Class PPGaussian
- java.lang.Object
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- com.actelion.research.chem.phesa.Gaussian3D
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- com.actelion.research.chem.phesa.pharmacophore.pp.PPGaussian
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public class PPGaussian extends Gaussian3D
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Field Summary
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Fields inherited from class com.actelion.research.chem.phesa.Gaussian3D
alpha, atomicNo, atomId, center, coeff, DIST_CUTOFF, volume, weight
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Constructor Summary
Constructors Constructor Description PPGaussian(int atomicNo, IPharmacophorePoint pp)
PPGaussian(PPGaussian original)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description double
calculateHeight()
double
calculateWidth()
void
decode(java.lang.String string64, StereoMolecule mol)
java.lang.String
encode()
static PPGaussian
fromString(java.lang.String encodedGaussian, StereoMolecule mol)
int
getAtomId()
double
getInteractionSimilarity(PPGaussian ppGauss2)
IPharmacophorePoint
getPharmacophorePoint()
Coordinates
getRotatedDirectionality(double[][] rotMatrix, double scaleFactor)
double
getSimilarity(PPGaussian ppGauss2)
double
getSimilarity(PPGaussian ppGauss2, Coordinates directionality)
double
getVectorSimilarity(PPGaussian ppGauss2)
double
getVectorSimilarity(PPGaussian ppGauss2, Coordinates directionalityMod)
void
setAtomId(int atomID)
void
setCenter(Coordinates center)
void
transform(Transformation transformation)
void
updateAtomIndeces(int[] map)
void
updateCoordinates(Coordinates[] coords)
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Methods inherited from class com.actelion.research.chem.phesa.Gaussian3D
calculateVolume, getAtomicNo, getCenter, getHeight, getVolume, getVolumeOverlap, getVolumeOverlap, getVolumeOverlap, getWeight, getWidth, setAtomicNo, setHeight, setWeight
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Constructor Detail
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PPGaussian
public PPGaussian(int atomicNo, IPharmacophorePoint pp)
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PPGaussian
public PPGaussian(PPGaussian original)
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Method Detail
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fromString
public static PPGaussian fromString(java.lang.String encodedGaussian, StereoMolecule mol)
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getRotatedDirectionality
public Coordinates getRotatedDirectionality(double[][] rotMatrix, double scaleFactor)
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getVectorSimilarity
public double getVectorSimilarity(PPGaussian ppGauss2, Coordinates directionalityMod)
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getVectorSimilarity
public double getVectorSimilarity(PPGaussian ppGauss2)
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getPharmacophorePoint
public IPharmacophorePoint getPharmacophorePoint()
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setAtomId
public void setAtomId(int atomID)
- Overrides:
setAtomId
in classGaussian3D
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getAtomId
public int getAtomId()
- Overrides:
getAtomId
in classGaussian3D
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getSimilarity
public double getSimilarity(PPGaussian ppGauss2, Coordinates directionality)
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getSimilarity
public double getSimilarity(PPGaussian ppGauss2)
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getInteractionSimilarity
public double getInteractionSimilarity(PPGaussian ppGauss2)
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setCenter
public void setCenter(Coordinates center)
- Overrides:
setCenter
in classGaussian3D
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encode
public java.lang.String encode()
- Specified by:
encode
in classGaussian3D
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decode
public void decode(java.lang.String string64, StereoMolecule mol)
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calculateHeight
public double calculateHeight()
- Specified by:
calculateHeight
in classGaussian3D
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transform
public void transform(Transformation transformation)
- Overrides:
transform
in classGaussian3D
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updateCoordinates
public void updateCoordinates(Coordinates[] coords)
- Overrides:
updateCoordinates
in classGaussian3D
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updateAtomIndeces
public void updateAtomIndeces(int[] map)
- Overrides:
updateAtomIndeces
in classGaussian3D
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calculateWidth
public double calculateWidth()
- Specified by:
calculateWidth
in classGaussian3D
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