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

Class ChargePoint

java.lang.Object

com.actelion.research.chem.phesa.pharmacophore.pp.ChargePoint

All Implemented Interfaces:

IPharmacophorePoint

public class ChargePoint
extends java.lang.Object
implements IPharmacophorePoint

Nested Class Summary

Nested classes/interfaces inherited from interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint

IPharmacophorePoint.Functionality

Constructor Summary

Constructors

Constructor	Description
ChargePoint(ChargePoint cP)
ChargePoint(StereoMolecule mol, int a, java.util.List<java.lang.Integer> neighbours, int charge)

Method Summary

Modifier and Type	Method	Description
IPharmacophorePoint	copyPharmacophorePoint()
java.lang.String	encode()
static ChargePoint	fromString(java.lang.String ppString, StereoMolecule mol)
Coordinates	getCenter()
int	getCenterID()
int	getCharge()
int	getChargeAtom()
Coordinates	getDirectionality()
void	getDirectionalityDerivativeCartesian(double[] grad, double[] v, Coordinates di, double sim)
int	getFunctionalityIndex()
java.util.List<java.lang.Integer>	getNeighbours()
Coordinates	getRotatedDirectionality(double[][] rotMatrix, double scaleFactor)
double	getSimilarity(IPharmacophorePoint pp)
double	getVectorSimilarity(IPharmacophorePoint pp2)
double	getVectorSimilarity(IPharmacophorePoint pp2, Coordinates directionalityMod)
void	setCenterID(int centerID)
void	setChargeAtom(int chargeAtom)
void	setDirectionality(Coordinates directionality)
void	setNeighbours(java.util.List<java.lang.Integer> neighbours)
void	updateAtomIndeces(int[] map)
void	updateCoordinates(Coordinates[] coords)

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.actelion.research.chem.phesa.pharmacophore.pp.IPharmacophorePoint

applyTransformation

Constructor Detail

ChargePoint

public ChargePoint(StereoMolecule mol,
                   int a,
                   java.util.List<java.lang.Integer> neighbours,
                   int charge)

ChargePoint

public ChargePoint(ChargePoint cP)

Method Detail

getCenter

public Coordinates getCenter()

Specified by:

getCenter in interface IPharmacophorePoint

updateCoordinates

public void updateCoordinates(Coordinates[] coords)

Specified by:

updateCoordinates in interface IPharmacophorePoint

getDirectionality

public Coordinates getDirectionality()

Specified by:

getDirectionality in interface IPharmacophorePoint

getRotatedDirectionality

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

Specified by:

getRotatedDirectionality in interface IPharmacophorePoint

fromString

public static ChargePoint fromString(java.lang.String ppString,
                                     StereoMolecule mol)

encode

public java.lang.String encode()

Specified by:

encode in interface IPharmacophorePoint

getSimilarity

public double getSimilarity(IPharmacophorePoint pp)

Specified by:

getSimilarity in interface IPharmacophorePoint

getCenterID

public int getCenterID()

Specified by:

getCenterID in interface IPharmacophorePoint

setCenterID

public void setCenterID(int centerID)

Specified by:

setCenterID in interface IPharmacophorePoint

setDirectionality

public void setDirectionality(Coordinates directionality)

Specified by:

setDirectionality in interface IPharmacophorePoint

getCharge

public int getCharge()

updateAtomIndeces

public void updateAtomIndeces(int[] map)

Specified by:

updateAtomIndeces in interface IPharmacophorePoint

copyPharmacophorePoint

public IPharmacophorePoint copyPharmacophorePoint()

Specified by:

copyPharmacophorePoint in interface IPharmacophorePoint

getDirectionalityDerivativeCartesian

public void getDirectionalityDerivativeCartesian(double[] grad,
                                                 double[] v,
                                                 Coordinates di,
                                                 double sim)

Specified by:

getDirectionalityDerivativeCartesian in interface IPharmacophorePoint

getVectorSimilarity

public double getVectorSimilarity(IPharmacophorePoint pp2,
                                  Coordinates directionalityMod)

Specified by:

getVectorSimilarity in interface IPharmacophorePoint

getVectorSimilarity

public double getVectorSimilarity(IPharmacophorePoint pp2)

Specified by:

getVectorSimilarity in interface IPharmacophorePoint

getFunctionalityIndex

public int getFunctionalityIndex()

Specified by:

getFunctionalityIndex in interface IPharmacophorePoint

getChargeAtom

public int getChargeAtom()

setChargeAtom

public void setChargeAtom(int chargeAtom)

getNeighbours

public java.util.List<java.lang.Integer> getNeighbours()

setNeighbours

public void setNeighbours(java.util.List<java.lang.Integer> neighbours)