Package org.openscience.cdk.qsar.descriptors.molecular
package org.openscience.cdk.qsar.descriptors.molecular
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ClassesClassDescriptionReturns the number of acidic groups.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 that returns the number of each amino acid in an atom container.Sum of the atomic polarizabilities (including implicit hydrogens).Class that returns the number of aromatic atoms in an atom container.This Class contains a method that returns the number of aromatic atoms in an AtomContainer.IDescriptor based on the number of atoms of a certain element type.This class calculates ATS autocorrelation descriptor, where the weight equal to the charges.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].This class calculates ATS autocorrelation descriptor, where the weight equal to the charges.Returns the number of basic groups.Eigenvalue based descriptor noted for its utility in chemical diversity.IDescriptor based on the number of bonds of a certain bond order.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.Topological descriptor characterizing the carbon connectivity.Evaluates chi chain descriptors.Evaluates chi cluster descriptors.Evaluates chi path cluster descriptors.Evaluates chi path descriptors.Calculates 29 Charged Partial Surface Area (CPSA) descriptors.A topological descriptor combining distance and adjacency information.An implementation of the FMF descriptor characterizing complexity of a molecule.An implementation of the Fractional CSP3 descriptor described in [Lovering, Frank et. al.. J. Med. Chem.. 2009. 52].Polar surface area expressed as a ratio to molecular size.Class that returns the complexity of a system.IDescriptor characterizing the mass distribution of the molecule.This descriptor calculates the number of hydrogen bond acceptors using a slightly simplified version of the PHACIR atom types.This descriptor calculates the number of hydrogen bond donors using a slightly simplified version of the PHACIR atom types.
IMolecularDescriptorthat reports the fraction of sp3 carbons to sp2 carbons.Deprecated.A logP model donated by Lhasa Limited.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.A fragment count descriptor that uses e-state fragments.Class that returns the number of atoms in the largest chain.Class that returns the number of atoms in the largest pi system.Evaluates length over breadth descriptors.Counts the number of atoms in the longest aliphatic chain.Prediction of logP based on the number of carbon and hetero atoms.Calculates the Molecular Distance Edge descriptor described in [Liu, S. et. al.. Journal of Chemical Information and Computer Sciences. 1998. 38].A descriptor that calculates the moment of inertia and radius of gyration.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.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.The number of rotatable bonds is given by the SMARTS specified by Daylight on SMARTS tutorialThis Class contains a method that returns the number failures of the Lipinski's Rule Of 5.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.Returns the number of spiro atoms.Calculation of topological polar surface area based on fragment contributions (TPSA) [Ertl, P. et. al.. J. Med. Chem.. 2000. 43].Volume descriptor using the method implemented in theVABCVolumeclass.Vertex adjacency information (magnitude): 1 + log2 m where m is the number of heavy-heavy bonds.IDescriptor based on the weight of atoms of a certain element type.Evaluates the weighted path descriptors.Holistic descriptors described by Todeschini et al [Todeschini, R. and Gramatica, P.. Persepectives in Drug Discovery and Design. 1998. null].This descriptor calculates the Wiener numbers.Prediction of logP based on the atom-type method called XLogP.Zagreb index: the sum of the squares of atom degree over all heavy atoms i.