Class AliphaticPoint
- java.lang.Object
-
- com.actelion.research.chem.phesa.pharmacophore.pp.AliphaticPoint
-
- All Implemented Interfaces:
IPharmacophorePoint
public class AliphaticPoint 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 AliphaticPoint(AliphaticPoint aP)
AliphaticPoint(StereoMolecule mol, int a, java.util.List<java.lang.Integer> atoms)
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description IPharmacophorePoint
copyPharmacophorePoint()
java.lang.String
encode()
static AliphaticPoint
fromString(java.lang.String ppString, StereoMolecule mol)
java.util.List<java.lang.Integer>
getAtoms()
Coordinates
getCenter()
int
getCenterID()
Coordinates
getDirectionality()
void
getDirectionalityDerivativeCartesian(double[] grad, double[] v, Coordinates di, double sim)
int
getFunctionalityIndex()
Coordinates
getRotatedDirectionality(double[][] m, double scaleFactor)
double
getSimilarity(IPharmacophorePoint pp)
double
getVectorSimilarity(IPharmacophorePoint pp2)
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
-
-
-
-
Constructor Detail
-
AliphaticPoint
public AliphaticPoint(StereoMolecule mol, int a, java.util.List<java.lang.Integer> atoms)
-
AliphaticPoint
public AliphaticPoint(AliphaticPoint aP)
-
-
Method Detail
-
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
-
getRotatedDirectionality
public Coordinates getRotatedDirectionality(double[][] m, double scaleFactor)
- Specified by:
getRotatedDirectionality
in interfaceIPharmacophorePoint
-
fromString
public static AliphaticPoint fromString(java.lang.String ppString, StereoMolecule mol)
-
encode
public java.lang.String encode()
- Specified by:
encode
in interfaceIPharmacophorePoint
-
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
-
getVectorSimilarity
public double getVectorSimilarity(IPharmacophorePoint pp2, Coordinates directionalityMod)
- Specified by:
getVectorSimilarity
in interfaceIPharmacophorePoint
-
getVectorSimilarity
public double getVectorSimilarity(IPharmacophorePoint pp2)
- Specified by:
getVectorSimilarity
in interfaceIPharmacophorePoint
-
getFunctionalityIndex
public int getFunctionalityIndex()
- Specified by:
getFunctionalityIndex
in interfaceIPharmacophorePoint
-
getAtoms
public java.util.List<java.lang.Integer> getAtoms()
-
-