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

Class Summary

Class	Description
AcidicGroupCountDescriptor	Returns the number of acidic groups.
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).
AminoAcidCountDescriptor	Class that returns the number of each amino acid in an atom container.
APolDescriptor	Sum of the atomic polarizabilities (including implicit hydrogens).
AromaticAtomsCountDescriptor	Class that returns the number of aromatic atoms in an atom container.
AromaticBondsCountDescriptor	This Class contains a method that returns the number of aromatic atoms in an AtomContainer.
AtomCountDescriptor	IDescriptor based on the number of atoms of a certain element type.
AutocorrelationDescriptorCharge	This class calculates ATS autocorrelation descriptor, where the weight equal to the charges.
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).
AutocorrelationDescriptorPolarizability	This class calculates ATS autocorrelation descriptor, where the weight equal to the charges.
BasicGroupCountDescriptor	Returns the number of basic groups.
BCUTDescriptor	Eigenvalue based descriptor noted for its utility in chemical diversity.
BondCountDescriptor	IDescriptor based on the number of bonds of a certain bond order.
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.
CarbonTypesDescriptor	Topological descriptor characterizing the carbon connectivity.
ChiChainDescriptor	Evaluates chi chain descriptors.
ChiClusterDescriptor	Evaluates chi cluster descriptors.
ChiPathClusterDescriptor	Evaluates chi path cluster descriptors.
ChiPathDescriptor	Evaluates chi path descriptors.
CPSADescriptor	Calculates 29 Charged Partial Surface Area (CPSA) descriptors.
EccentricConnectivityIndexDescriptor	A topological descriptor combining distance and adjacency information.
FMFDescriptor	An implementation of the FMF descriptor characterizing complexity of a molecule.
FractionalCSP3Descriptor	An implementation of the Fractional CSP3 descriptor described in (Lovering, Frank et. al.. J. Med. Chem.. 2009. 52).
FractionalPSADescriptor	Polar surface area expressed as a ratio to molecular size.
FragmentComplexityDescriptor	Class that returns the complexity of a system.
GravitationalIndexDescriptor	IDescriptor characterizing the mass distribution of the molecule.
HBondAcceptorCountDescriptor	This descriptor calculates the number of hydrogen bond acceptors using a slightly simplified version of the PHACIR atom types.
HBondDonorCountDescriptor	This descriptor calculates the number of hydrogen bond donors using a slightly simplified version of the PHACIR atom types.
HybridizationRatioDescriptor	IMolecularDescriptor that reports the fraction of sp3 carbons to sp2 carbons.
IPMolecularLearningDescriptor	Deprecated
JPlogPDescriptor	A logP model donated by Lhasa Limited.
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.
KierHallSmartsDescriptor	A fragment count descriptor that uses e-state fragments.
LargestChainDescriptor	Class that returns the number of atoms in the largest chain.
LargestPiSystemDescriptor	Class that returns the number of atoms in the largest pi system.
LengthOverBreadthDescriptor	Evaluates length over breadth descriptors.
LongestAliphaticChainDescriptor	Counts the number of atoms in the longest aliphatic chain.
MannholdLogPDescriptor	Prediction of logP based on the number of carbon and hetero atoms.
MDEDescriptor	Calculates the Molecular Distance Edge descriptor described in (Liu, S. et. al.. Journal of Chemical Information and Computer Sciences. 1998. 38).
MomentOfInertiaDescriptor	A descriptor that calculates the moment of inertia and radius of gyration.
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.
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.
RotatableBondsCountDescriptor	The number of rotatable bonds is given by the SMARTS specified by Daylight on SMARTS tutorial
RuleOfFiveDescriptor	This Class contains a method that returns the number failures of the Lipinski's Rule Of 5.
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.
SpiroAtomCountDescriptor	Returns the number of spiro atoms.
TPSADescriptor	Calculation of topological polar surface area based on fragment contributions (TPSA) (Ertl, P. et. al.. J. Med. Chem.. 2000. 43).
VABCDescriptor	Volume descriptor using the method implemented in the VABCVolume class.
VAdjMaDescriptor	Vertex adjacency information (magnitude): 1 + log2 m where m is the number of heavy-heavy bonds.
WeightDescriptor	IDescriptor based on the weight of atoms of a certain element type.
WeightedPathDescriptor	Evaluates the weighted path descriptors.
WHIMDescriptor	Holistic descriptors described by Todeschini et al (Todeschini, R. and Gramatica, P.. Persepectives in Drug Discovery and Design. 1998. null).
WienerNumbersDescriptor	This descriptor calculates the Wiener numbers.
XLogPDescriptor	Prediction of logP based on the atom-type method called XLogP.
ZagrebIndexDescriptor	Zagreb index: the sum of the squares of atom degree over all heavy atoms i.