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