Package com.actelion.research.chem.phesa
Class MolecularVolume
- java.lang.Object
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- com.actelion.research.chem.phesa.ShapeVolume
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- com.actelion.research.chem.phesa.MolecularVolume
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public class MolecularVolume extends ShapeVolume
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Field Summary
Fields Modifier and Type Field Description static double
alpha_pref
static double
p
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Fields inherited from class com.actelion.research.chem.phesa.ShapeVolume
atomicGaussians, com, ppGaussians
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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)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
calcCOM()
calculates volume weighted center of mass of the molecular VolumeMatrix
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 moleculedouble[]
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()
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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
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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)
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
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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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getSelfAtomOverlap
public double getSelfAtomOverlap()
calculate the self-overlap of the base molecule- Overrides:
getSelfAtomOverlap
in classShapeVolume
- Returns:
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getTotalAtomOverlap
public double[] getTotalAtomOverlap(double[] transform, MolecularVolume fitVol)
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rotate180DegreeAroundAxis
protected void rotate180DegreeAroundAxis(PheSAAlignment.axis a)
- Overrides:
rotate180DegreeAroundAxis
in classShapeVolume
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calcCOM
public void calcCOM()
calculates volume weighted center of mass of the molecular Volume- Overrides:
calcCOM
in classShapeVolume
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getCovarianceMatrix
public Matrix getCovarianceMatrix()
- Overrides:
getCovarianceMatrix
in classShapeVolume
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getVolumeGaussians
public java.util.ArrayList<VolumeGaussian> getVolumeGaussians()
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transformGaussians
protected void transformGaussians(Transformation transform)
- Overrides:
transformGaussians
in classShapeVolume
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getHydrogens
public java.util.ArrayList<Coordinates> getHydrogens()
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update
public void update(StereoMolecule mol)
- Overrides:
update
in classShapeVolume
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update
public void update(Conformer conf)
- Overrides:
update
in classShapeVolume
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createCanonicalOrientation
public Matrix createCanonicalOrientation(Conformer conf)
- Overrides:
createCanonicalOrientation
in classShapeVolume
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translateToCOM
public void translateToCOM(Coordinates com)
- Overrides:
translateToCOM
in classShapeVolume
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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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