Package com.actelion.research.chem.phesa

Class MolecularVolume

java.lang.Object

com.actelion.research.chem.phesa.ShapeVolume

com.actelion.research.chem.phesa.MolecularVolume

public class MolecularVolume
extends ShapeVolume

Field Summary

Fields

Modifier and Type	Field	Description
static double	alpha_pref
static double	p

Fields inherited from class com.actelion.research.chem.phesa.ShapeVolume

atomicGaussians, com, ppGaussians

Constructor Summary

Constructors

Constructor	Description
MolecularVolume(MolecularVolume original)	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)
MolecularVolume(MolecularVolume original, Conformer conf)
MolecularVolume(StereoMolecule mol)
MolecularVolume(java.util.List<AtomicGaussian> atomicGaussiansInp, java.util.List<PPGaussian> ppGaussiansInp, java.util.List<VolumeGaussian> volGaussians, java.util.List<Coordinates> hydrogenCoords)

Method Summary

Modifier and Type	Method	Description
void	calcCOM()	calculates volume weighted center of mass of the molecular Volume
Matrix	createCanonicalOrientation(Conformer conf)
static MolecularVolume	decodeCoordsOnly(java.lang.String string, MolecularVolume reference)
static MolecularVolume	decodeFull(java.lang.String string, StereoMolecule refMol)
java.lang.String	encodeCoordsOnly()
java.lang.String	encodeFull()
Matrix	getCovarianceMatrix()
java.util.ArrayList<Coordinates>	getHydrogens()
double	getSelfAtomOverlap()	calculate the self-overlap of the base molecule
double[]	getTotalAtomOverlap(double[] transform, MolecularVolume fitVol)
java.util.ArrayList<VolumeGaussian>	getVolumeGaussians()
protected void	rotate180DegreeAroundAxis(PheSAAlignment.axis a)
protected void	transformGaussians(Transformation transform)
void	translateToCOM(Coordinates com)
void	update(Conformer conf)
void	update(StereoMolecule mol)
void	updateAtomIndeces(int[] map)
void	updateCOM()

Methods inherited from class com.actelion.research.chem.phesa.ShapeVolume

addAtomVolume, addPharmacophorePoint, decode, encode, getAtomicGaussians, getCOM, getExitVectorGaussians, getPPGaussians, getSelfPPOverlap, getTotalAtomOverlap, getTotalPPOverlap, isCanonicalOrientation, preProcess, removeRings, rotateGaussian, rotateGaussians180DegreeAroundAxis, setAtomicGaussians, setPPGaussians, transform, transformGaussians, updateCoordinates

Methods inherited from class java.lang.Object

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

Field Detail

p

public static final double p

See Also:

Constant Field Values

alpha_pref

public static final double alpha_pref

See Also:

Constant Field Values

Constructor Detail

MolecularVolume

public MolecularVolume(java.util.List<AtomicGaussian> atomicGaussiansInp,
                       java.util.List<PPGaussian> ppGaussiansInp,
                       java.util.List<VolumeGaussian> volGaussians,
                       java.util.List<Coordinates> hydrogenCoords)

MolecularVolume

public MolecularVolume(StereoMolecule mol)

MolecularVolume

public MolecularVolume(MolecularVolume original,
                       Conformer conf)

MolecularVolume

public MolecularVolume(MolecularVolume original)

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 -

Method Detail

updateCOM

public void updateCOM()

updateAtomIndeces

public void updateAtomIndeces(int[] map)

getSelfAtomOverlap

public double getSelfAtomOverlap()

calculate the self-overlap of the base molecule

Overrides:

getSelfAtomOverlap in class ShapeVolume

Returns:

getTotalAtomOverlap

public double[] getTotalAtomOverlap(double[] transform,
                                    MolecularVolume fitVol)

rotate180DegreeAroundAxis

protected void rotate180DegreeAroundAxis(PheSAAlignment.axis a)

Overrides:

rotate180DegreeAroundAxis in class ShapeVolume

calcCOM

public void calcCOM()

calculates volume weighted center of mass of the molecular Volume

Overrides:

calcCOM in class ShapeVolume

getCovarianceMatrix

public Matrix getCovarianceMatrix()

Overrides:

getCovarianceMatrix in class ShapeVolume

getVolumeGaussians

public java.util.ArrayList<VolumeGaussian> getVolumeGaussians()

transformGaussians

protected void transformGaussians(Transformation transform)

Overrides:

transformGaussians in class ShapeVolume

getHydrogens

public java.util.ArrayList<Coordinates> getHydrogens()

update

public void update(StereoMolecule mol)

Overrides:

update in class ShapeVolume

update

public void update(Conformer conf)

Overrides:

update in class ShapeVolume

createCanonicalOrientation

public Matrix createCanonicalOrientation(Conformer conf)

Overrides:

createCanonicalOrientation in class ShapeVolume

translateToCOM

public void translateToCOM(Coordinates com)

Overrides:

translateToCOM in class ShapeVolume

encodeFull

public java.lang.String encodeFull()

encodeCoordsOnly

public java.lang.String encodeCoordsOnly()

decodeCoordsOnly

public static MolecularVolume decodeCoordsOnly(java.lang.String string,
                                               MolecularVolume reference)

decodeFull

public static MolecularVolume decodeFull(java.lang.String string,
                                         StereoMolecule refMol)