Package | Description |
---|---|
org.openscience.cdk.qsar.descriptors.molecular | |
org.openscience.cdk.qsar.descriptors.protein |
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 |
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 |
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.
|
Modifier and Type | Class and Description |
---|---|
class |
TaeAminoAcidDescriptor
An implementation of the TAE descriptors for amino acids.
|
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