Uses of Class
com.actelion.research.chem.phesa.ShapeVolume

Packages that use ShapeVolume

Package	Description
com.actelion.research.chem.alignment3d
com.actelion.research.chem.docking.receptorpharmacophore
com.actelion.research.chem.docking.shape
com.actelion.research.chem.phesa
com.actelion.research.chem.phesaflex

Uses of ShapeVolume in com.actelion.research.chem.alignment3d

Methods in com.actelion.research.chem.alignment3d with parameters of type ShapeVolume

Modifier and Type	Method	Description
static java.util.List<PheSAAlignmentOptimizer.AlignmentResult>	PheSAAlignmentOptimizer.alignToNegRecImg(ShapeVolume ref, java.util.List<? extends ShapeVolume> fitVols, double ppWeight, boolean optimize)

Method parameters in com.actelion.research.chem.alignment3d with type arguments of type ShapeVolume

Modifier and Type	Method	Description
static java.util.List<PheSAAlignmentOptimizer.AlignmentResult>	PheSAAlignmentOptimizer.alignToNegRecImg(ShapeVolume ref, java.util.List<? extends ShapeVolume> fitVols, double ppWeight, boolean optimize)
static java.util.NavigableSet<PheSAAlignmentOptimizer.AlignmentResult>	PheSAAlignmentOptimizer.createAlignmentSolutions(java.util.List<? extends ShapeVolume> refVols, java.util.List<? extends ShapeVolume> fitVols, double ppWeight, boolean optimize, boolean tversky, boolean useDirectionality)

Uses of ShapeVolume in com.actelion.research.chem.docking.receptorpharmacophore

Methods in com.actelion.research.chem.docking.receptorpharmacophore that return ShapeVolume

Modifier and Type	Method	Description
ShapeVolume	NegativeReceptorImage.calculate()
static ShapeVolume	NegativeReceptorImageCreator.create(StereoMolecule lig, StereoMolecule rec, TransformationSequence transformation)

Uses of ShapeVolume in com.actelion.research.chem.docking.shape

Constructors in com.actelion.research.chem.docking.shape with parameters of type ShapeVolume

Constructor	Description
ShapeDocking(ShapeVolume negRecImage, Transformation transformation)

Uses of ShapeVolume in com.actelion.research.chem.phesa

Subclasses of ShapeVolume in com.actelion.research.chem.phesa

Modifier and Type	Class	Description
class	MolecularVolume

Methods in com.actelion.research.chem.phesa that return ShapeVolume

Modifier and Type	Method	Description
static ShapeVolume	ShapeVolume.decode(java.lang.String s)
ShapeVolume	PheSAAlignment.getMolGauss()
ShapeVolume	PheSAAlignment.getRefMolGauss()

Methods in com.actelion.research.chem.phesa with parameters of type ShapeVolume

Modifier and Type	Method	Description
double[]	ShapeVolume.getTotalAtomOverlap(double[] transform, ShapeVolume fitVol)	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	ShapeVolume.getTotalPPOverlap(double[] transform, ShapeVolume fitVol)

Constructors in com.actelion.research.chem.phesa with parameters of type ShapeVolume

Constructor	Description
PheSAAlignment(ShapeVolume refMolGauss, ShapeVolume molGauss, double ppWeight)
ShapeVolume(ShapeVolume original)

Uses of ShapeVolume in com.actelion.research.chem.phesaflex

Methods in com.actelion.research.chem.phesaflex with parameters of type ShapeVolume

Modifier and Type	Method	Description
double	EvaluableFlexibleOverlap.getFGValueSelfPP(double[] grad, ShapeVolume molVol, boolean rigid)
double	EvaluableFlexibleOverlap.getFGValueShapeSelf(double[] grad, ShapeVolume molGauss, boolean rigid)