Package com.actelion.research.chem.phesa

Class Gaussian3D

java.lang.Object

com.actelion.research.chem.phesa.Gaussian3D

Direct Known Subclasses:

AtomicGaussian, PPGaussian, SimplePPGaussian, VolumeGaussian

public abstract class Gaussian3D
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field	Description
protected double	alpha
protected int	atomicNo
protected int	atomId
protected Coordinates	center
protected double	coeff
static double	DIST_CUTOFF
protected double	volume
protected double	weight

Constructor Summary

Constructors

Constructor	Description
Gaussian3D()
Gaussian3D(int atomId, int atomicNo, Coordinates center, double weight)
Gaussian3D(Gaussian3D original)

Method Summary

Modifier and Type	Method	Description
abstract double	calculateHeight()
double	calculateVolume()
abstract double	calculateWidth()
abstract java.lang.String	encode()
int	getAtomicNo()
int	getAtomId()
Coordinates	getCenter()
double	getHeight()
Coordinates	getRotatedCenter(double[][] rotMatrix, double scaleFactor, double[] translation)
double	getVolume()
double	getVolumeOverlap(Gaussian3D g2)
double	getVolumeOverlap(Gaussian3D g2, double distCutoff)
double	getVolumeOverlap(Gaussian3D g2, Coordinates c2, double distCutoff)
double	getWeight()
double	getWidth()
void	setAtomicNo(int atomicNo)
void	setAtomId(int atomId)
void	setCenter(Coordinates center)
void	setHeight(double height)
void	setWeight(double weight)
void	updateAtomIndeces(int[] map)
void	updateCoordinates(Conformer conf)
void	updateCoordinates(StereoMolecule mol)

Methods inherited from class java.lang.Object

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

Field Detail

DIST_CUTOFF

public static final double DIST_CUTOFF

See Also:

Constant Field Values

atomId

protected int atomId

atomicNo

protected int atomicNo

center

protected Coordinates center

coeff

protected double coeff

alpha

protected double alpha

volume

protected double volume

weight

protected double weight

Constructor Detail

Gaussian3D

public Gaussian3D(int atomId,
                  int atomicNo,
                  Coordinates center,
                  double weight)

Gaussian3D

public Gaussian3D(Gaussian3D original)

Gaussian3D

public Gaussian3D()

Method Detail

calculateHeight

public abstract double calculateHeight()

calculateWidth

public abstract double calculateWidth()

calculateVolume

public double calculateVolume()

getHeight

public double getHeight()

setHeight

public void setHeight(double height)

getWidth

public double getWidth()

getVolume

public double getVolume()

getCenter

public Coordinates getCenter()

setCenter

public void setCenter(Coordinates center)

getAtomicNo

public int getAtomicNo()

setAtomicNo

public void setAtomicNo(int atomicNo)

getAtomId

public int getAtomId()

setAtomId

public void setAtomId(int atomId)

getWeight

public double getWeight()

setWeight

public void setWeight(double weight)

getRotatedCenter

public Coordinates getRotatedCenter(double[][] rotMatrix,
                                    double scaleFactor,
                                    double[] translation)

getVolumeOverlap

public double getVolumeOverlap(Gaussian3D g2,
                               Coordinates c2,
                               double distCutoff)

getVolumeOverlap

public double getVolumeOverlap(Gaussian3D g2)

getVolumeOverlap

public double getVolumeOverlap(Gaussian3D g2,
                               double distCutoff)

updateCoordinates

public void updateCoordinates(StereoMolecule mol)

updateCoordinates

public void updateCoordinates(Conformer conf)

updateAtomIndeces

public void updateAtomIndeces(int[] map)

encode

public abstract java.lang.String encode()