Package com.actelion.research.chem.phesa

Class MolecularVolume

java.lang.Object

com.actelion.research.chem.phesa.MolecularVolume

public class MolecularVolume
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field	Description
static double	alpha_pref
static double	p

Constructor Summary

Constructors

Constructor	Description
MolecularVolume(MolecularVolume original)
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
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()
java.util.ArrayList<AtomicGaussian>	getAtomicGaussians()
Coordinates	getCOM()
java.util.List<PPGaussian>	getExitVectorGaussians()
java.util.ArrayList<Coordinates>	getHydrogens()
java.util.ArrayList<PPGaussian>	getPPGaussians()
java.util.ArrayList<VolumeGaussian>	getVolumeGaussians()
void	translateToCOM(Coordinates com)
void	update(Conformer conf)
void	update(StereoMolecule mol)
void	updateAtomIndeces(int[] map)
void	updateCOM()

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)

Method Detail

updateCOM

public void updateCOM()

updateAtomIndeces

public void updateAtomIndeces(int[] map)

getCOM

public Coordinates getCOM()

getAtomicGaussians

public java.util.ArrayList<AtomicGaussian> getAtomicGaussians()

getPPGaussians

public java.util.ArrayList<PPGaussian> getPPGaussians()

getVolumeGaussians

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

getHydrogens

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

update

public void update(StereoMolecule mol)

update

public void update(Conformer conf)

translateToCOM

public void translateToCOM(Coordinates com)

getExitVectorGaussians

public java.util.List<PPGaussian> getExitVectorGaussians()

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)