Uses of Class
org.openscience.cdk.qsar.DescriptorValue
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Uses of DescriptorValue in org.openscience.cdk.qsar
Methods in org.openscience.cdk.qsar that return DescriptorValue Modifier and Type Method Description DescriptorValue
IAtomicDescriptor. calculate(IAtom atom, IAtomContainer container)
Calculates the descriptor value for the given IAtom.DescriptorValue
IAtomPairDescriptor. calculate(IAtom atom, IAtom atom2, IAtomContainer container)
Calculates the descriptor value for the given IAtom.DescriptorValue
IBondDescriptor. calculate(IBond bond, IAtomContainer atomContainer)
Calculates the descriptor value for the given IBond.DescriptorValue
IMolecularDescriptor. calculate(IAtomContainer container)
Calculates the descriptor value for the given IAtomContainer. -
Uses of DescriptorValue in org.openscience.cdk.qsar.descriptors.atomic
Methods in org.openscience.cdk.qsar.descriptors.atomic that return DescriptorValue Modifier and Type Method Description DescriptorValue
AtomDegreeDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculates the number of not-H substituents of an atom.DescriptorValue
AtomHybridizationDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculates the hybridization of an atom.DescriptorValue
AtomHybridizationVSEPRDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculates the hybridization of an atom.DescriptorValue
AtomValenceDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculates the valence of an atom.DescriptorValue
BondsToAtomDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculate the number of bonds on the shortest path between two atoms.DescriptorValue
CovalentRadiusDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculates the Covalent radius of an atom.DescriptorValue
DistanceToAtomDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculate the 3D distance between two atoms.DescriptorValue
EffectiveAtomPolarizabilityDescriptor. calculate(IAtom atom, IAtomContainer ac)
The method calculates the Effective Atom Polarizability of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
InductiveAtomicHardnessDescriptor. calculate(IAtom atom, IAtomContainer ac)
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder, and 3D coordinates.DescriptorValue
InductiveAtomicSoftnessDescriptor. calculate(IAtom atom, IAtomContainer ac)
It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder, and 3D coordinates.DescriptorValue
IPAtomicHOSEDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculates the ionization potential of an atom.DescriptorValue
IPAtomicLearningDescriptor. calculate(IAtom atom, IAtomContainer container)
Deprecated.This method calculates the ionization potential of an atom.DescriptorValue
IsProtonInAromaticSystemDescriptor. calculate(IAtom atom, IAtomContainer atomContainer)
The method is a proton descriptor that evaluate if a proton is bonded to an aromatic system or if there is distance of 2 bonds.DescriptorValue
IsProtonInConjugatedPiSystemDescriptor. calculate(IAtom atom, IAtomContainer atomContainer)
The method is a proton descriptor that evaluates if a proton is joined to a conjugated system.DescriptorValue
PartialPiChargeDescriptor. calculate(IAtom atom, IAtomContainer ac)
The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
PartialSigmaChargeDescriptor. calculate(IAtom atom, IAtomContainer ac)
The method returns apha partial charges assigned to an heavy atom through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
PartialTChargeMMFF94Descriptor. calculate(IAtom atom, IAtomContainer org)
The method returns partial charges assigned to an heavy atom through MMFF94 method.DescriptorValue
PartialTChargePEOEDescriptor. calculate(IAtom atom, IAtomContainer ac)
The method returns partial total charges assigned to an heavy atom through PEOE method.DescriptorValue
PeriodicTablePositionDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculates the period of an atom.DescriptorValue
PiElectronegativityDescriptor. calculate(IAtom atom, IAtomContainer atomContainer)
The method calculates the pi electronegativity of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
ProtonAffinityHOSEDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculates the protonation affinity of an atom.DescriptorValue
ProtonTotalPartialChargeDescriptor. calculate(IAtom atom, IAtomContainer ac)
The method returns partial charges assigned to an heavy atom and its protons through Gasteiger Marsili It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
RDFProtonDescriptor_G3R. calculate(IAtom atom, IAtomContainer varAtomContainerSet)
DescriptorValue
RDFProtonDescriptor_G3R. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
DescriptorValue
RDFProtonDescriptor_GDR. calculate(IAtom atom, IAtomContainer varAtomContainerSet)
DescriptorValue
RDFProtonDescriptor_GDR. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
DescriptorValue
RDFProtonDescriptor_GHR_topol. calculate(IAtom atom, IAtomContainer varAtomContainerSet)
DescriptorValue
RDFProtonDescriptor_GHR_topol. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
DescriptorValue
RDFProtonDescriptor_GHR. calculate(IAtom atom, IAtomContainer varAtomContainerSet)
DescriptorValue
RDFProtonDescriptor_GHR. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
DescriptorValue
RDFProtonDescriptor_GSR. calculate(IAtom atom, IAtomContainer varAtomContainerSet)
DescriptorValue
RDFProtonDescriptor_GSR. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
DescriptorValue
SigmaElectronegativityDescriptor. calculate(IAtom atom, IAtomContainer ac)
The method calculates the sigma electronegativity of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
StabilizationPlusChargeDescriptor. calculate(IAtom atom, IAtomContainer container)
The method calculates the stabilization of charge of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
VdWRadiusDescriptor. calculate(IAtom atom, IAtomContainer container)
This method calculate the Van der Waals radius of an atom. -
Uses of DescriptorValue in org.openscience.cdk.qsar.descriptors.atompair
Methods in org.openscience.cdk.qsar.descriptors.atompair that return DescriptorValue Modifier and Type Method Description DescriptorValue
PiContactDetectionDescriptor. calculate(IAtom first, IAtom second, IAtomContainer atomContainer)
The method returns if two atoms have pi-contact. -
Uses of DescriptorValue in org.openscience.cdk.qsar.descriptors.bond
Methods in org.openscience.cdk.qsar.descriptors.bond that return DescriptorValue Modifier and Type Method Description DescriptorValue
AtomicNumberDifferenceDescriptor. calculate(IBond bond, IAtomContainer ac)
DescriptorValue
BondPartialPiChargeDescriptor. calculate(IBond bond, IAtomContainer ac)
The method calculates the bond-pi Partial charge of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
BondPartialSigmaChargeDescriptor. calculate(IBond bond, IAtomContainer ac)
The method calculates the bond-sigma Partial charge of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
BondPartialTChargeDescriptor. calculate(IBond bond, IAtomContainer ac)
The method calculates the bond total Partial charge of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
BondSigmaElectronegativityDescriptor. calculate(IBond aBond, IAtomContainer atomContainer)
The method calculates the sigma electronegativity of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
IPBondLearningDescriptor. calculate(IBond bond, IAtomContainer atomContainer)
Deprecated.This method calculates the ionization potential of a bond. -
Uses of DescriptorValue in org.openscience.cdk.qsar.descriptors.molecular
Methods in org.openscience.cdk.qsar.descriptors.molecular that return DescriptorValue Modifier and Type Method Description DescriptorValue
AcidicGroupCountDescriptor. calculate(IAtomContainer atomContainer)
Calculates the descriptor value for the given IAtomContainer.DescriptorValue
ALOGPDescriptor. calculate(IAtomContainer container)
The AlogP descriptor.DescriptorValue
AminoAcidCountDescriptor. calculate(IAtomContainer ac)
Determine the number of amino acids groups the suppliedIAtomContainer
.DescriptorValue
APolDescriptor. calculate(IAtomContainer container)
Calculate the sum of atomic polarizabilities in anIAtomContainer
.DescriptorValue
AromaticAtomsCountDescriptor. calculate(IAtomContainer atomContainer)
Calculate the count of aromatic atoms in the suppliedIAtomContainer
.DescriptorValue
AromaticBondsCountDescriptor. calculate(IAtomContainer atomContainer)
Calculate the count of aromatic atoms in the suppliedIAtomContainer
.DescriptorValue
AtomCountDescriptor. calculate(IAtomContainer container)
This method calculate the number of atoms of a given type in anIAtomContainer
.DescriptorValue
AutocorrelationDescriptorCharge. calculate(IAtomContainer atomContainer)
DescriptorValue
AutocorrelationDescriptorMass. calculate(IAtomContainer atomContainer)
This method calculate the ATS Autocorrelation descriptor.DescriptorValue
AutocorrelationDescriptorPolarizability. calculate(IAtomContainer container)
This method calculate the ATS Autocorrelation descriptor.DescriptorValue
BasicGroupCountDescriptor. calculate(IAtomContainer atomContainer)
Calculates the descriptor value for the given IAtomContainer.DescriptorValue
BCUTDescriptor. calculate(IAtomContainer container)
Calculates the three classes of BCUT descriptors.DescriptorValue
BondCountDescriptor. calculate(IAtomContainer container)
This method calculate the number of bonds of a given type in an atomContainerDescriptorValue
BPolDescriptor. calculate(IAtomContainer container)
This method calculate the sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the moleculeDescriptorValue
CarbonTypesDescriptor. calculate(IAtomContainer container)
Calculates the 9 carbon types descriptorsDescriptorValue
ChiChainDescriptor. calculate(IAtomContainer container)
DescriptorValue
ChiClusterDescriptor. calculate(IAtomContainer container)
DescriptorValue
ChiPathClusterDescriptor. calculate(IAtomContainer container)
DescriptorValue
ChiPathDescriptor. calculate(IAtomContainer container)
DescriptorValue
CPSADescriptor. calculate(IAtomContainer atomContainer)
Evaluates the 29 CPSA descriptors using Gasteiger-Marsilli charges.DescriptorValue
EccentricConnectivityIndexDescriptor. calculate(IAtomContainer container)
Calculates the eccentric connectivityDescriptorValue
FMFDescriptor. calculate(IAtomContainer container)
Calculates the FMF descriptor value for the givenIAtomContainer
.DescriptorValue
FractionalCSP3Descriptor. calculate(IAtomContainer mol)
Calculates the Fsp3 descriptor value for the givenIAtomContainer
.DescriptorValue
FractionalPSADescriptor. calculate(IAtomContainer mol)
Calculates the topological polar surface area and expresses it as a ratio to molecule size.DescriptorValue
FragmentComplexityDescriptor. calculate(IAtomContainer container)
Calculate the complexity in the suppliedIAtomContainer
.DescriptorValue
GravitationalIndexDescriptor. calculate(IAtomContainer container)
Calculates the 9 gravitational indices.DescriptorValue
HBondAcceptorCountDescriptor. calculate(IAtomContainer atomContainer)
Calculates the number of H bond acceptors.DescriptorValue
HBondDonorCountDescriptor. calculate(IAtomContainer atomContainer)
Calculates the number of H bond donors.DescriptorValue
HybridizationRatioDescriptor. calculate(IAtomContainer container)
Calculate sp3/sp2 hybridization ratio in the suppliedIAtomContainer
.DescriptorValue
IPMolecularLearningDescriptor. calculate(IAtomContainer atomContainer)
Deprecated.It calculates the first ionization energy of a molecule.DescriptorValue
JPlogPDescriptor. calculate(IAtomContainer container)
DescriptorValue
KappaShapeIndicesDescriptor. calculate(IAtomContainer container)
calculates the kier shape indices for an atom containerDescriptorValue
KierHallSmartsDescriptor. calculate(IAtomContainer container)
This method calculates occurrences of the Kier & Hall E-state fragments.DescriptorValue
LargestChainDescriptor. calculate(IAtomContainer atomContainer)
Calculate the count of atoms of the largest chain in the suppliedIAtomContainer
.DescriptorValue
LargestPiSystemDescriptor. calculate(IAtomContainer container)
Calculate the count of atoms of the largest pi system in the suppliedIAtomContainer
.DescriptorValue
LengthOverBreadthDescriptor. calculate(IAtomContainer atomContainer)
Evaluate the descriptor for the molecule.DescriptorValue
LongestAliphaticChainDescriptor. calculate(IAtomContainer mol)
Calculate the count of atoms of the longest aliphatic chain in the suppliedIAtomContainer
.DescriptorValue
MannholdLogPDescriptor. calculate(IAtomContainer atomContainer)
Calculates the Mannhold LogP for an atom container.DescriptorValue
MDEDescriptor. calculate(IAtomContainer container)
Calculate the weight of specified element type in the suppliedIAtomContainer
.DescriptorValue
MomentOfInertiaDescriptor. calculate(IAtomContainer container)
Calculates the 3 MI's, 3 ration and the R_gyr value.DescriptorValue
PetitjeanNumberDescriptor. calculate(IAtomContainer atomContainer)
Evaluate the descriptor for the molecule.DescriptorValue
PetitjeanShapeIndexDescriptor. calculate(IAtomContainer container)
Calculates the two Petitjean shape indices.DescriptorValue
RotatableBondsCountDescriptor. calculate(IAtomContainer ac)
The method calculates the number of rotatable bonds of an atom container.DescriptorValue
RuleOfFiveDescriptor. calculate(IAtomContainer mol)
the method take a boolean checkAromaticity: if the boolean is true, it means that aromaticity has to be checked.DescriptorValue
SmallRingDescriptor. calculate(IAtomContainer mol)
Performs the calculation: the graph will be analyzed and ring information will be determined and wrapped up into descriptors.DescriptorValue
SpiroAtomCountDescriptor. calculate(IAtomContainer atomContainer)
Calculates the descriptor value for the given IAtomContainer.DescriptorValue
TPSADescriptor. calculate(IAtomContainer atomContainer)
Calculates the TPSA for an atom container.DescriptorValue
VABCDescriptor. calculate(IAtomContainer atomContainer)
Calculates the descriptor value using theVABCVolume
class.DescriptorValue
VAdjMaDescriptor. calculate(IAtomContainer atomContainer)
calculates the VAdjMa descriptor for an atom containerDescriptorValue
WeightDescriptor. calculate(IAtomContainer container)
Calculate the natural weight of specified elements type in the suppliedIAtomContainer
.DescriptorValue
WeightedPathDescriptor. calculate(IAtomContainer container)
Calculates the weighted path descriptors.DescriptorValue
WHIMDescriptor. calculate(IAtomContainer container)
Calculates 11 directional and 6 non-directional WHIM descriptors for.DescriptorValue
WienerNumbersDescriptor. calculate(IAtomContainer atomContainer)
Calculate the Wiener numbers.DescriptorValue
XLogPDescriptor. calculate(IAtomContainer atomContainer)
Calculates the xlogP for an atom container.DescriptorValue
ZagrebIndexDescriptor. calculate(IAtomContainer atomContainer)
Evaluate the Zagreb Index for a molecule.DescriptorValue
IPMolecularLearningDescriptor. calculatePlus(IAtomContainer container)
Deprecated.It calculates the 1,2,.. -
Uses of DescriptorValue in org.openscience.cdk.qsar.descriptors.protein
Methods in org.openscience.cdk.qsar.descriptors.protein that return DescriptorValue Modifier and Type Method Description DescriptorValue
TaeAminoAcidDescriptor. calculate(IAtomContainer container)
Calculates the 147 TAE descriptors for amino acids. -
Uses of DescriptorValue in org.openscience.cdk.qsar.descriptors.substance
Methods in org.openscience.cdk.qsar.descriptors.substance that return DescriptorValue Modifier and Type Method Description DescriptorValue
ISubstanceDescriptor. calculate(ISubstance substance)
Calculates the descriptor value for the givenISubstance
.DescriptorValue
OxygenAtomCountDescriptor. calculate(ISubstance substance)
Calculates the descriptor value for the givenISubstance
.
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