Uses of Class
com.actelion.research.chem.phesa.MolecularVolume
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Packages that use MolecularVolume Package Description com.actelion.research.chem.phesa com.actelion.research.chem.phesaflex -
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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)
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 MolecularVolume
MolecularVolume. decodeCoordsOnly(java.lang.String string, MolecularVolume reference)
StereoMolecule
PheSAMolecule. getConformer(MolecularVolume molVol)
Returns the corresponding conformer of a molecular volumedouble[]
MolecularVolume. getTotalAtomOverlap(double[] transform, MolecularVolume fitVol)
Constructors in com.actelion.research.chem.phesa with parameters of type MolecularVolume 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)
PheSAAlignment(MolecularVolume refMolGauss, MolecularVolume molGauss)
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)
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Uses of MolecularVolume in com.actelion.research.chem.phesaflex
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)
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