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

Packages that use IMolecularDescriptor

Package	Description
org.openscience.cdk.qsar
org.openscience.cdk.qsar.descriptors.molecular
org.openscience.cdk.qsar.descriptors.protein

Uses of IMolecularDescriptor in org.openscience.cdk.qsar

Classes in org.openscience.cdk.qsar that implement IMolecularDescriptor

Modifier and Type	Class and Description
class	AbstractMolecularDescriptor A super class for molecular descriptors allowing default implementations for interface methods.

Uses of IMolecularDescriptor in org.openscience.cdk.qsar.descriptors.molecular

Classes in org.openscience.cdk.qsar.descriptors.molecular that implement IMolecularDescriptor

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 [Ghose, A.K. and Crippen, G.M. , Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships. I. Partition coefficients as a measure of hydrophobicity, Journal of Computational Chemistry, 1986, 7:565-577, doi:10.1002/jcc.540070419, Ghose, A.K. and Crippen, G.M. , Atomic physicochemical parameters for three-dimensional-structure-directed quantitative structure-activity relationships. 2. Modeling dispersive and hydrophobic interactions, Journal of Chemical Information and Computer Science, 1987, 27:21-35, doi:10.1021/ci00053a005].
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., The autocorrelation of a topological structure: A new molecular descriptor, Nouveau Journal de Chimie, 1980, ?:359-360].
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	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	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 [Liu, S. and Cao, C. and Li, Z. , Approach to Estimation and Prediction for Normal Boiling Point (NBP) of Alkanes Based on a Novel Molecular Distance Edge (MDE) Vector, lambda, Journal of Chemical Information and Computer Sciences, 1998, 38:387-394].
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. , Applications of the radius-diameter diagram to the classification of topological and geometrical shapes of chemical compounds, Journal of Chemical Information and Computer Science, 1992, 32:331-337]) 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 enumeration of all the small rings (sizes 3 to 9) in a molecule, which can be obtained quickly and deterministically.
class	TPSADescriptor Calculation of topological polar surface area based on fragment contributions (TPSA) [Ertl, P. and Rohde, B. and Selzer, P., Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-Based Contributions and Its Application to the Prediction of Drug Transport Properties, J. Med. Chem., 2000, 43:3714-3717, doi:10.1021/jm000942e].
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., New 3D Molecular Descriptors: The WHIM theory and QAR Applications, Persepectives in Drug Discovery and Design, 1998, ?:355-380].
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 IMolecularDescriptor in org.openscience.cdk.qsar.descriptors.protein

Classes in org.openscience.cdk.qsar.descriptors.protein that implement IMolecularDescriptor

Modifier and Type	Class and Description
class	TaeAminoAcidDescriptor An implementation of the TAE descriptors for amino acids.