Package org.biojava.nbio.structure.contact

Class BoundingBox

java.lang.Object

org.biojava.nbio.structure.contact.BoundingBox

All Implemented Interfaces:

Serializable

public class BoundingBox
extends Object
implements Serializable

A bounding box for short cutting some geometrical calculations. See http://en.wikipedia.org/wiki/Bounding_volume

Author:

Jose Duarte

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
double	xmax
double	xmin
double	ymax
double	ymin
double	zmax
double	zmin

Constructor Summary

Constructors

Constructor	Description
BoundingBox(double xmin, double xmax, double ymin, double ymax, double zmin, double zmax)
BoundingBox(javax.vecmath.Point3d[] atoms)	Constructs a BoundingBox by calculating maxs and mins of given array of atoms.
BoundingBox(BoundingBox bb)
BoundingBox(BoundingBox[] boxes)	Given a set of bounding boxes returns a bounding box that bounds all of them.

Method Summary

Modifier and Type	Method	Description
boolean	contains(javax.vecmath.Point3d atom)	Check if a given point falls within this box
double[]	getDimensions()	Returns the dimensions of this bounding box.
double[]	getMinMax(double[] array)	Returns an array of size 2 with min and max values of given double array
boolean	overlaps(BoundingBox o, double cutoff)	Returns true if this bounding box overlaps given one, i.e. they are within one cutoff distance in one of their 3 dimensions.
String	toString()
void	translate(javax.vecmath.Vector3d translation)

Methods inherited from class java.lang.Object

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

Field Details

xmin

public double xmin

xmax

public double xmax

ymin

public double ymin

ymax

public double ymax

zmin

public double zmin

zmax

public double zmax

Constructor Details

BoundingBox

public BoundingBox(double xmin,
 double xmax,
 double ymin,
 double ymax,
 double zmin,
 double zmax)

BoundingBox

public BoundingBox(BoundingBox bb)

BoundingBox

public BoundingBox(javax.vecmath.Point3d[] atoms)

Constructs a BoundingBox by calculating maxs and mins of given array of atoms.

Parameters:

atoms - the atom array

Throws:

IllegalArgumentException - if atom array is empty

NullPointerException - if input is null

BoundingBox

public BoundingBox(BoundingBox[] boxes)

Given a set of bounding boxes returns a bounding box that bounds all of them.

Parameters:

boxes - an array of bounding boxes

Throws:

IllegalArgumentException - if input array is empty

NullPointerException - if input is null

Method Details

getDimensions

public double[] getDimensions()

Returns the dimensions of this bounding box.

Returns:

a double array (x,y,z) with the dimensions of the box.

overlaps

public boolean overlaps(BoundingBox o,
 double cutoff)

Returns true if this bounding box overlaps given one, i.e. they are within one cutoff distance in one of their 3 dimensions.

Parameters:

cutoff -

Returns:

contains

public boolean contains(javax.vecmath.Point3d atom)

Check if a given point falls within this box

Parameters:

atom -

Returns:

translate

public void translate(javax.vecmath.Vector3d translation)

getMinMax

public double[] getMinMax(double[] array)

Returns an array of size 2 with min and max values of given double array

Parameters:

array -

Returns:

toString

public String toString()

Overrides:

toString in class Object