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

Constructor Summary

Constructors

Constructor	Description
PheSAAlignment(MolecularVolume refMolGauss, MolecularVolume molGauss)
PheSAAlignment(MolecularVolume refMolGauss, MolecularVolume molGauss, double ppWeight)
PheSAAlignment(StereoMolecule refMol, StereoMolecule mol)
PheSAAlignment(StereoMolecule refMol, StereoMolecule mol, double ppWeight)

Method Summary

Modifier and Type	Method	Description
static Matrix	createCanonicalOrientation(Conformer conf, MolecularVolume molGauss)
double[]	findAlignment(double[][] transforms)
double[]	findAlignment(double[][] transforms, boolean optimize)
MolecularVolume	getMolGauss()
MolecularVolume	getRefMolGauss()
static void	getRotationMatrix(double theta, Coordinates axis, double[][] r)
double	getSelfAtomOverlap(MolecularVolume molGauss)	calculate the self-overlap of the base molecule
double	getSelfAtomOverlapFit()
double	getSelfAtomOverlapRef()
double	getSelfPPOverlap(MolecularVolume molGauss)
double	getSelfPPOverlapFit()
double	getSelfPPOverlapRef()
double[]	getTotalAtomOverlap(double[] transform)	calculate the Overlap of the two molecular volumes as a function a transform vector that is applied to the query molecule overlap Volume of two molecular Volumes formulated as a summed overlap of atomic Gaussians taken from Grant, Gallardo, Pickup, Journal of Computational Chemistry, 17, 1653-1666, 1996 returns a double[2]: the first double is the total overlap, whereas the second value is the specific contribution of additional volume gaussians (inclusion, exclusion)
double	getTotalPPOverlap(double[] transform)
static double[][]	initialTransform(int mode)	.
static void	multiplyInverseMatrix(double[][] r, double[][] s, double[][] rs)
static void	multiplyMatrix(double[][] r, double[][] s, double[][] rs)
static Matrix	preProcess(Conformer conf, MolecularVolume molVol)	Move COM of the molecular volume to the origin of the lab-frame and orient molecules so that their principal moments of inertia coincide with the 3 axis of the coordinate system
static void	rotateMol(Conformer conf, double[] transform)
static void	rotateMol(Conformer conf, Matrix rotMat)
static void	rotateMol(Conformer conf, Quaternion rotor, double[] transl)
static void	rotateMol(StereoMolecule mol, double[] transform)
static void	rotateMol(StereoMolecule mol, double[][] m)
static void	rotateMol(StereoMolecule mol, Matrix rotMat)
static void	rotateMol(StereoMolecule mol, Quaternion rotor, double[] transl)
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

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(MolecularVolume refMolGauss,
                      MolecularVolume molGauss,
                      double ppWeight)

Method Detail

getRefMolGauss

public MolecularVolume getRefMolGauss()

getMolGauss

public MolecularVolume getMolGauss()

preProcess

public static Matrix preProcess(Conformer conf,
                                MolecularVolume molVol)

Move COM of the molecular volume to the origin of the lab-frame and orient molecules so that their principal moments of inertia coincide with the 3 axis of the coordinate system

Parameters:

mol -

molVol -

createCanonicalOrientation

public static Matrix createCanonicalOrientation(Conformer conf,
                                                MolecularVolume molGauss)

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:

getTotalAtomOverlap

public double[] getTotalAtomOverlap(double[] transform)

calculate the Overlap of the two molecular volumes as a function a transform vector that is applied to the query molecule overlap Volume of two molecular Volumes formulated as a summed overlap of atomic Gaussians taken from Grant, Gallardo, Pickup, Journal of Computational Chemistry, 17, 1653-1666, 1996 returns a double[2]: the first double is the total overlap, whereas the second value is the specific contribution of additional volume gaussians (inclusion, exclusion)

Parameters:

transform -

Returns:

getTotalPPOverlap

public double getTotalPPOverlap(double[] transform)

getSelfAtomOverlap

public double getSelfAtomOverlap(MolecularVolume molGauss)

calculate the self-overlap of the base molecule

Returns:

getSelfPPOverlap

public double getSelfPPOverlap(MolecularVolume molGauss)

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)

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[][] transforms)

findAlignment

public double[] findAlignment(double[][] transforms,
                              boolean optimize)

rotateMol

public static void rotateMol(Conformer conf,
                             Matrix rotMat)

rotateMol

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

rotateMol

public static void rotateMol(StereoMolecule mol,
                             Matrix rotMat)

rotateMol

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