Package com.actelion.research.chem.phesa
Class MolecularVolume
- java.lang.Object
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- com.actelion.research.chem.phesa.MolecularVolume
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public class MolecularVolume extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description static double
alpha_pref
static double
p
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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)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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()
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Field Detail
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p
public static final double p
- See Also:
- Constant Field Values
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alpha_pref
public static final double alpha_pref
- See Also:
- Constant Field Values
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Constructor Detail
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MolecularVolume
public MolecularVolume(java.util.List<AtomicGaussian> atomicGaussiansInp, java.util.List<PPGaussian> ppGaussiansInp, java.util.List<VolumeGaussian> volGaussians, java.util.List<Coordinates> hydrogenCoords)
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MolecularVolume
public MolecularVolume(StereoMolecule mol)
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MolecularVolume
public MolecularVolume(MolecularVolume original, Conformer conf)
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MolecularVolume
public MolecularVolume(MolecularVolume original)
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Method Detail
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updateCOM
public void updateCOM()
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updateAtomIndeces
public void updateAtomIndeces(int[] map)
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getCOM
public Coordinates getCOM()
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getAtomicGaussians
public java.util.ArrayList<AtomicGaussian> getAtomicGaussians()
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getPPGaussians
public java.util.ArrayList<PPGaussian> getPPGaussians()
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getVolumeGaussians
public java.util.ArrayList<VolumeGaussian> getVolumeGaussians()
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getHydrogens
public java.util.ArrayList<Coordinates> getHydrogens()
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update
public void update(StereoMolecule mol)
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update
public void update(Conformer conf)
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translateToCOM
public void translateToCOM(Coordinates com)
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getExitVectorGaussians
public java.util.List<PPGaussian> getExitVectorGaussians()
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encodeFull
public java.lang.String encodeFull()
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encodeCoordsOnly
public java.lang.String encodeCoordsOnly()
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decodeCoordsOnly
public static MolecularVolume decodeCoordsOnly(java.lang.String string, MolecularVolume reference)
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decodeFull
public static MolecularVolume decodeFull(java.lang.String string, StereoMolecule refMol)
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