astex
Class Map

java.lang.Object
  astex.Symmetry
      astex.Map

public class Map
extends Symmetry

A class for storing an electron density map.

Field Summary

static int	ASTEX_ASCII
int[]	axis
static int	CCP4_BINARY Various definitions of map types.
int[]	centerGrid The center grid point for the current stored map data.
float[]	data
int[]	grid Size of map grid.
boolean	headerInitialised Is header initialised.
boolean	initialiseContours
static int	INSIGHT_ASCII
static int	Lines Types for the display style.
static int	MaximumContourLevels Maximum number of contour levels.
int[]	maximumGrid The maximum grid point for the current stored map data.
int[]	minimumGrid The minimum grid point for the current stored map data.
int[]	ngrid The number of grid points along each axis.
static int	O_BINARY
Point3d	origin The position of the first grid point.
Point3d	spacing The spacing along each axis.
static int	Surface
static int	SYBYL_ASCII
int	volumeColor Volume color.
double	volumeMax Volume max.
double	volumeMin Volume min.
boolean	volumeRender Volume render.

Fields inherited from class astex.Symmetry

cartesianToFractional, fractionalToCartesian, matricesAssigned, scale, unitCell

Method Summary

void	absoluteGridToCartesian(double ix, double iy, double iz, Point3d p) Convert grid coordiantes to cartesian.
static int	convertBigToLittle(int i) Convert from big to little endian byte ordering.
static Map	create() Public interface to map creation.
static Map	createSimpleMap() Create a simple map for internal use.
void	ensureMapCapacity(int dataPoints) Ensure we have enough room to store the map.
int	getContourColor(int i) Get the specified contour color.
boolean	getContourDisplayed(int i) Get if the specified contour is displayed.
double	getContourLevel(int i) Get the specified contour level.
int	getContourStyle(int i) Get the specified contour color.
float[]	getDataArray() Get the actual data array.
java.lang.String	getFile() Get the filename.
void	getMapBoxDimensions(int[] dims) Return the size of map we have loaded.
int	getMapType() Get the value of mapType.
java.lang.String	getName() Get the map name.
double	getRadius() Get the radius of the current map region.
int	getRelativeGridIndex(int gx, int gy, int gz) Calculate the relative grid index.
double	getSigma() Return the sigma value for the map.
double	getValueAtRelativeGrid(int gx, int gy, int gz) Get the map value at relative grid point.
boolean	hasContoursDisplayed()
void	lowerRelativeGrid(Point3d p, int[] g) Find nearest relative grid point to the specified point.
static void	main(java.lang.String[] args) Test program.
void	nearestRelativeGrid(Point3d p, int[] g) Find nearest relative grid point to the specified point.
boolean	needsReading() Does the map need reading.
static void	printArray(java.lang.String name, double[] array) Print an array.
static void	printArray(java.lang.String name, int[] array) Print an array.
void	printHeader(java.io.PrintStream printStream) Print the header for the map.
void	read() Read a map from the specified file object.
void	readHeader() Read a map from the specified file object.
void	readRegion() Read the determined region from the map.
void	relativeGridToCartesian(double ix, double iy, double iz, Point3d p) Convert grid coordiantes to cartesian.
void	setCenter(double x, double y, double z) Set the center point of the region we will contour.
void	setCenter(Point3d p) Set the center point of the region we will contour.
void	setContourColor(int i, int color) Set the specified contour color.
void	setContourDisplayed(int i, boolean displayed) Set if the specified contour is displayed.
void	setContourLevel(int i, double level) Set the specified contour level.
void	setContourStyle(int i, int style) Set the specified contour color.
void	setFile(java.lang.String file) Set the filename.
void	setMapType(int v) Set the value of mapType.
void	setName(java.lang.String mapName) Set the map name.
void	setNeedsReading(boolean flag) Set whether the map needs reading.
void	setRadius(double r) Set the radis of the region we will contour.
void	setSigma(double s) Set the sigma level.

Methods inherited from class astex.Symmetry

cnxSpaceGroupNameToNumber, decodeSymmetryToken, generateMatrices, getCartesianToFractionalMatrix, getFractionalToCartesianMatrix, getOriginalSpaceGroupName, getSpaceGroupName, getSpaceGroupName, getSpaceGroupNumber, getSymmetryOperators, getUnitCellCode, prepareSymmetry, readSymmetryOperator, setOriginalSpaceGroupName, setSpaceGroupName, setSpaceGroupNumber, setUnitCell, setUnitCellCode, SQ, transformPoint2

Methods inherited from class java.lang.Object

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

Field Detail

volumeRender

public boolean volumeRender

Volume render.

volumeColor

public int volumeColor

Volume color.

volumeMin

public double volumeMin

Volume min.

volumeMax

public double volumeMax

Volume max.

MaximumContourLevels

public static int MaximumContourLevels

Maximum number of contour levels.

Lines

public static final int Lines

Types for the display style.

See Also:

Constant Field Values

Surface

public static final int Surface

See Also:

Constant Field Values

grid

public int[] grid

Size of map grid.

headerInitialised

public boolean headerInitialised

Is header initialised.

CCP4_BINARY

public static final int CCP4_BINARY

Various definitions of map types.

See Also:

Constant Field Values

SYBYL_ASCII

public static final int SYBYL_ASCII

See Also:

Constant Field Values

INSIGHT_ASCII

public static final int INSIGHT_ASCII

See Also:

Constant Field Values

ASTEX_ASCII

public static final int ASTEX_ASCII

See Also:

Constant Field Values

O_BINARY

public static final int O_BINARY

See Also:

Constant Field Values

centerGrid

public int[] centerGrid

The center grid point for the current stored map data.

minimumGrid

public int[] minimumGrid

The minimum grid point for the current stored map data.

maximumGrid

public int[] maximumGrid

The maximum grid point for the current stored map data.

axis

public int[] axis

data

public float[] data

origin

public Point3d origin

The position of the first grid point.

spacing

public Point3d spacing

The spacing along each axis.

ngrid

public int[] ngrid

The number of grid points along each axis.

initialiseContours

public boolean initialiseContours

Method Detail

create

public static Map create()

Public interface to map creation.

createSimpleMap

public static Map createSimpleMap()

Create a simple map for internal use.

getSigma

public double getSigma()

Return the sigma value for the map.

setSigma

public void setSigma(double s)

Set the sigma level.

needsReading

public boolean needsReading()

Does the map need reading.

setNeedsReading

public void setNeedsReading(boolean flag)

Set whether the map needs reading.

getMapType

public int getMapType()

Get the value of mapType.

Returns:

value of mapType.

setMapType

public void setMapType(int v)

Set the value of mapType.

Parameters:

v - Value to assign to mapType.

read

public void read()

Read a map from the specified file object.

convertBigToLittle

public static int convertBigToLittle(int i)

Convert from big to little endian byte ordering.

readHeader

public void readHeader()

Read a map from the specified file object.

printHeader

public void printHeader(java.io.PrintStream printStream)

Print the header for the map.

setCenter

public void setCenter(double x,
                      double y,
                      double z)

Set the center point of the region we will contour.

setCenter

public void setCenter(Point3d p)

Set the center point of the region we will contour.

setRadius

public void setRadius(double r)

Set the radis of the region we will contour.

getRadius

public double getRadius()

Get the radius of the current map region.

setName

public void setName(java.lang.String mapName)

Set the map name.

getName

public java.lang.String getName()

Get the map name.

setFile

public void setFile(java.lang.String file)

Set the filename. We need to know where it came from so we can reread the map when we recenter.

getFile

public java.lang.String getFile()

Get the filename.

ensureMapCapacity

public void ensureMapCapacity(int dataPoints)

Ensure we have enough room to store the map.

readRegion

public void readRegion()

Read the determined region from the map.

relativeGridToCartesian

public void relativeGridToCartesian(double ix,
                                    double iy,
                                    double iz,
                                    Point3d p)

Convert grid coordiantes to cartesian.

getValueAtRelativeGrid

public double getValueAtRelativeGrid(int gx,
                                     int gy,
                                     int gz)

Get the map value at relative grid point.

getRelativeGridIndex

public int getRelativeGridIndex(int gx,
                                int gy,
                                int gz)

Calculate the relative grid index.

getMapBoxDimensions

public void getMapBoxDimensions(int[] dims)

Return the size of map we have loaded.

getDataArray

public float[] getDataArray()

Get the actual data array.

absoluteGridToCartesian

public void absoluteGridToCartesian(double ix,
                                    double iy,
                                    double iz,
                                    Point3d p)

Convert grid coordiantes to cartesian.

nearestRelativeGrid

public void nearestRelativeGrid(Point3d p,
                                int[] g)

Find nearest relative grid point to the specified point.

lowerRelativeGrid

public void lowerRelativeGrid(Point3d p,
                              int[] g)

Find nearest relative grid point to the specified point.

printArray

public static void printArray(java.lang.String name,
                              int[] array)

Print an array.

printArray

public static void printArray(java.lang.String name,
                              double[] array)

Print an array.

setContourLevel

public void setContourLevel(int i,
                            double level)

Set the specified contour level.

setContourColor

public void setContourColor(int i,
                            int color)

Set the specified contour color.

setContourStyle

public void setContourStyle(int i,
                            int style)

Set the specified contour color.

setContourDisplayed

public void setContourDisplayed(int i,
                                boolean displayed)

Set if the specified contour is displayed.

getContourLevel

public double getContourLevel(int i)

Get the specified contour level.

getContourColor

public int getContourColor(int i)

Get the specified contour color.

getContourStyle

public int getContourStyle(int i)

Get the specified contour color.

getContourDisplayed

public boolean getContourDisplayed(int i)

Get if the specified contour is displayed.

hasContoursDisplayed

public boolean hasContoursDisplayed()

main

public static void main(java.lang.String[] args)

Test program.