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

Packages that use MolecularVolume

Package	Description
com.actelion.research.chem.alignment3d
com.actelion.research.chem.phesa
com.actelion.research.chem.phesaflex

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

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

Modifier and Type	Method	Description
static double	PheSAAlignmentOptimizer.align(PheSAMolecule fitShape, MolecularVolume refVol, MolecularVolume fitVol, StereoMolecule aligned, double ppWeight)

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

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

Modifier and Type	Method	Description
static MolecularVolume	MolecularVolume.decodeCoordsOnly(java.lang.String string, MolecularVolume reference)
static MolecularVolume	MolecularVolume.decodeFull(java.lang.String string, StereoMolecule refMol)
MolecularVolume	PheSAAlignment.getMolGauss()
MolecularVolume	PheSAAlignment.getRefMolGauss()

Methods in com.actelion.research.chem.phesa that return types with arguments of type MolecularVolume

Modifier and Type	Method	Description
java.util.ArrayList<MolecularVolume>	PheSAMolecule.getVolumes()

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

Modifier and Type	Method	Description
static Matrix	PheSAAlignment.createCanonicalOrientation(Conformer conf, MolecularVolume molGauss)
static MolecularVolume	MolecularVolume.decodeCoordsOnly(java.lang.String string, MolecularVolume reference)
StereoMolecule	PheSAMolecule.getConformer(MolecularVolume molVol)	Returns the corresponding conformer of a molecular volume
double	PheSAAlignment.getSelfAtomOverlap(MolecularVolume molGauss)	calculate the self-overlap of the base molecule
double	PheSAAlignment.getSelfPPOverlap(MolecularVolume molGauss)
static Matrix	PheSAAlignment.preProcess(Conformer conf, MolecularVolume molVol)	Move COM of the molecular volume to the origin of the lab-frame and orient molecules so that their principal moments of inertia coincide with the 3 axis of the coordinate system

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

Constructor	Description
MolecularVolume(MolecularVolume original)
MolecularVolume(MolecularVolume original, Conformer conf)
PheSAAlignment(MolecularVolume refMolGauss, MolecularVolume molGauss)
PheSAAlignment(MolecularVolume refMolGauss, MolecularVolume molGauss, double ppWeight)
PheSAMolecule(StereoMolecule mol, MolecularVolume shape)

Constructor parameters in com.actelion.research.chem.phesa with type arguments of type MolecularVolume

Constructor	Description
PheSAMolecule(StereoMolecule mol, java.util.ArrayList<MolecularVolume> shape)

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

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

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

Constructors in com.actelion.research.chem.phesaflex with parameters of type MolecularVolume

Constructor	Description
FlexibleShapeAlignment(StereoMolecule refMol, StereoMolecule fitMol, MolecularVolume refVol, MolecularVolume fitVol, double ppWeight)