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 volumedouble
PheSAAlignment. getSelfAtomOverlap(MolecularVolume molGauss)
calculate the self-overlap of the base moleculedouble
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 systemConstructors 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)
-