Uses of Interface
org.openscience.cdk.qsar.IDescriptor
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Uses of IDescriptor in org.openscience.cdk.qsar
Subinterfaces of IDescriptor in org.openscience.cdk.qsar Modifier and Type Interface 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 forIAtomContainer
objects.Classes in org.openscience.cdk.qsar that implement IDescriptor Modifier and Type Class 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
AbstractAtomPairDescriptor
A super class for atom pair descriptors allowing default implementations for interface methods.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.class
AbstractMolecularDescriptor
A super class for molecular descriptors allowing default implementations for interface methods.Methods in org.openscience.cdk.qsar that return types with arguments of type IDescriptor Modifier and Type Method Description List<IDescriptor>
DescriptorEngine. getDescriptorInstances()
Returns a List containing the instantiated descriptor classes.List<IDescriptor>
DescriptorEngine. instantiateDescriptors(List<String> descriptorClassNames)
Method parameters in org.openscience.cdk.qsar with type arguments of type IDescriptor Modifier and Type Method Description List<IImplementationSpecification>
DescriptorEngine. initializeSpecifications(List<IDescriptor> descriptors)
void
DescriptorEngine. setDescriptorInstances(List<IDescriptor> descriptors)
Set the list ofDescriptor
objects.Constructor parameters in org.openscience.cdk.qsar with type arguments of type IDescriptor Constructor Description DescriptorEngine(Class<? extends IDescriptor> c, IChemObjectBuilder builder)
Create a descriptor engine for all descriptor types. -
Uses of IDescriptor in org.openscience.cdk.qsar.descriptors.atomic
Classes in org.openscience.cdk.qsar.descriptors.atomic that implement IDescriptor Modifier and Type Class 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 returns the covalent radius of a given atom.class
DistanceToAtomDescriptor
This class returns the 3D distance between two atoms.class
EffectiveAtomPolarizabilityDescriptor
Effective polarizability of a heavy atom Parameters for this descriptor: Name Default Description no parametersclass
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 containing lone pair electrons.class
IPAtomicLearningDescriptor
Deprecated.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 Parameters for this descriptor: Name Default Description no parametersclass
PiElectronegativityDescriptor
Pi electronegativity is given by X = a + bq + c(q*q) Parameters for this descriptor: Name Default Description maxIterations 0 Number of maximum iterationsclass
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 [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74].class
RDFProtonDescriptor_GDR
This class calculates GDR proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74].class
RDFProtonDescriptor_GHR
This class calculates GHR proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74].class
RDFProtonDescriptor_GHR_topol
This class calculates GHR topological proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74].class
RDFProtonDescriptor_GSR
This class calculates GDR proton descriptors used in neural networks for H1 NMR shift [Aires-de-Sousa, J. et. al.. J. Chem. Inf. Mod.. 2002. 74].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. -
Uses of IDescriptor in org.openscience.cdk.qsar.descriptors.atompair
Classes in org.openscience.cdk.qsar.descriptors.atompair that implement IDescriptor Modifier and Type Class 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 neighbours of the atoms). -
Uses of IDescriptor in org.openscience.cdk.qsar.descriptors.bond
Classes in org.openscience.cdk.qsar.descriptors.bond that implement IDescriptor Modifier and Type Class 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
Deprecated. -
Uses of IDescriptor in org.openscience.cdk.qsar.descriptors.molecular
Classes in org.openscience.cdk.qsar.descriptors.molecular that implement IDescriptor Modifier and Type Class Description class
AcidicGroupCountDescriptor
Returns the number of acidic groups.class
ALOGPDescriptor
This class calculates ALOGP (Ghose-Crippen LogKow) and the Ghose-Crippen molar refractivity [Ghose, A.K. and Crippen, G.M. . Journal of Computational Chemistry. 1986. 7, Ghose, A.K. and Crippen, G.M. . Journal of Chemical Information and Computer Science. 1987. 27].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 [Moreau G. and Broto P.. Nouveau Journal de Chimie. 1980. null].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
FractionalCSP3Descriptor
An implementation of the Fractional CSP3 descriptor described in [Lovering, Frank et. al.. J. Med. Chem.. 2009. 52].class
FractionalPSADescriptor
Polar surface area expressed as a ratio to molecular size.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
Deprecated.class
JPlogPDescriptor
A logP model donated by Lhasa Limited.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
Counts 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 [Liu, S. et. al.. Journal of Chemical Information and Computer Sciences. 1998. 38].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 ([ Petitjean, M. . Journal of Chemical Information and Computer Science. 1992. 32]) and considered the molecular graph.class
RotatableBondsCountDescriptor
The number of rotatable bonds is given by the SMARTS specified by Daylight on SMARTS tutorialclass
RuleOfFiveDescriptor
This Class contains a method that returns the number failures of the Lipinski's Rule Of 5.class
SmallRingDescriptor
Small ring descriptors: these are based on enumeration of all the small rings (sizes 3 to 9) in a molecule, which can be obtained quickly and deterministically.class
SpiroAtomCountDescriptor
Returns the number of spiro atoms.class
TPSADescriptor
Calculation of topological polar surface area based on fragment contributions (TPSA) [Ertl, P. et. al.. J. Med. Chem.. 2000. 43].class
VABCDescriptor
Volume descriptor using the method implemented in theVABCVolume
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 [Todeschini, R. and Gramatica, P.. Persepectives in Drug Discovery and Design. 1998. null].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. -
Uses of IDescriptor in org.openscience.cdk.qsar.descriptors.protein
Classes in org.openscience.cdk.qsar.descriptors.protein that implement IDescriptor Modifier and Type Class Description class
TaeAminoAcidDescriptor
An implementation of the TAE descriptors for amino acids. -
Uses of IDescriptor in org.openscience.cdk.qsar.descriptors.substance
Subinterfaces of IDescriptor in org.openscience.cdk.qsar.descriptors.substance Modifier and Type Interface Description interface
ISubstanceDescriptor
Classes that implement this interface are QSAR substance calculators.Classes in org.openscience.cdk.qsar.descriptors.substance that implement IDescriptor Modifier and Type Class Description class
OxygenAtomCountDescriptor
Descriptor that returns the number of oxygens in the chemical formula.
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