOperatorsSg,
                           int numPolyChainsAu)

Method Detail

setBbs

public void setBbs(Structure structure,
                   javax.vecmath.Matrix4d[] ops,
                   boolean includeHetAtoms)

getChainBoundingBox

public BoundingBox getChainBoundingBox(int cellIdx,
                                       int chainIdx)

Get the chain BoundingBox for the given cell index (cellIdx=0 would be original AU) and chain index

Parameters:

cellIdx -

chainIdx -

Returns:

getAuBoundingBox

public BoundingBox getAuBoundingBox(int cellIdx)

Get the AU BoundingBox for the given cell index (cellIdx=0 would be original AU) The AU BoundingBox is the BoundingBox that bounds all chains belonging to the AU

Parameters:

cellIdx -

Returns:

getTranslatedBbs

public UnitCellBoundingBox getTranslatedBbs(javax.vecmath.Vector3d translation)

Returns a new BoundingBoxes object containing the same bounds as this BoundingBoxes object translated by the given translation

Parameters:

translation -

Returns: