Package com.actelion.research.chem.phesa
Class PheSAAlignment
- java.lang.Object
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- com.actelion.research.chem.phesa.PheSAAlignment
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public class PheSAAlignment extends java.lang.Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
PheSAAlignment.axis
static class
PheSAAlignment.PheSAResult
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Field Summary
Fields Modifier and Type Field Description static double
TVERSKY_COEFFICIENT
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Constructor Summary
Constructors Constructor Description PheSAAlignment(MolecularVolume refMolGauss, MolecularVolume molGauss)
PheSAAlignment(ShapeVolume refMolGauss, ShapeVolume molGauss, double ppWeight)
PheSAAlignment(StereoMolecule refMol, StereoMolecule mol)
PheSAAlignment(StereoMolecule refMol, StereoMolecule mol, double ppWeight)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description double[]
findAlignment(double[][] initialTransforms, TransformationSequence optimizedTransform)
double[]
findAlignment(double[][] initialTransforms, TransformationSequence optimizedTransform, boolean optimize)
double[]
findAlignment(double[][] initialTransforms, TransformationSequence optimizedTransform, boolean optimize, boolean tversky)
ShapeVolume
getMolGauss()
ShapeVolume
getRefMolGauss()
static void
getRotationMatrix(double theta, Coordinates axis, double[][] r)
double
getSelfAtomOverlapFit()
double
getSelfAtomOverlapRef()
double
getSelfPPOverlapFit()
double
getSelfPPOverlapRef()
static double[][]
initialTransform(int mode)
.static void
multiplyInverseMatrix(double[][] r, double[][] s, double[][] rs)
static void
multiplyMatrix(double[][] r, double[][] s, double[][] rs)
static void
rotateCoordsAroundAxis180(Coordinates coords, PheSAAlignment.axis a)
static void
rotateMol(Conformer conf, double[][] m)
static void
rotateMol(Conformer conf, Quaternion rotor, double[] transl)
static void
rotateMol(StereoMolecule mol, double[][] m)
static void
rotateMol(StereoMolecule mol, Quaternion rotor, double[] transl)
static void
rotateMolAroundAxis180(Conformer conf, PheSAAlignment.axis a)
static void
translateMol(StereoMolecule mol, double[] translate)
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Field Detail
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TVERSKY_COEFFICIENT
public static final double TVERSKY_COEFFICIENT
- See Also:
- Constant Field Values
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Constructor Detail
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PheSAAlignment
public PheSAAlignment(StereoMolecule refMol, StereoMolecule mol, double ppWeight)
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PheSAAlignment
public PheSAAlignment(StereoMolecule refMol, StereoMolecule mol)
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PheSAAlignment
public PheSAAlignment(MolecularVolume refMolGauss, MolecularVolume molGauss)
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PheSAAlignment
public PheSAAlignment(ShapeVolume refMolGauss, ShapeVolume molGauss, double ppWeight)
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Method Detail
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getRefMolGauss
public ShapeVolume getRefMolGauss()
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getMolGauss
public ShapeVolume getMolGauss()
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rotateMolAroundAxis180
public static void rotateMolAroundAxis180(Conformer conf, PheSAAlignment.axis a)
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rotateCoordsAroundAxis180
public static void rotateCoordsAroundAxis180(Coordinates coords, PheSAAlignment.axis a)
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initialTransform
public static double[][] initialTransform(int mode)
. generate initial orientations of the molecule: mode1: 4 orientations: initial orientation and 180 degree rotation about each axis mode2: mode1 and 90 degree rotations about each axis a transformation vector consists of 7 elements: the first 4 elements form a Quaternion and describe the rotation the last three elements are the translation vector- Parameters:
mode
-- Returns:
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getSelfAtomOverlapRef
public double getSelfAtomOverlapRef()
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getSelfAtomOverlapFit
public double getSelfAtomOverlapFit()
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getSelfPPOverlapRef
public double getSelfPPOverlapRef()
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getSelfPPOverlapFit
public double getSelfPPOverlapFit()
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rotateMol
public static void rotateMol(Conformer conf, Quaternion rotor, double[] transl)
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rotateMol
public static void rotateMol(StereoMolecule mol, Quaternion rotor, double[] transl)
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rotateMol
public static void rotateMol(StereoMolecule mol, double[][] m)
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rotateMol
public static void rotateMol(Conformer conf, double[][] m)
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translateMol
public static void translateMol(StereoMolecule mol, double[] translate)
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multiplyMatrix
public static void multiplyMatrix(double[][] r, double[][] s, double[][] rs)
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multiplyInverseMatrix
public static void multiplyInverseMatrix(double[][] r, double[][] s, double[][] rs)
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getRotationMatrix
public static void getRotationMatrix(double theta, Coordinates axis, double[][] r)
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findAlignment
public double[] findAlignment(double[][] initialTransforms, TransformationSequence optimizedTransform)
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findAlignment
public double[] findAlignment(double[][] initialTransforms, TransformationSequence optimizedTransform, boolean optimize)
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findAlignment
public double[] findAlignment(double[][] initialTransforms, TransformationSequence optimizedTransform, boolean optimize, boolean tversky)
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