Modifier and Type | Interface and Description |
---|---|
interface |
IAtomicDescriptor
Classes that implement this interface are QSAR descriptor calculators.
|
interface |
IAtomPairDescriptor
Classes that implement this interface are QSAR descriptor calculators.
|
interface |
IBondDescriptor
Classes that implement this interface are QSAR descriptor calculators.
|
interface |
IMolecularDescriptor
Classes that implement this interface are QSAR descriptor calculators
for
IMolecule objects. |
Modifier and Type | Class and Description |
---|---|
class |
AbstractAtomicDescriptor
Abstract atomic descriptor class with helper functions for descriptors
that require the whole molecule to calculate the descriptor values,
which in turn need to be cached for all atoms, so that they can be
retrieved one by one.
|
class |
AbstractBondDescriptor
Abstract bond descriptor class with helper functions for descriptors
that require the whole molecule to calculate the descriptor values,
which in turn need to be cached for all bonds, so that they can be
retrieved one by one.
|
Modifier and Type | Method and Description |
---|---|
List<IDescriptor> |
DescriptorEngine.getDescriptorInstances()
Returns a List containing the instantiated descriptor classes.
|
List<IDescriptor> |
DescriptorEngine.instantiateDescriptors(List<String> descriptorClassNames) |
Modifier and Type | Method and Description |
---|---|
List<DescriptorSpecification> |
DescriptorEngine.initializeSpecifications(List<IDescriptor> descriptors) |
void |
DescriptorEngine.setDescriptorInstances(List<IDescriptor> descriptors)
Set the list of
Descriptor objects. |
Modifier and Type | Class and Description |
---|---|
class |
AtomDegreeDescriptor
This class returns the number of not-Hs substituents of an atom, also defined as "atom degree".
|
class |
AtomHybridizationDescriptor
This class returns the hybridization of an atom.
|
class |
AtomHybridizationVSEPRDescriptor
This class returns the hybridization of an atom.
|
class |
AtomValenceDescriptor
This class returns the valence of an atom.
|
class |
BondsToAtomDescriptor
This class returns the number of bonds on the shortest path between two atoms.
|
class |
CovalentRadiusDescriptor
This class return the covalent radius of a given atom.
|
class |
DistanceToAtomDescriptor
This class returns the 3D distance between two atoms.
|
class |
EffectiveAtomPolarizabilityDescriptor
Effective polarizability of an heavy atom
|
class |
InductiveAtomicHardnessDescriptor
Inductive atomic hardness of an atom in a polyatomic system can be defined
as the "resistance" to a change of the atomic charge.
|
class |
InductiveAtomicSoftnessDescriptor
Inductive atomic softness of an atom in a polyatomic system can be defined
as charge delocalizing ability.
|
class |
IPAtomicHOSEDescriptor
This class returns the ionization potential of an atom containg lone
pair electrons.
|
class |
IPAtomicLearningDescriptor
This class returns the ionization potential of an atom containing lone
pair electrons.
|
class |
IsProtonInAromaticSystemDescriptor
This descriptor returns 1 if the protons is directly bonded to an aromatic system,
it returns 2 if the distance between aromatic system and proton is 2 bonds,
and it return 0 for other positions.
|
class |
IsProtonInConjugatedPiSystemDescriptor
This class evaluates if a proton is joined to a conjugated system.
|
class |
PartialPiChargeDescriptor
The calculation of pi partial charges in pi-bonded systems of an heavy
atom was made by Saller-Gasteiger.
|
class |
PartialSigmaChargeDescriptor
The calculation of sigma partial charges in sigma-bonded systems of an heavy atom
was made by Marsilli-Gasteiger.
|
class |
PartialTChargeMMFF94Descriptor
The calculation of total partial charges of an heavy atom is based on MMFF94 model.
|
class |
PartialTChargePEOEDescriptor
The calculation of total partial charges of an heavy atom is based on
Partial Equalization of Electronegativity method (PEOE-PEPE) from Gasteiger.
|
class |
PeriodicTablePositionDescriptor
This class returns the period in the periodic table of an atom belonging to an atom container
|
class |
PiElectronegativityDescriptor
Pi electronegativity is given by X = a + bq + c(q*q)
|
class |
ProtonAffinityHOSEDescriptor
This class returns the proton affinity of an atom containing.
|
class |
ProtonTotalPartialChargeDescriptor
The calculation of partial charges of an heavy atom and its protons is based on Gasteiger Marsili (PEOE).
|
class |
RDFProtonDescriptor_G3R
This class calculates G3R proton descriptors used in neural networks for H1
NMR shift .
|
class |
RDFProtonDescriptor_GDR
This class calculates GDR proton descriptors used in neural networks for H1 NMR
shift .
|
class |
RDFProtonDescriptor_GHR
This class calculates GHR proton descriptors used in neural networks for H1 NMR
shift .
|
class |
RDFProtonDescriptor_GHR_topol
This class calculates GHR topological proton descriptors used in neural networks for H1 NMR
shift .
|
class |
RDFProtonDescriptor_GSR
This class calculates GDR proton descriptors used in neural networks for H1 NMR
shift .
|
class |
SigmaElectronegativityDescriptor
Atomic descriptor that reflects that Gasteiger-Marsili sigma electronegativity.
|
class |
StabilizationPlusChargeDescriptor
The stabilization of the positive charge
(e.g.) obtained in the polar breaking of a bond is calculated from the sigma- and
lone pair-electronegativity values of the atoms that are in conjugation to the atoms
obtaining the charges.
|
class |
VdWRadiusDescriptor
This class return the VdW radius of a given atom.
|
Modifier and Type | Class and Description |
---|---|
class |
PiContactDetectionDescriptor
This class checks if two atoms have pi-contact (this is true when there is
one and the same conjugated pi-system which contains both atoms, or directly
linked neighboors of the atoms).
|
Modifier and Type | Class and Description |
---|---|
class |
AtomicNumberDifferenceDescriptor
Describes the imbalance in atomic number of the IBond.
|
class |
BondPartialPiChargeDescriptor
The calculation of bond-pi Partial charge is calculated
determining the difference the Partial Pi Charge on atoms
A and B of a bond.
|
class |
BondPartialSigmaChargeDescriptor
The calculation of bond-sigma Partial charge is calculated
determining the difference the Partial Sigma Charge on atoms
A and B of a bond.
|
class |
BondPartialTChargeDescriptor
The calculation of bond total Partial charge is calculated
determining the difference the Partial Total Charge on atoms
A and B of a bond.
|
class |
BondSigmaElectronegativityDescriptor
The calculation of bond-Polarizability is calculated determining the
difference the Sigma electronegativity on atoms A and B of a bond.
|
class |
IPBondLearningDescriptor
This class returns the ionization potential of a Bond.
|
Modifier and Type | Class and Description |
---|---|
class |
AcidicGroupCountDescriptor
Returns the number of acidic groups.
|
class |
ALOGPDescriptor
This class calculates ALOGP (Ghose-Crippen LogKow) and the
Ghose-Crippen molar refractivity .
|
class |
AminoAcidCountDescriptor
Class that returns the number of each amino acid in an atom container.
|
class |
APolDescriptor
Sum of the atomic polarizabilities (including implicit hydrogens).
|
class |
AromaticAtomsCountDescriptor
Class that returns the number of aromatic atoms in an atom container.
|
class |
AromaticBondsCountDescriptor
This Class contains a method that returns the number of aromatic atoms in an AtomContainer.
|
class |
AtomCountDescriptor
IDescriptor based on the number of atoms of a certain element type.
|
class |
AutocorrelationDescriptorCharge
This class calculates ATS autocorrelation descriptor, where the weight equal
to the charges.
|
class |
AutocorrelationDescriptorMass
This class calculates ATS autocorrelation descriptor, where the weight equal
to the scaled atomic mass .
|
class |
AutocorrelationDescriptorPolarizability
This class calculates ATS autocorrelation descriptor, where the weight equal
to the charges.
|
class |
BasicGroupCountDescriptor
Returns the number of basic groups.
|
class |
BCUTDescriptor
Eigenvalue based descriptor noted for its utility in chemical diversity.
|
class |
BondCountDescriptor
IDescriptor based on the number of bonds of a certain bond order.
|
class |
BPolDescriptor
Sum of the absolute value of the difference between atomic polarizabilities
of all bonded atoms in the molecule (including implicit hydrogens) with polarizabilities taken from
http://www.sunysccc.edu/academic/mst/ptable/p-table2.htm
This descriptor assumes 2-centered bonds.
|
class |
CarbonTypesDescriptor
Topological descriptor characterizing the carbon connectivity.
|
class |
ChiChainDescriptor
Evaluates chi chain descriptors.
|
class |
ChiClusterDescriptor
Evaluates chi cluster descriptors.
|
class |
ChiPathClusterDescriptor
Evaluates chi path cluster descriptors.
|
class |
ChiPathDescriptor
Evaluates chi path descriptors.
|
class |
CPSADescriptor
Calculates 29 Charged Partial Surface Area (CPSA) descriptors.
|
class |
EccentricConnectivityIndexDescriptor
A topological descriptor combining distance and adjacency information.
|
class |
FMFDescriptor
An implementation of the FMF descriptor characterizing complexity of a molecule.
|
class |
FragmentComplexityDescriptor
Class that returns the complexity of a system.
|
class |
GravitationalIndexDescriptor
IDescriptor characterizing the mass distribution of the molecule.
|
class |
HBondAcceptorCountDescriptor
This descriptor calculates the number of hydrogen bond acceptors using a slightly simplified version of the
PHACIR atom types.
|
class |
HBondDonorCountDescriptor
This descriptor calculates the number of hydrogen bond donors using a slightly simplified version of the
PHACIR atom types.
|
class |
HybridizationRatioDescriptor
IMolecularDescriptor that reports the fraction of sp3 carbons to sp2 carbons. |
class |
IPMolecularLearningDescriptor
This class returns the ionization potential of a molecule.
|
class |
KappaShapeIndicesDescriptor
Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs;
a description is given at: http://www.chemcomp.com/Journal_of_CCG/Features/descr.htm#KH :
"they are intended to capture different aspects of molecular shape.
|
class |
KierHallSmartsDescriptor
A fragment count descriptor that uses e-state fragments.
|
class |
LargestChainDescriptor
Class that returns the number of atoms in the largest chain.
|
class |
LargestPiSystemDescriptor
Class that returns the number of atoms in the largest pi system.
|
class |
LengthOverBreadthDescriptor
Evaluates length over breadth descriptors.
|
class |
LongestAliphaticChainDescriptor
Class that returns the number of atoms in the longest aliphatic chain.
|
class |
MannholdLogPDescriptor
Prediction of logP based on the number of carbon and hetero atoms.
|
class |
MDEDescriptor
Calculates the Molecular Distance Edge descriptor described in .
|
class |
MomentOfInertiaDescriptor
A descriptor that calculates the moment of inertia and radius of gyration.
|
class |
PetitjeanNumberDescriptor
According to the Petitjean definition, the eccentricity of a vertex corresponds to
the distance from that vertex to the most remote vertex in the graph.
|
class |
PetitjeanShapeIndexDescriptor
Evaluates the Petitjean shape indices,
These original Petitjean number was described by Petitjean ()
and considered the molecular graph.
|
class |
RotatableBondsCountDescriptor
The number of rotatable bonds is given by the SMARTS specified by Daylight on
SMARTS tutorial
|
class |
RuleOfFiveDescriptor
This Class contains a method that returns the number failures of the
Lipinski's Rule Of 5.
|
class |
TPSADescriptor
Calculation of topological polar surface area based on fragment
contributions (TPSA) .
|
class |
VABCDescriptor
Volume descriptor using the method implemented in the
VABCVolume class. |
class |
VAdjMaDescriptor
Vertex adjacency information (magnitude):
1 + log2 m where m is the number of heavy-heavy bonds.
|
class |
WeightDescriptor
IDescriptor based on the weight of atoms of a certain element type.
|
class |
WeightedPathDescriptor
Evaluates the weighted path descriptors.
|
class |
WHIMDescriptor
Holistic descriptors described by Todeschini et al .
|
class |
WienerNumbersDescriptor
This descriptor calculates the Wiener numbers.
|
class |
XLogPDescriptor
Prediction of logP based on the atom-type method called XLogP.
|
class |
ZagrebIndexDescriptor
Zagreb index: the sum of the squares of atom degree over all heavy atoms i.
|
Modifier and Type | Class and Description |
---|---|
class |
TaeAminoAcidDescriptor
An implementation of the TAE descriptors for amino acids.
|