org.openscience.cdk.tools

Class GridGenerator

java.lang.Object

org.openscience.cdk.tools.GridGenerator

public class GridGenerator
extends Object

Generates a grid of points in 3D space within given boundaries.

Author:

cho

Source code:

master

Created on:

2005-09-30

Constructor Summary

Constructors

Constructor and Description
GridGenerator()
GridGenerator(double[] minMax, double initialValue, boolean cubicGridFlag)
GridGenerator(double min, double max)
GridGenerator(double min, double max, double initialValue)

Method Summary

Methods

Modifier and Type	Method and Description
void	generateGrid() Main method creates a grid between given boundaries (dimensions).
javax.vecmath.Point3d	getCoordinatesFromGridPoint(int gridPoint) Method calculates coordinates from a given grid array position.
javax.vecmath.Point3d	getCoordinatesFromGridPoint(javax.vecmath.Point3d gridPoint) Method calculates coordinates from a given grid point.
int[]	getDim()
double	getExtendGrid()
double[][][]	getGrid()
double[]	getGridArray()
javax.vecmath.Point3d	getGridPointFrom3dCoordinates(javax.vecmath.Point3d coord) Method calculates the nearest grid point from given coordinates.
double	getLatticeConstant()
double	getMaxx()
double	getMaxy()
double	getMaxz()
double	getMinx()
double	getMiny()
double	getMinz()
double[]	gridToGridArray(double[][][] grid) Method transforms the grid to an array.
void	initializeGrid(double value) Method initialise the given grid points with a value.
double[][][]	initializeGrid(double[][][] grid, double value) Method initialise the given grid points with a value.
void	setDim(int[] dim)
void	setDimension(double[] minMax, boolean cubicGridFlag) Method sets the maximal 3d dimensions to given min and max values.
void	setDimension(double min, double max) Method sets the maximal 3d dimensions to given min and max values.
void	setDimension(double minx, double maxx, double miny, double maxy, double minz, double maxz) Method sets the maximal 3d dimensions to given min and max values.
void	setExtendGrid(double extendGrid)
void	setGrid(double[][][] grid)
void	setLatticeConstant(double latticeConstant)
String	toString()
void	writeGridInPmeshFormat(String outPutFileName) Method transforms the grid into pmesh format.
void	writeGridInPmeshFormat(String outPutFileName, double cutOff) Method transforms the grid into pmesh format.

Methods inherited from class java.lang.Object

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

Constructor Detail

GridGenerator

public GridGenerator()

GridGenerator

public GridGenerator(double min,
             double max)

GridGenerator

public GridGenerator(double min,
             double max,
             double initialValue)

Parameters:

initialValue - used as initial value for the grid points

GridGenerator

public GridGenerator(double[] minMax,
             double initialValue,
             boolean cubicGridFlag)

Method Detail

setDimension

public void setDimension(double min,
                double max)

Method sets the maximal 3d dimensions to given min and max values.

setDimension

public void setDimension(double[] minMax,
                boolean cubicGridFlag)

Method sets the maximal 3d dimensions to given min and max values.

setDimension

public void setDimension(double minx,
                double maxx,
                double miny,
                double maxy,
                double minz,
                double maxz)

Method sets the maximal 3d dimensions to given min and max values.

generateGrid

public void generateGrid()

Main method creates a grid between given boundaries (dimensions). The grid my be extended over the given boundaries with the variable extendGrid.

initializeGrid

public void initializeGrid(double value)

Method initialise the given grid points with a value.

initializeGrid

public double[][][] initializeGrid(double[][][] grid,
                          double value)

Method initialise the given grid points with a value.

gridToGridArray

public double[] gridToGridArray(double[][][] grid)

Method transforms the grid to an array.

getCoordinatesFromGridPoint

public javax.vecmath.Point3d getCoordinatesFromGridPoint(javax.vecmath.Point3d gridPoint)

Method calculates coordinates from a given grid point.

getCoordinatesFromGridPoint

public javax.vecmath.Point3d getCoordinatesFromGridPoint(int gridPoint)

Method calculates coordinates from a given grid array position.

getGridPointFrom3dCoordinates

public javax.vecmath.Point3d getGridPointFrom3dCoordinates(javax.vecmath.Point3d coord)
                                                    throws Exception

Method calculates the nearest grid point from given coordinates.

Throws:

Exception

writeGridInPmeshFormat

public void writeGridInPmeshFormat(String outPutFileName)
                            throws IOException

Method transforms the grid into pmesh format.

Throws:

IOException

writeGridInPmeshFormat

public void writeGridInPmeshFormat(String outPutFileName,
                          double cutOff)
                            throws IOException

Method transforms the grid into pmesh format. Only grid points with specific value defined with cutoff are considered.

cutoff <0, the values considered must be <=cutoff
 cutoff >0, the values considered must be >=cutoff
 

Throws:

IOException

toString

public String toString()

Overrides:

toString in class Object

getDim

public int[] getDim()

Returns:

Returns the dim.

setDim

public void setDim(int[] dim)

Parameters:

dim - The dim to set.

getExtendGrid

public double getExtendGrid()

Returns:

Returns the extendGrid.

setExtendGrid

public void setExtendGrid(double extendGrid)

Parameters:

extendGrid - The extendGrid to set.

getGrid

public double[][][] getGrid()

Returns:

Returns the grid.

setGrid

public void setGrid(double[][][] grid)

Parameters:

grid - The grid to set.

getLatticeConstant

public double getLatticeConstant()

Returns:

Returns the latticeConstant.

setLatticeConstant

public void setLatticeConstant(double latticeConstant)

Parameters:

latticeConstant - The latticeConstant to set.

getGridArray

public double[] getGridArray()

Returns:

Returns the gridArray.

getMaxx

public double getMaxx()

Returns:

Returns the maxx.

getMaxy

public double getMaxy()

Returns:

Returns the maxy.

getMaxz

public double getMaxz()

Returns:

Returns the maxz.

getMinx

public double getMinx()

Returns:

Returns the minx.

getMiny

public double getMiny()

Returns:

Returns the miny.

getMinz

public double getMinz()

Returns:

Returns the minz.