Uses of Interface
org.openscience.cdk.qsar.IDescriptor

Packages that use IDescriptor

Package	Description
org.openscience.cdk.qsar
org.openscience.cdk.qsar.descriptors.atomic
org.openscience.cdk.qsar.descriptors.atompair
org.openscience.cdk.qsar.descriptors.bond
org.openscience.cdk.qsar.descriptors.molecular
org.openscience.cdk.qsar.descriptors.protein
org.openscience.cdk.qsar.descriptors.substance

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 for IAtomContainer 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 of Descriptor objects.

Constructor parameters in org.openscience.cdk.qsar with type arguments of type IDescriptor

Modifier	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 parameters
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 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 parameters
class	PiElectronegativityDescriptor	Pi electronegativity is given by X = a + bq + c(q*q) Parameters for this descriptor: Name Default Description maxIterations 0 Number of maximum iterations
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 [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 tutorial
class	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 an 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 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 [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.