Package com.actelion.research.chem.phesa.pharmacophore

Class PPGaussian

java.lang.Object

com.actelion.research.chem.phesa.Gaussian3D

com.actelion.research.chem.phesa.pharmacophore.PPGaussian

public class PPGaussian
extends Gaussian3D

Field Summary

Fields inherited from class com.actelion.research.chem.phesa.Gaussian3D

alpha, atomicNo, atomId, center, coeff, DIST_CUTOFF, volume, weight

Constructor Summary

Constructors

Constructor	Description
PPGaussian(int atomicNo, IPharmacophorePoint pp)
PPGaussian(PPGaussian original)

Method Summary

Modifier and Type	Method	Description
double	calculateHeight()
double	calculateWidth()
void	decode(java.lang.String string64, StereoMolecule mol)
java.lang.String	encode()
static PPGaussian	fromString(java.lang.String encodedGaussian, StereoMolecule mol)
double	getInteractionSimilarity(PPGaussian ppGauss2)
IPharmacophorePoint	getPharmacophorePoint()
Coordinates	getRotatedDirectionality(double[][] rotMatrix, double scaleFactor)
double	getSimilarity(PPGaussian ppGauss2)
double	getSimilarity(PPGaussian ppGauss2, Coordinates directionality)
double	getVectorSimilarity(PPGaussian ppGauss2)
double	getVectorSimilarity(PPGaussian ppGauss2, Coordinates directionalityMod)
void	setCenter(Coordinates center)
void	updateAtomIndeces(int[] map)
void	updateCoordinates(Conformer conf)
void	updateCoordinates(StereoMolecule mol)

Methods inherited from class com.actelion.research.chem.phesa.Gaussian3D

calculateVolume, getAtomicNo, getAtomId, getCenter, getHeight, getRotatedCenter, getVolume, getVolumeOverlap, getVolumeOverlap, getVolumeOverlap, getWeight, getWidth, setAtomicNo, setAtomId, setHeight, setWeight

Methods inherited from class java.lang.Object

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

Constructor Detail

PPGaussian

public PPGaussian(int atomicNo,
                  IPharmacophorePoint pp)

PPGaussian

public PPGaussian(PPGaussian original)

Method Detail

fromString

public static PPGaussian fromString(java.lang.String encodedGaussian,
                                    StereoMolecule mol)

getRotatedDirectionality

public Coordinates getRotatedDirectionality(double[][] rotMatrix,
                                            double scaleFactor)

getVectorSimilarity

public double getVectorSimilarity(PPGaussian ppGauss2,
                                  Coordinates directionalityMod)

getVectorSimilarity

public double getVectorSimilarity(PPGaussian ppGauss2)

getPharmacophorePoint

public IPharmacophorePoint getPharmacophorePoint()

getSimilarity

public double getSimilarity(PPGaussian ppGauss2,
                            Coordinates directionality)

getSimilarity

public double getSimilarity(PPGaussian ppGauss2)

getInteractionSimilarity

public double getInteractionSimilarity(PPGaussian ppGauss2)

setCenter

public void setCenter(Coordinates center)

Overrides:

setCenter in class Gaussian3D

encode

public java.lang.String encode()

Specified by:

encode in class Gaussian3D

decode

public void decode(java.lang.String string64,
                   StereoMolecule mol)

calculateHeight

public double calculateHeight()

Specified by:

calculateHeight in class Gaussian3D

updateCoordinates

public void updateCoordinates(StereoMolecule mol)

Overrides:

updateCoordinates in class Gaussian3D

updateCoordinates

public void updateCoordinates(Conformer conf)

Overrides:

updateCoordinates in class Gaussian3D

updateAtomIndeces

public void updateAtomIndeces(int[] map)

Overrides:

updateAtomIndeces in class Gaussian3D

calculateWidth

public double calculateWidth()

Specified by:

calculateWidth in class Gaussian3D