Package com.actelion.research.chem.phesa

Class PheSAAlignment

java.lang.Object

com.actelion.research.chem.phesa.PheSAAlignment

public class PheSAAlignment
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	PheSAAlignment.axis
static class	PheSAAlignment.PheSAResult

Field Summary

Fields

Modifier and Type	Field	Description
static double	TVERSKY_COEFFICIENT

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)

Method Summary

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)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

TVERSKY_COEFFICIENT

public static final double TVERSKY_COEFFICIENT

See Also:

Constant Field Values

Constructor Detail

PheSAAlignment

public PheSAAlignment(StereoMolecule refMol,
                      StereoMolecule mol,
                      double ppWeight)

PheSAAlignment

public PheSAAlignment(StereoMolecule refMol,
                      StereoMolecule mol)

PheSAAlignment

public PheSAAlignment(MolecularVolume refMolGauss,
                      MolecularVolume molGauss)

PheSAAlignment

public PheSAAlignment(ShapeVolume refMolGauss,
                      ShapeVolume molGauss,
                      double ppWeight)

Method Detail

getRefMolGauss

public ShapeVolume getRefMolGauss()

getMolGauss

public ShapeVolume getMolGauss()

rotateMolAroundAxis180

public static void rotateMolAroundAxis180(Conformer conf,
                                          PheSAAlignment.axis a)

rotateCoordsAroundAxis180

public static void rotateCoordsAroundAxis180(Coordinates coords,
                                             PheSAAlignment.axis a)

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:

getSelfAtomOverlapRef

public double getSelfAtomOverlapRef()

getSelfAtomOverlapFit

public double getSelfAtomOverlapFit()

getSelfPPOverlapRef

public double getSelfPPOverlapRef()

getSelfPPOverlapFit

public double getSelfPPOverlapFit()

rotateMol

public static void rotateMol(Conformer conf,
                             Quaternion rotor,
                             double[] transl)

rotateMol

public static void rotateMol(StereoMolecule mol,
                             Quaternion rotor,
                             double[] transl)

rotateMol

public static void rotateMol(StereoMolecule mol,
                             double[][] m)

rotateMol

public static void rotateMol(Conformer conf,
                             double[][] m)

translateMol

public static void translateMol(StereoMolecule mol,
                                double[] translate)

multiplyMatrix

public static void multiplyMatrix(double[][] r,
                                  double[][] s,
                                  double[][] rs)

multiplyInverseMatrix

public static void multiplyInverseMatrix(double[][] r,
                                         double[][] s,
                                         double[][] rs)

getRotationMatrix

public static void getRotationMatrix(double theta,
                                     Coordinates axis,
                                     double[][] r)

findAlignment

public double[] findAlignment(double[][] initialTransforms,
                              TransformationSequence optimizedTransform)

findAlignment

public double[] findAlignment(double[][] initialTransforms,
                              TransformationSequence optimizedTransform,
                              boolean optimize)

findAlignment

public double[] findAlignment(double[][] initialTransforms,
                              TransformationSequence optimizedTransform,
                              boolean optimize,
                              boolean tversky)