edu.sdsc.mbt.util
Class Octree

java.lang.Object
  edu.sdsc.mbt.util.Octree

public class Octree

extends java.lang.Object

Octree class constructed with recursion in mind. Each child is itself a tree.

Author:

Apostol Gramada

Field Summary

static int	countAppBondOp
static int	countChildren
int	levels
java.lang.String	path
static int	rejectedPaths

Constructor Summary

Octree(int spaceDimension, OctreeDataItem[] data, double[] offset)
Constructor that is mostly used for instantiating the root tree.

Octree(Octree root, Octree parent, int id, OctreeDataItem[] data, double[] firstCorner, double[] secondCorner)
Construct an octree as a child of "parent" in a tree rooted at "root" with given data and corners.

Method Summary

double[]	add(double[] v1, double[] v2) ???
void	appendBonds(OctreeDataItem dataItem, double cutOff, java.util.Vector bondVector) ???
void	appendHBondInfo(double[] coords1, int index1, double cutOff, int indexCutOff, java.util.Vector bondList)
void	appendHBonds(OctreeDataItem dataItem, double cutOff, int indexCutOff, java.util.Vector bondVector) ???
void	build() Build the whole tree recursively.
void	build(OctreeDataItem[] data) Build a subtree recursively.
java.lang.Object[]	getBonds(double cutOff) ???
java.util.Vector	getBondsVector(double cutOff) Return the vector of all potential covalent bonds.
int	getDimension() ???
double	getDistance(double[] coord1, double[] coord2) Methods to operate with vectors.
java.util.Vector	getHBondInfoVector(double cutOff)
java.lang.Object[]	getHBonds(double cutOff) ???
java.util.Vector	getHBondsVector(double cutOff) ???
int	getMaxNumberOfChildren() ???
int	getNumberOfChildren() ???
int	getWeight() ???
void	printChildNamingScheme() ???
double[]	scale(double[] v1, double scaleFactor) ???
void	setChildId(int child) ???
void	setData(OctreeDataItem[] data) ???
double[]	setGeometricalCenter() ???
void	setLeafCutOffCriterion(int leafCutOff) ???
void	setLeafFlag(boolean leafFlag) ???
void	setParent(Octree parentTree) ???
void	setRoot(Octree rootTree) ???
void	setWeight(int weight) ???

Methods inherited from class java.lang.Object

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

Field Detail

path

public java.lang.String path

levels

public int levels

countChildren

public static int countChildren

countAppBondOp

public static int countAppBondOp

rejectedPaths

public static int rejectedPaths

Constructor Detail

Octree

public Octree(Octree root,
              Octree parent,
              int id,
              OctreeDataItem[] data,
              double[] firstCorner,
              double[] secondCorner)

Construct an octree as a child of "parent" in a tree rooted at "root" with given data and corners.

Octree

public Octree(int spaceDimension,
              OctreeDataItem[] data,
              double[] offset)

Constructor that is mostly used for instantiating the root tree.

Method Detail

build

public void build()

Build the whole tree recursively.

build

public void build(OctreeDataItem[] data)

Build a subtree recursively.

getDistance

public final double getDistance(double[] coord1,
                                double[] coord2)

Methods to operate with vectors.

add

public final double[] add(double[] v1,
                          double[] v2)

???

scale

public final double[] scale(double[] v1,
                            double scaleFactor)

???

setRoot

public void setRoot(Octree rootTree)

???

setParent

public void setParent(Octree parentTree)

???

setData

public void setData(OctreeDataItem[] data)

???

setLeafFlag

public void setLeafFlag(boolean leafFlag)

???

setLeafCutOffCriterion

public void setLeafCutOffCriterion(int leafCutOff)

???

setChildId

public void setChildId(int child)

???

setWeight

public void setWeight(int weight)

???

setGeometricalCenter

public double[] setGeometricalCenter()

???

getBonds

public java.lang.Object[] getBonds(double cutOff)

???

getBondsVector

public java.util.Vector getBondsVector(double cutOff)

Return the vector of all potential covalent bonds.

getHBonds

public java.lang.Object[] getHBonds(double cutOff)

???

getHBondsVector

public java.util.Vector getHBondsVector(double cutOff)

???

getHBondInfoVector

public java.util.Vector getHBondInfoVector(double cutOff)

appendHBondInfo

public void appendHBondInfo(double[] coords1,
                            int index1,
                            double cutOff,
                            int indexCutOff,
                            java.util.Vector bondList)

appendBonds

public void appendBonds(OctreeDataItem dataItem,
                        double cutOff,
                        java.util.Vector bondVector)

???

appendHBonds

public void appendHBonds(OctreeDataItem dataItem,
                         double cutOff,
                         int indexCutOff,
                         java.util.Vector bondVector)

???

getDimension

public int getDimension()

???

getMaxNumberOfChildren

public int getMaxNumberOfChildren()

???

getNumberOfChildren

public int getNumberOfChildren()

???

getWeight

public int getWeight()

???

printChildNamingScheme

public void printChildNamingScheme()

???