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

Class SimplePharmacophorePoint

java.lang.Object

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

All Implemented Interfaces:

IPharmacophorePoint

public class SimplePharmacophorePoint
extends java.lang.Object
implements IPharmacophorePoint

doesn't possess directionality terms (only a dummy vector) and is used to represent receptor pharmacophores (not dependent on a molecular conformation, as opposed to ligand-based pharmacophores)

Author:

wahljo1

Nested Class Summary

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

IPharmacophorePoint.Functionality

Constructor Summary

Constructors

Constructor	Description
SimplePharmacophorePoint(int atomID, Coordinates center, IPharmacophorePoint.Functionality functionality)
SimplePharmacophorePoint(SimplePharmacophorePoint point)

Method Summary

Modifier and Type	Method	Description
IPharmacophorePoint	copyPharmacophorePoint()
static SimplePharmacophorePoint	decode(java.lang.String encoded)
java.lang.String	encode()
static SimplePharmacophorePoint	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()
Coordinates	getRotatedDirectionality(double[][] rotMatrix, double scaleFactor)
double	getSimilarity(IPharmacophorePoint pp)
double	getVectorSimilarity(IPharmacophorePoint pp2, Coordinates directionalityMod)
void	setCenterID(int centerID)
void	setDirectionality(Coordinates directionality)
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, getVectorSimilarity

Constructor Detail

SimplePharmacophorePoint

public SimplePharmacophorePoint(int atomID,
                                Coordinates center,
                                IPharmacophorePoint.Functionality functionality)

SimplePharmacophorePoint

public SimplePharmacophorePoint(SimplePharmacophorePoint point)

Method Detail

fromString

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

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

encode

public java.lang.String encode()

Specified by:

encode in interface IPharmacophorePoint

decode

public static SimplePharmacophorePoint decode(java.lang.String encoded)

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

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

getRotatedDirectionality

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

Specified by:

getRotatedDirectionality in interface IPharmacophorePoint

getFunctionalityIndex

public int getFunctionalityIndex()

Specified by:

getFunctionalityIndex in interface IPharmacophorePoint

getVectorSimilarity

public double getVectorSimilarity(IPharmacophorePoint pp2,
                                  Coordinates directionalityMod)

Specified by:

getVectorSimilarity in interface IPharmacophorePoint