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

Class AromRingPoint

java.lang.Object

com.actelion.research.chem.phesa.pharmacophore.AromRingPoint

All Implemented Interfaces:

IPharmacophorePoint

public class AromRingPoint
extends java.lang.Object
implements IPharmacophorePoint

Nested Class Summary

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

IPharmacophorePoint.Functionality

Constructor Summary

Constructors

Constructor	Description
AromRingPoint(AromRingPoint aP)
AromRingPoint(StereoMolecule mol, int a, java.util.List<java.lang.Integer> ringAtoms)

Method Summary

Modifier and Type	Method	Description
IPharmacophorePoint	copyPharmacophorePoint()
java.lang.String	encode()
static AromRingPoint	fromString(java.lang.String ppString, StereoMolecule mol)
Coordinates	getCenter()
int	getCenterID()
Coordinates	getDirectionality()
void	getDirectionalityDerivativeCartesian(double[] grad, double[] v, Coordinates di, double sim)
int	getFunctionalityIndex()
double	getSimilarity(IPharmacophorePoint pp)
double	getVectorSimilarity(IPharmacophorePoint pp2)
double	getVectorSimilarity(IPharmacophorePoint pp2, Coordinates directionalityMod)
void	setDirectionality(Coordinates directionality)
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

Constructor Detail

AromRingPoint

public AromRingPoint(StereoMolecule mol,
                     int a,
                     java.util.List<java.lang.Integer> ringAtoms)

AromRingPoint

public AromRingPoint(AromRingPoint aP)

Method Detail

getCenter

public Coordinates getCenter()

Specified by:

getCenter in interface IPharmacophorePoint

updateCoordinates

public void updateCoordinates(StereoMolecule mol)

Specified by:

updateCoordinates in interface IPharmacophorePoint

updateCoordinates

public void updateCoordinates(Conformer conf)

Specified by:

updateCoordinates in interface IPharmacophorePoint

getDirectionality

public Coordinates getDirectionality()

Specified by:

getDirectionality in interface IPharmacophorePoint

fromString

public static AromRingPoint 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

setDirectionality

public void setDirectionality(Coordinates directionality)

Specified by:

setDirectionality in interface IPharmacophorePoint

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