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

Class AcceptorPoint

java.lang.Object

com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint

All Implemented Interfaces:

IPharmacophorePoint

public class AcceptorPoint
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
AcceptorPoint(AcceptorPoint aP)
AcceptorPoint(StereoMolecule mol, int a, java.util.List<java.lang.Integer> neighbours, int interactionClass)
AcceptorPoint(StereoMolecule mol, int a, java.util.List<java.lang.Integer> neighbours, int interactionClass, int acceptorID)

Method Summary

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

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

getVectorSimilarity, getVectorSimilarity

Constructor Detail

AcceptorPoint

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

AcceptorPoint

public AcceptorPoint(AcceptorPoint aP)

AcceptorPoint

public AcceptorPoint(StereoMolecule mol,
                     int a,
                     java.util.List<java.lang.Integer> neighbours,
                     int interactionClass,
                     int acceptorID)

Method Detail

fromString

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

updateCoordinates

public void updateCoordinates(StereoMolecule mol)

Specified by:

updateCoordinates in interface IPharmacophorePoint

updateCoordinates

public void updateCoordinates(Conformer conf)

Specified by:

updateCoordinates in interface IPharmacophorePoint

getCenter

public Coordinates getCenter()

Specified by:

getCenter in interface IPharmacophorePoint

getDirectionality

public Coordinates getDirectionality()

Specified by:

getDirectionality in interface IPharmacophorePoint

encode

public java.lang.String encode()

Specified by:

encode in interface IPharmacophorePoint

getSimilarity

public double getSimilarity(IPharmacophorePoint pp)

Specified by:

getSimilarity in interface IPharmacophorePoint

getInteractionClass

public int getInteractionClass()

getCenterID

public int getCenterID()

Specified by:

getCenterID in interface IPharmacophorePoint

setDirectionality

public void setDirectionality(Coordinates directionality)

Specified by:

setDirectionality in interface IPharmacophorePoint

getAcceptorID

public int getAcceptorID()

getDirectionalityDerivativeCartesian

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

Specified by:

getDirectionalityDerivativeCartesian 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

getFunctionalityIndex

public int getFunctionalityIndex()

Specified by:

getFunctionalityIndex in interface IPharmacophorePoint