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 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 IAtomContainer objects.

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

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	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 and 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 and 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

Constructor and 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 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 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 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 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 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 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 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. . 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 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 and 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 and 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 and Description class OxygenAtomCountDescriptor Descriptor that returns the number of oxygens in the chemical formula. Skip navigation links Overview Package Class Use Tree Deprecated Index Help Prev Next Frames No Frames All Classes Copyright © 2021. All rights reserved.