charite.christo.protein
Class Matrix3D

java.lang.Object
  charite.christo.protein.Matrix3D

All Implemented Interfaces:

HasModiCount

public final class Matrix3D
extends java.lang.Object
implements HasModiCount

A matrix defines an affine transformation in 3D space.

Field Summary

static int	FORMAT_EXPLAIN
static int	FORMAT_JMOL
static int	FORMAT_PLAIN
static int	FORMAT_PYMOL
static int	FORMAT_ROUNDED
static Matrix3D[]	NONE

Constructor Summary

Matrix3D()
Create a new unit matrix

Matrix3D(BA ba)

Matrix3D(double xx, double xy, double xz, double xo, double yx, double yy, double yz, double yo, double zx, double zy, double zz, double zo)

Matrix3D(Matrix3D m)

Method Summary

boolean	equals(java.lang.Object o)
int	getBiomolecule()
double	getDeterminant(boolean normalize)
java.lang.String	getName()
double[][]	getRotation()
double[]	getTranslation()
int	hashCode()
boolean	isUnit()
int	modificationCount()
static void	mostDistantPoints3(float[] xyz, int len, int[] result)
Matrix3D	mult(Matrix3D rhs) Multiply this matrix by a second: M=M*R
Matrix3D	newInverse()
boolean	parse(BA ba)
boolean	parsePlain(byte[] text, int begin, int end)
Matrix3D	rotate(char axis, double theta) rotate theta degrees about the x,y,z axis
Matrix3D	scale(double f) Scale by f in all dimensions
Matrix3D	setRotation(double[][] r)
Matrix3D	setTranslation(double[] t)
Matrix3D	setTranslation(double tx, double ty, double tz)
java.lang.String	toString()
java.lang.String	toText(int format, java.lang.String linePrefix)
float[]	transformPoints(float[] v, float[] tv0, int n0)
Matrix3D	unit() Set to unit matrix

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Field Detail

NONE

public static final Matrix3D[] NONE

FORMAT_PLAIN

public static final int FORMAT_PLAIN

See Also:

Constant Field Values

FORMAT_JMOL

public static final int FORMAT_JMOL

See Also:

Constant Field Values

FORMAT_PYMOL

public static final int FORMAT_PYMOL

See Also:

Constant Field Values

FORMAT_EXPLAIN

public static final int FORMAT_EXPLAIN

See Also:

Constant Field Values

FORMAT_ROUNDED

public static final int FORMAT_ROUNDED

See Also:

Constant Field Values

Constructor Detail

Matrix3D

public Matrix3D()

Create a new unit matrix

Matrix3D

public Matrix3D(BA ba)

Matrix3D

public Matrix3D(double xx,
                double xy,
                double xz,
                double xo,
                double yx,
                double yy,
                double yz,
                double yo,
                double zx,
                double zy,
                double zz,
                double zo)

Matrix3D

public Matrix3D(Matrix3D m)

Method Detail

getRotation

public double[][] getRotation()

getTranslation

public double[] getTranslation()

getName

public java.lang.String getName()

getBiomolecule

public int getBiomolecule()

scale

public Matrix3D scale(double f)

Scale by f in all dimensions

rotate

public Matrix3D rotate(char axis,
                       double theta)

rotate theta degrees about the x,y,z axis

mult

public Matrix3D mult(Matrix3D rhs)

Multiply this matrix by a second: M=M*R

newInverse

public Matrix3D newInverse()

unit

public Matrix3D unit()

Set to unit matrix

setTranslation

public Matrix3D setTranslation(double tx,
                               double ty,
                               double tz)

setTranslation

public Matrix3D setTranslation(double[] t)

setRotation

public Matrix3D setRotation(double[][] r)

parsePlain

public boolean parsePlain(byte[] text,
                          int begin,
                          int end)

parse

public boolean parse(BA ba)

isUnit

public boolean isUnit()

getDeterminant

public double getDeterminant(boolean normalize)

transformPoints

public float[] transformPoints(float[] v,
                               float[] tv0,
                               int n0)

mostDistantPoints3

public static void mostDistantPoints3(float[] xyz,
                                      int len,
                                      int[] result)

modificationCount

public int modificationCount()

Specified by:

modificationCount in interface HasModiCount

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

toText

public java.lang.String toText(int format,
                               java.lang.String linePrefix)