Modifier and Type | Method and Description |
---|---|
DescriptorValue |
IMolecularDescriptor.calculate(IAtomContainer container)
Calculates the descriptor value for the given IAtomContainer.
|
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.
|
Modifier and Type | Method and Description |
---|---|
DescriptorValue |
IPAtomicLearningDescriptor.calculate(IAtom atom,
IAtomContainer container)
Deprecated.
This method calculates the ionization potential of an atom.
|
DescriptorValue |
PartialTChargeMMFF94Descriptor.calculate(IAtom atom,
IAtomContainer org)
The method returns partial charges assigned to an heavy atom through
MMFF94 method.
|
DescriptorValue |
IPAtomicHOSEDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the ionization potential of an atom.
|
DescriptorValue |
CovalentRadiusDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the Covalent radius of an atom.
|
DescriptorValue |
RDFProtonDescriptor_GDR.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
DescriptorValue |
RDFProtonDescriptor_GHR.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
DescriptorValue |
AtomValenceDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the valence of an atom.
|
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 |
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 |
AtomHybridizationDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the hybridization of an atom.
|
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 |
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 |
DistanceToAtomDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculate the 3D distance between two atoms.
|
DescriptorValue |
VdWRadiusDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculate the Van der Waals radius of an atom.
|
DescriptorValue |
InductiveAtomicHardnessDescriptor.calculate(IAtom atom,
IAtomContainer ac)
It is needed to call the addExplicitHydrogensToSatisfyValency method from
the class tools.HydrogenAdder, and 3D coordinates.
|
DescriptorValue |
BondsToAtomDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculate the number of bonds on the shortest path between two atoms.
|
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 |
RDFProtonDescriptor_GSR.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
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 |
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 |
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 |
RDFProtonDescriptor_GHR_topol.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
DescriptorValue |
PeriodicTablePositionDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the period of an atom.
|
DescriptorValue |
AtomHybridizationVSEPRDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the hybridization of an atom.
|
DescriptorValue |
InductiveAtomicSoftnessDescriptor.calculate(IAtom atom,
IAtomContainer ac)
It is needed to call the addExplicitHydrogensToSatisfyValency method from
the class tools.HydrogenAdder, and 3D coordinates.
|
DescriptorValue |
AtomDegreeDescriptor.calculate(IAtom atom,
IAtomContainer container)
This method calculates the number of not-H substituents of an atom.
|
DescriptorValue |
RDFProtonDescriptor_G3R.calculate(IAtom atom,
IAtomContainer varAtomContainerSet) |
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 |
PartialTChargePEOEDescriptor.calculate(IAtom atom,
IAtomContainer ac)
The method returns partial total charges assigned to an heavy atom through PEOE method.
|
DescriptorValue |
RDFProtonDescriptor_GDR.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_GHR.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_GSR.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_GHR_topol.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_G3R.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
Modifier and Type | Method and Description |
---|---|
DescriptorValue |
PiContactDetectionDescriptor.calculate(IAtom first,
IAtom second,
IAtomContainer atomContainer)
The method returns if two atoms have pi-contact.
|
Modifier and Type | Method and Description |
---|---|
DescriptorValue |
IPBondLearningDescriptor.calculate(IBond bond,
IAtomContainer atomContainer)
Deprecated.
This method calculates the ionization potential of a bond.
|
DescriptorValue |
AtomicNumberDifferenceDescriptor.calculate(IBond bond,
IAtomContainer ac) |
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 |
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 |
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 |
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.
|
Modifier and Type | Method and Description |
---|---|
DescriptorValue |
IPMolecularLearningDescriptor.calculate(IAtomContainer atomContainer)
Deprecated.
It calculates the first ionization energy of a molecule.
|
DescriptorValue |
AminoAcidCountDescriptor.calculate(IAtomContainer ac)
Determine the number of amino acids groups the supplied
IAtomContainer . |
DescriptorValue |
BondCountDescriptor.calculate(IAtomContainer container)
This method calculate the number of bonds of a given type in an atomContainer
|
DescriptorValue |
HBondAcceptorCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the number of H bond acceptors.
|
DescriptorValue |
AutocorrelationDescriptorPolarizability.calculate(IAtomContainer container)
This method calculate the ATS Autocorrelation descriptor.
|
DescriptorValue |
AromaticAtomsCountDescriptor.calculate(IAtomContainer atomContainer)
Calculate the count of aromatic atoms in the supplied
IAtomContainer . |
DescriptorValue |
KappaShapeIndicesDescriptor.calculate(IAtomContainer container)
calculates the kier shape indices for an atom container
|
DescriptorValue |
FragmentComplexityDescriptor.calculate(IAtomContainer container)
Calculate the complexity in the supplied
IAtomContainer . |
DescriptorValue |
AutocorrelationDescriptorMass.calculate(IAtomContainer atomContainer)
This method calculate the ATS Autocorrelation descriptor.
|
DescriptorValue |
LargestPiSystemDescriptor.calculate(IAtomContainer container)
Calculate the count of atoms of the largest pi system in the supplied
IAtomContainer . |
DescriptorValue |
FractionalPSADescriptor.calculate(IAtomContainer mol)
Calculates the topological polar surface area and expresses it as a ratio to molecule size.
|
DescriptorValue |
ChiPathClusterDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
CarbonTypesDescriptor.calculate(IAtomContainer container)
Calculates the 9 carbon types descriptors
|
DescriptorValue |
ChiChainDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
LengthOverBreadthDescriptor.calculate(IAtomContainer atomContainer)
Evaluate the descriptor for the molecule.
|
DescriptorValue |
GravitationalIndexDescriptor.calculate(IAtomContainer container)
Calculates the 9 gravitational indices.
|
DescriptorValue |
CPSADescriptor.calculate(IAtomContainer atomContainer)
Evaluates the 29 CPSA descriptors using Gasteiger-Marsilli charges.
|
DescriptorValue |
AutocorrelationDescriptorCharge.calculate(IAtomContainer atomContainer) |
DescriptorValue |
TPSADescriptor.calculate(IAtomContainer atomContainer)
Calculates the TPSA for an atom container.
|
DescriptorValue |
FMFDescriptor.calculate(IAtomContainer container)
Calculates the FMF descriptor value for the given
IAtomContainer . |
DescriptorValue |
MomentOfInertiaDescriptor.calculate(IAtomContainer container)
Calculates the 3 MI's, 3 ration and the R_gyr value.
|
DescriptorValue |
RotatableBondsCountDescriptor.calculate(IAtomContainer ac)
The method calculates the number of rotatable bonds of an atom container.
|
DescriptorValue |
ChiPathDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
WeightDescriptor.calculate(IAtomContainer container)
Calculate the natural weight of specified elements type in the supplied
IAtomContainer . |
DescriptorValue |
WeightedPathDescriptor.calculate(IAtomContainer container)
Calculates the weighted path descriptors.
|
DescriptorValue |
ZagrebIndexDescriptor.calculate(IAtomContainer atomContainer)
Evaluate the Zagreb Index for a molecule.
|
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 |
APolDescriptor.calculate(IAtomContainer container)
Calculate the sum of atomic polarizabilities in an
IAtomContainer . |
DescriptorValue |
XLogPDescriptor.calculate(IAtomContainer atomContainer)
Calculates the xlogP for an atom container.
|
DescriptorValue |
AcidicGroupCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the descriptor value for the given IAtomContainer.
|
DescriptorValue |
LargestChainDescriptor.calculate(IAtomContainer atomContainer)
Calculate the count of atoms of the largest chain in the supplied
IAtomContainer . |
DescriptorValue |
JPlogPDescriptor.calculate(IAtomContainer container) |
DescriptorValue |
VAdjMaDescriptor.calculate(IAtomContainer atomContainer)
calculates the VAdjMa descriptor for an atom container
|
DescriptorValue |
EccentricConnectivityIndexDescriptor.calculate(IAtomContainer container)
Calculates the eccentric connectivity
|
DescriptorValue |
VABCDescriptor.calculate(IAtomContainer atomContainer)
Calculates the descriptor value using the
VABCVolume class. |
DescriptorValue |
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 molecule
|
DescriptorValue |
SpiroAtomCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the descriptor value for the given IAtomContainer.
|
DescriptorValue |
PetitjeanShapeIndexDescriptor.calculate(IAtomContainer container)
Calculates the two Petitjean shape indices.
|
DescriptorValue |
PetitjeanNumberDescriptor.calculate(IAtomContainer atomContainer)
Evaluate the descriptor for the molecule.
|
DescriptorValue |
FractionalCSP3Descriptor.calculate(IAtomContainer mol)
Calculates the Fsp3 descriptor value for the given
IAtomContainer . |
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 |
HBondDonorCountDescriptor.calculate(IAtomContainer atomContainer)
Calculates the number of H bond donors.
|
DescriptorValue |
KierHallSmartsDescriptor.calculate(IAtomContainer container)
This method calculates occurrences of the Kier & Hall E-state fragments.
|
DescriptorValue |
WHIMDescriptor.calculate(IAtomContainer container)
Calculates 11 directional and 6 non-directional WHIM descriptors for.
|
DescriptorValue |
ALOGPDescriptor.calculate(IAtomContainer container)
The AlogP descriptor.
|
DescriptorValue |
MDEDescriptor.calculate(IAtomContainer container)
Calculate the weight of specified element type in the supplied
IAtomContainer . |
DescriptorValue |
LongestAliphaticChainDescriptor.calculate(IAtomContainer mol)
Calculate the count of atoms of the longest aliphatic chain in the supplied
IAtomContainer . |
DescriptorValue |
AromaticBondsCountDescriptor.calculate(IAtomContainer atomContainer)
Calculate the count of aromatic atoms in the supplied
IAtomContainer . |
DescriptorValue |
AtomCountDescriptor.calculate(IAtomContainer container)
This method calculate the number of atoms of a given type in an
IAtomContainer . |
DescriptorValue |
HybridizationRatioDescriptor.calculate(IAtomContainer container)
Calculate sp3/sp2 hybridization ratio in the supplied
IAtomContainer . |
DescriptorValue |
ChiClusterDescriptor.calculate(IAtomContainer container) |
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 |
MannholdLogPDescriptor.calculate(IAtomContainer atomContainer)
Calculates the Mannhold LogP for an atom container.
|
DescriptorValue |
WienerNumbersDescriptor.calculate(IAtomContainer atomContainer)
Calculate the Wiener numbers.
|
DescriptorValue |
IPMolecularLearningDescriptor.calculatePlus(IAtomContainer container)
Deprecated.
It calculates the 1,2,..
|
Modifier and Type | Method and Description |
---|---|
DescriptorValue |
TaeAminoAcidDescriptor.calculate(IAtomContainer container)
Calculates the 147 TAE descriptors for amino acids.
|
Modifier and Type | Method and Description |
---|---|
DescriptorValue |
OxygenAtomCountDescriptor.calculate(ISubstance substance)
Calculates the descriptor value for the given
ISubstance . |
DescriptorValue |
ISubstanceDescriptor.calculate(ISubstance substance)
Calculates the descriptor value for the given
ISubstance . |
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