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
All Methods Static Methods Instance Methods Concrete Methods 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 interfaceIPharmacophorePoint
-
updateCoordinates
public void updateCoordinates(Coordinates[] coords)
- Specified by:
updateCoordinates
in interfaceIPharmacophorePoint
-
getDirectionality
public Coordinates getDirectionality()
- Specified by:
getDirectionality
in interfaceIPharmacophorePoint
-
encode
public java.lang.String encode()
- Specified by:
encode
in interfaceIPharmacophorePoint
-
decode
public static SimplePharmacophorePoint decode(java.lang.String encoded)
-
getSimilarity
public double getSimilarity(IPharmacophorePoint pp)
- Specified by:
getSimilarity
in interfaceIPharmacophorePoint
-
getCenterID
public int getCenterID()
- Specified by:
getCenterID
in interfaceIPharmacophorePoint
-
setCenterID
public void setCenterID(int centerID)
- Specified by:
setCenterID
in interfaceIPharmacophorePoint
-
setDirectionality
public void setDirectionality(Coordinates directionality)
- Specified by:
setDirectionality
in interfaceIPharmacophorePoint
-
updateAtomIndeces
public void updateAtomIndeces(int[] map)
- Specified by:
updateAtomIndeces
in interfaceIPharmacophorePoint
-
copyPharmacophorePoint
public IPharmacophorePoint copyPharmacophorePoint()
- Specified by:
copyPharmacophorePoint
in interfaceIPharmacophorePoint
-
getDirectionalityDerivativeCartesian
public void getDirectionalityDerivativeCartesian(double[] grad, double[] v, Coordinates di, double sim)
- Specified by:
getDirectionalityDerivativeCartesian
in interfaceIPharmacophorePoint
-
getRotatedDirectionality
public Coordinates getRotatedDirectionality(double[][] rotMatrix, double scaleFactor)
- Specified by:
getRotatedDirectionality
in interfaceIPharmacophorePoint
-
getFunctionalityIndex
public int getFunctionalityIndex()
- Specified by:
getFunctionalityIndex
in interfaceIPharmacophorePoint
-
getVectorSimilarity
public double getVectorSimilarity(IPharmacophorePoint pp2, Coordinates directionalityMod)
- Specified by:
getVectorSimilarity
in interfaceIPharmacophorePoint
-
-