Modifier and Type | Class and Description |
---|---|
class |
Association
Base class for storing interactions like hydrogen bonds and ionic interactions.
|
class |
CDK
Helper class to provide general information about this CDK library.
|
class |
CDKConstants
An interface providing predefined values for a number of
constants used throughout the CDK.
|
class |
ConformerContainer
A memory-efficient data structure to store conformers for a single molecule.
|
Modifier and Type | Class and Description |
---|---|
class |
AromaticityCalculator |
class |
CDKHueckelAromaticityDetector
This aromaticity detector detects the aromaticity based on the Hückel
4n+2 pi-electrons rule applied to isolated ring systems.
|
class |
DoubleBondAcceptingAromaticityDetector
This aromaticity detector detects the aromaticity based on the Hückel
4n+2 pi-electrons rule applied to isolated ring systems.
|
Modifier and Type | Class and Description |
---|---|
class |
CDKAtomTypeMatcher
Atom Type matcher that perceives atom types as defined in the CDK atom type list
org/openscience/cdk/dict/data/cdk-atom-types.owl . |
class |
EStateAtomTypeMatcher
Determines the EState atom types.
|
class |
SybylAtomTypeMatcher
Atom Type matcher for Sybyl atom types.
|
Modifier and Type | Class and Description |
---|---|
class |
AtomTypeMapper
An
AtomTypeMapper allows the mapping of atom types between atom type
schemes. |
Modifier and Type | Class and Description |
---|---|
class |
AtomTypeCharges
Assigns charges to atom types.
|
class |
Electronegativity
Calculation of the electronegativity of orbitals of a molecule
by the method Gasteiger based on electronegativity is given by X = a + bq + c(q*q).
|
class |
GasteigerMarsiliPartialCharges
The calculation of the Gasteiger Marsili (PEOE) partial charges is based on
.
|
class |
GasteigerPEPEPartialCharges
The calculation of the Gasteiger (PEPE) partial charges is based on
.
|
class |
InductivePartialCharges
The calculation of the inductive partial atomic charges and equalization of
effective electronegativities is based on .
|
class |
PiElectronegativity
Calculation of the electronegativity of orbitals of a molecule
by the method Gasteiger based on electronegativity is given by X = a + bq + c(q*q).
|
class |
Polarizability
Calculation of the polarizability of a molecule by the method of Kang and
Jhon and Gasteiger based on and
Limitations in parameterization of atoms:
H, Csp3, Csp2, Csp2arom, Csp3, Nsp3, Nsp2, Nsp3,
P, Osp3 and Osp2.
|
class |
StabilizationCharges
The stabilization of the positive and the negative charge
obtained (e.g 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.
|
Modifier and Type | Class and Description |
---|---|
class |
AtomTypeFactory
General class for defining AtomTypes.
|
class |
CDKBasedAtomTypeConfigurator
AtomType resource that reads the atom type configuration from an XML file.
|
class |
IsotopeFactory
Used to store and return data of a particular isotope.
|
class |
OWLBasedAtomTypeConfigurator
AtomType resource that reads the atom type configuration from an OWL file.
|
class |
TXTBasedAtomTypeConfigurator
AtomType list configurator that uses the AtomTypes originally
defined in Jmol v5.
|
Modifier and Type | Class and Description |
---|---|
class |
AtomTypeHandler
SAX Handler for the AtomTypeReader.
|
class |
AtomTypeReader
XML Reader for the CDKBasedAtomTypeConfigurator.
|
class |
OWLAtomTypeHandler
SAX Handler for the
OWLAtomTypeReader . |
class |
OWLAtomTypeMappingHandler
SAX Handler for the
OWLAtomTypeMappingReader . |
class |
OWLAtomTypeMappingReader
XML Reader for the
OWLBasedAtomTypeConfigurator . |
class |
OWLAtomTypeReader
XML Reader for the
OWLBasedAtomTypeConfigurator . |
Modifier and Type | Class and Description |
---|---|
class |
IsotopeHandler
Reads an isotope list in CML2 format.
|
class |
IsotopeReader
Reader that instantiates an XML parser and customized handler to process
the isotope information in the CML2 isotope data file.
|
Modifier and Type | Class and Description |
---|---|
class |
DictRef
Object that can be used as key in IChemObject.setProperty(key, value) to
denote that this property is a dictionary reference for this IChemObject.
|
Modifier and Type | Class and Description |
---|---|
class |
CDKException
Exception that is thrown by CDK classes when some problem has occured.
|
class |
InvalidSmilesException |
class |
NoSuchAtomException
Exception that is thrown when an Atom is requested or required that
does not exist in the relevant environment.
|
class |
NoSuchAtomTypeException
Exception that may be thrown when an atom type is looked up or perceived
but no such atom type was found.
|
class |
UnsupportedChemObjectException |
Modifier and Type | Class and Description |
---|---|
class |
EStateFingerprinter
This fingerprinter generates 79 bit fingerprints using the E-State
fragments.
|
class |
ExtendedFingerprinter
Generates an extended fingerprint for a given
IAtomContainer , that
extends the Fingerprinter with additional bits describing ring
features. |
class |
Fingerprinter
Generates a fingerprint for a given AtomContainer.
|
class |
FingerprinterTool
Tool with helper methods for IFingerprint.
|
class |
GraphOnlyFingerprinter
Specialized version of the
Fingerprinter which does not take bond orders
into account. |
class |
HybridizationFingerprinter
Generates a fingerprint for a given
IAtomContainer . |
class |
KlekotaRothFingerprinter
SMARTS based substructure fingerprint based on
|
class |
MACCSFingerprinter
This fingerprinter generates 166 bit MACCS keys.
|
class |
PubchemFingerprinter
Generates a Pubchem fingerprint for a molecule.
|
class |
StandardSubstructureSets
Default sets of atom containers aimed for use with the substructure
|
class |
SubstructureFingerprinter
IFingerprinter that gives a bit set which has a size equal to the number
of substructures it was constructed from. |
Modifier and Type | Class and Description |
---|---|
class |
AdductFormula
Class defining an adduct object in a MolecularFormula.
|
class |
IsotopeContainer
This class defines a isotope container.
|
class |
IsotopePattern
This class defines the properties of a deisotoped
pattern distribution.
|
class |
IsotopePatternGenerator
Generates all Combinatorial chemical isotopes given a structure.
|
class |
IsotopePatternManipulator
Class to manipulate IsotopePattern objects.
|
class |
IsotopePatternSimilarity
This class gives a score hit of similarity between two different
isotope abundance pattern.
|
class |
MassToFormulaTool
Tool to determine molecular formula consistent with a given accurate mass.
|
class |
MolecularFormula
Class defining a molecular formula object.
|
class |
MolecularFormulaChecker
Validate a molecular formula given in IMolecularformula object.
|
class |
MolecularFormulaRange
Class defining a expanded molecular formula object.
|
class |
MolecularFormulaSet
Class defining an set object of MolecularFormulas.
|
Modifier and Type | Class and Description |
---|---|
class |
ExhaustiveFragmenter
Generate fragments exhaustively.
|
class |
FragmentUtils
Helper methods for fragmentation algorithms.
|
class |
MurckoFragmenter
An implementation of the Murcko fragmenation method .
|
Modifier and Type | Class and Description |
---|---|
class |
BondTools
A set of static utility classes for geometric calculations on
IBond s. |
class |
CrystalGeometryTools
A set of static methods for working with crystal coordinates.
|
Modifier and Type | Class and Description |
---|---|
class |
KabschAlignment
Aligns two structures to minimize the RMSD using the Kabsch algorithm.
|
Modifier and Type | Class and Description |
---|---|
class |
CIPTool
Tool to help determine the R,S and stereochemistry definitions of a subset of the
CIP rules .
|
class |
ImplicitHydrogenLigand
Subclass of
Ligand to which no further recursion must be applied. |
class |
Ligand
Concept of a ligand in CIP terms, reflecting a side chain of a central atom that can
have precedence over another.
|
class |
VisitedAtoms
Helper class for the
CIPTool to keep track of which atoms have
already been visited. |
Modifier and Type | Class and Description |
---|---|
class |
CIPLigandRule
Compares to
ILigand s based on CIP sequences sub rules. |
Modifier and Type | Class and Description |
---|---|
class |
VABCVolume
Calculates the Van der Waals volume using the method proposed
in .
|
Modifier and Type | Class and Description |
---|---|
class |
BFSShortestPath
Utility class that finds the shortest bond path between two atoms using
a breadth first search.
|
class |
BiconnectivityInspector
Finds the biconnected components of a graph.
|
class |
ConnectivityChecker
Tool class for checking whether the (sub)structure in an
AtomContainer is connected.
|
class |
MinimalPathIterator
Iterates over all shortest paths between two vertices in an undirected, unweighted graph.
|
class |
MoleculeGraphs
Utility class to create a molecule graph for use with JGraphT.
|
class |
PathTools
Tools class with methods for handling molecular graphs.
|
class |
SpanningTree
Spanning tree of a molecule.
|
Modifier and Type | Class and Description |
---|---|
class |
CanonicalLabeler
Canonically labels an atom container implementing
the algorithm published in David Weininger et.al.
|
class |
ConjugatedPiSystemsDetector |
class |
InChINumbersTools
Tool for calculating atom numbers using the InChI algorithm.
|
class |
MorganNumbersTools
Tool for calculating Morgan numbers .
|
Modifier and Type | Class and Description |
---|---|
class |
AdjacencyMatrix
Calculator for a adjacency matrix representation of this AtomContainer.
|
class |
ConnectionMatrix
Calculator for a connection matrix representation of this AtomContainer.
|
Modifier and Type | Class and Description |
---|---|
class |
Bspt
BSP-Tree stands for Binary Space Partitioning Tree.
|
class |
Point |
class |
RebondTool
Provides tools to rebond a molecule from 3D coordinates only.
|
Modifier and Type | Class and Description |
---|---|
class |
InChIGenerator
This class generates the IUPAC International Chemical Identifier (InChI) for
a CDK IAtomContainer.
|
class |
InChIGeneratorFactory
Factory providing access to
InChIGenerator and InChIToStructure . |
class |
InChIToStructure
This class generates a CDK IAtomContainer from an InChI string.
|
Modifier and Type | Class and Description |
---|---|
class |
CASNumber
Tools to work with CAS registry numbers.
|
Modifier and Type | Class and Description |
---|---|
class |
CDKSourceCodeWriter
Converts a Molecule into CDK source code that would build the same
molecule.
|
class |
CIFReader
This is not a reader for the CIF and mmCIF crystallographic formats.
|
class |
CMLReader
Reads a molecule in CML 1.x and 2.0 format.
|
class |
CMLWriter
Serializes a
IMoleculeSet or a IMolecule object to CML 2 code. |
class |
CrystClustReader |
class |
CrystClustWriter
Rather stupid file format used for storing crystal information.
|
class |
CTXReader
Reader that extracts information from the IDENT, NAME, ATOMS and BONDS
blocks in CTX files.
|
class |
FormatFactory
A factory for recognizing chemical file formats.
|
class |
GamessReader
A reader for GAMESS log file.
|
class |
Gaussian98Reader
A reader for Gaussian98 output.
|
class |
GhemicalMMReader
Reads Ghemical (
http://www.uku.fi/~thassine/ghemical/)
molecular mechanics (*.mm1gp) files.
|
class |
HINReader
Reads an object from HIN formated input.
|
class |
HINWriter
Writer that outputs in the HIN format.
|
class |
INChIPlainTextReader
Reads the content of a IUPAC/NIST Chemical Identifier (INChI) plain text
document.
|
class |
INChIReader
Reads the content of a IUPAC/NIST Chemical Identifier (INChI) document.
|
class |
MDLReader
Reads a molecule from the original MDL MOL or SDF file .
|
class |
MDLRXNReader
Reads a molecule from an MDL RXN file .
|
class |
MDLRXNV2000Reader
Reads a molecule from an MDL RXN file .
|
class |
MDLRXNV3000Reader
Class that implements the new MDL mol format introduced in August 2002.
|
class |
MDLRXNWriter
Writes a reaction to a MDL rxn or SDF file.
|
class |
MDLV2000Reader
Reads content from MDL molfiles and SD files.
|
class |
MDLV2000Writer
Writes MDL molfiles, which contains a single molecule (see ).
|
class |
MDLV3000Reader
Class that implements the MDL mol V3000 format.
|
class |
Mol2Reader
Reads a molecule from an Mol2 file, such as written by Sybyl.
|
class |
Mol2Writer
An output Writer that writes molecular data into the
Tripos Mol2 format.
|
class |
MoSSOutputReader
Reader for MoSS output files which present the results
of a substructure mining study.
|
class |
PCCompoundASNReader
Reads an object from ASN formated input for PubChem Compound entries.
|
class |
PCCompoundXMLReader
Reads an object from ASN.1 XML formated input for PubChem Compound entries.
|
class |
PCSubstanceXMLReader
Reads an object from ASN formated input for PubChem Compound entries.
|
class |
PDBReader
Reads the contents of a PDBFile.
|
class |
PDBWriter
Saves small molecules in a rudimentary PDB format.
|
class |
PMPReader
Reads an frames from a PMP formated input.
|
class |
RGroupQueryReader
A reader for Symyx' Rgroup files (RGFiles).
|
class |
RssWriter
Generates an RSS feed.
|
class |
SDFWriter
Writes MDL SD files ().
|
class |
ShelXReader
A reader for ShelX output (RES) files.
|
class |
ShelXWriter
Serializes a MoleculeSet or a Molecule object to ShelX code.
|
class |
SMILESReader
This Reader reads files which has one SMILES string on each
line, where the format is given as below:
|
class |
SMILESWriter
Writes the SMILES strings to a plain text file.
|
class |
VASPReader
Read output files generated with the VASP software.
|
class |
XYZReader
Reads an object from XYZ formated input.
|
class |
XYZWriter |
class |
ZMatrixReader
It reads Z matrices like in Gaussian input files.
|
Modifier and Type | Class and Description |
---|---|
class |
CMLStack
Low weigth alternative to Sun's Stack class.
|
Modifier and Type | Class and Description |
---|---|
class |
IteratingMDLConformerReader
Iterate over conformers of a collection of molecules stored in SDF format.
|
class |
IteratingSMILESReader
Iterating SMILES file reader.
|
Modifier and Type | Class and Description |
---|---|
class |
GaussianInputWriter
File writer thats generates input files for Gaussian calculation
jobs.
|
Modifier and Type | Class and Description |
---|---|
class |
CDKOWLReader
Reads content from a CDK OWL serialization.
|
Modifier and Type | Class and Description |
---|---|
class |
IsomorphismTester
A too simplistic implementation of an isomorphism test for chemical graphs.
|
Modifier and Type | Class and Description |
---|---|
class |
AtomPlacer
Methods for generating coordinates for atoms in various situations.
|
class |
TemplateHandler
Helper class for Structure Diagram Generation.
|
Modifier and Type | Class and Description |
---|---|
class |
FortranFormat
Converts a String representation of a Fortran double to a double.
|
class |
MathTools
Class providing convenience methods for simple mathematical operations.
|
class |
Primes |
class |
RandomNumbersTool
Class supplying useful methods to generate random numbers.
|
Modifier and Type | Class and Description |
---|---|
class |
Normalizer
Adjusts parts of an AtomContainer to the congiguratin of a fragment.
|
class |
SMSDNormalizer
This class containes set of modules required to clean a molecule
before subjecting it for MCS search.
|
Modifier and Type | Class and Description |
---|---|
class |
PharmacophoreAngleBond
Represents an angle relationship between three pharmacophore groups.
|
class |
PharmacophoreAtom
A representation of a pharmacophore group.
|
class |
PharmacophoreBond
Represents a distance relationship between two pharmacophore groups.
|
class |
PharmacophoreMatcher
Identifies atoms whose 3D arrangement matches a specified pharmacophore query.
|
class |
PharmacophoreQuery
Represents a colleciton of pharmacophore groups and constraints.
|
class |
PharmacophoreQueryAngleBond
Represents a pharmacophore query angle constraint.
|
class |
PharmacophoreQueryAtom
Represents a query pharmacophore group.
|
class |
PharmacophoreQueryBond
Represents a pharmacophore query distance constraint.
|
class |
PharmacophoreUtils
Provides some utility methods for pharmacophore handling.
|
Modifier and Type | Class and Description |
---|---|
class |
DescriptorEngine
A class that provides access to automatic descriptor calculation and more.
|
class |
DescriptorException
Exception that is thrown by descriptor routines when a problem has occured.
|
class |
DescriptorSpecification
Class that is used to distribute descriptor specifications.
|
class |
DescriptorValue
Class that is used to store descriptor values as IChemObject properties.
|
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 return the covalent radius of a given atom.
|
class |
DistanceToAtomDescriptor
This class returns the 3D distance between two atoms.
|
class |
EffectiveAtomPolarizabilityDescriptor
Effective polarizability of an heavy atom
|
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 containg lone
pair electrons.
|
class |
IPAtomicLearningDescriptor
This class returns the ionization potential of an atom containing lone
pair electrons.
|
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
|
class |
PiElectronegativityDescriptor
Pi electronegativity is given by X = a + bq + c(q*q)
|
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 .
|
class |
RDFProtonDescriptor_GDR
This class calculates GDR proton descriptors used in neural networks for H1 NMR
shift .
|
class |
RDFProtonDescriptor_GHR
This class calculates GHR proton descriptors used in neural networks for H1 NMR
shift .
|
class |
RDFProtonDescriptor_GHR_topol
This class calculates GHR topological proton descriptors used in neural networks for H1 NMR
shift .
|
class |
RDFProtonDescriptor_GSR
This class calculates GDR proton descriptors used in neural networks for H1 NMR
shift .
|
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.
|
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
This class returns the ionization potential of a Bond.
|
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 .
|
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 .
|
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 |
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
This class returns the ionization potential of a molecule.
|
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 .
|
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 ()
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 |
TPSADescriptor
Calculation of topological polar surface area based on fragment
contributions (TPSA) .
|
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 .
|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
BooleanResult
Object that provides access to the calculated descriptor value.
|
class |
BooleanResultType
IDescriptorResult type for booleans.
|
class |
DoubleArrayResult |
class |
DoubleArrayResultType
IDescriptorResult type for booleans.
|
class |
DoubleResult |
class |
DoubleResultType
IDescriptorResult type for booleans.
|
class |
IntegerArrayResult |
class |
IntegerArrayResultType
IDescriptorResult type for booleans.
|
class |
IntegerResult
Object that provides access to the calculated descriptor value.
|
class |
IntegerResultType
IDescriptorResult type for booleans.
|
Modifier and Type | Class and Description |
---|---|
class |
ReactionChain
Classes that extends the definition of reaction to a chain reaction.
|
class |
ReactionEngine
The base class for all chemical reactions objects in this cdk.
|
class |
ReactionSpecification
Class that is used to distribute reactions specifications.
|
Modifier and Type | Class and Description |
---|---|
class |
AdductionLPMechanism
This mechanism adduct together two fragments.
|
class |
AdductionPBMechanism
This mechanism adduct together two fragments due to a double bond.
|
class |
HeterolyticCleavageMechanism
This mechanism displaces the chemical bond to an Atom.
|
class |
HomolyticCleavageMechanism
This mechanism breaks the chemical bond between atoms.
|
class |
RadicalSiteIonizationMechanism
This mechanism extracts an atom because of the stabilization of a radical.
|
class |
RadicalSiteRearrangementMechanism
This mechanism displaces an Atom or substructure (R) from one position to an other.
|
class |
RearrangementChargeMechanism
This mechanism displaces the charge(radical, charge + or charge -) because of
a double bond which is associated.
|
class |
RemovingSEofBMechanism
This mechanism extracts a single electron from a bonding orbital which located in
an bond.
|
class |
RemovingSEofNBMechanism
This mechanism extracts a single electron from a non-bonding orbital which located in
a ILonePair container.
|
class |
SharingElectronMechanism
This mechanism displaces the charge (lonePair) because of
deficiency of charge.
|
class |
TautomerizationMechanism
This mechanism produces the tautomerization chemical reaction between two tautomers.
|
Modifier and Type | Class and Description |
---|---|
class |
AdductionProtonLPReaction
IReactionProcess which produces a protonation.
|
class |
AdductionProtonPBReaction
IReactionProcess which produces a protonation to double bond.
|
class |
AdductionSodiumLPReaction
IReactionProcess which produces an adduction of the Sodium.
|
class |
CarbonylEliminationReaction
IReactionProcess which participate mass spectrum process.
|
class |
ElectronImpactNBEReaction
IReactionProcess which make an electron impact for for Non-Bonding Electron Lost.
|
class |
ElectronImpactPDBReaction
IReactionProcess which make an electron impact for pi-Bond Dissociation.
|
class |
ElectronImpactSDBReaction
IReactionProcess which make an electron impact for Sigma Bond Dissociation.
|
class |
HeterolyticCleavagePBReaction
IReactionProcess which a bond is broken displacing the electron to one of the
atoms.
|
class |
HeterolyticCleavageSBReaction
IReactionProcess which a bond is broken displacing the electron to one of the
atoms.
|
class |
HomolyticCleavageReaction
IReactionProcess which breaks the bond homogeneously leading to radical ions.
|
class |
HyperconjugationReaction
HyperconjugationReaction is the stabilizing interaction that results
from the interaction of the electrons in a s-bond (for our case only C-H)
with an adjacent empty (or partially filled) p-orbital.
|
class |
PiBondingMovementReaction
IReactionProcess which tries to reproduce the delocalization of electrons
which are unsaturated bonds from conjugated rings.
|
class |
RadicalChargeSiteInitiationHReaction
IReactionProcess which participate mass spectrum process.
|
class |
RadicalChargeSiteInitiationReaction
IReactionProcess which participate mass spectrum process.
|
class |
RadicalSiteHrAlphaReaction
This reaction could be represented as [A*]-(C)_2-C3[H] => A([H])-(C_2)-[C3*].
|
class |
RadicalSiteHrBetaReaction
This reaction could be represented as [A*]-(C)_3-C4[H] => A([H])-(C_3)-[C4*].
|
class |
RadicalSiteHrDeltaReaction
This reaction could be represented as [A*]-(C)_4-C5[H] => A([H])-(C_4)-[C5*].
|
class |
RadicalSiteHrGammaReaction
This reaction could be represented as [A*]-C1-C2-C3[H] => A([H])-C1-C2-[C3*].
|
class |
RadicalSiteInitiationHReaction
IReactionProcess which participate mass spectrum process.
|
class |
RadicalSiteInitiationReaction
IReactionProcess which participate mass spectrum process.
|
class |
RadicalSiteRrAlphaReaction
This reaction could be represented as [A*]-(C)_2-C3[R] => A([RH])-(C_2)-[C3*].
|
class |
RadicalSiteRrBetaReaction
This reaction could be represented as [A*]-(C)_3-C4[R] => A([R])-(C_3)-[C4*].
|
class |
RadicalSiteRrDeltaReaction
This reaction could be represented as [A*]-(C)_4-C5[R] => A([R])-(C_4)-[C5*].
|
class |
RadicalSiteRrGammaReaction
This reaction could be represented as [A*]-(C)_5-C6[R] => A([R])-(C_5)-[C6*].
|
class |
RearrangementAnionReaction
IReactionProcess which participate in movement resonance.
|
class |
RearrangementCationReaction
IReactionProcess which participate in movement resonance.
|
class |
RearrangementLonePairReaction
IReactionProcess which participate in movement resonance.
|
class |
RearrangementRadicalReaction
IReactionProcess which participate in movement resonance.
|
class |
SharingAnionReaction
IReactionProcess which participate in movement resonance.
|
class |
SharingChargeDBReaction
IReactionProcess which participate in movement resonance.
|
class |
SharingChargeSBReaction
IReactionProcess which participate in movement resonance.
|
class |
SharingLonePairReaction
IReactionProcess which participate in movement resonance.
|
class |
TautomerizationReaction
IReactionProcess which produces a tautomerization chemical reaction.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IParameterReact
Interface for classes that generate parameters used in reactions.
|
class |
ParameterReact
Class which defines the allowed parameters of a reaction.
|
class |
SetReactionCenter
Class extension of ParameterReact class which defines if a reaction is set already the reaction center
in the reactants.
|
Modifier and Type | Class and Description |
---|---|
class |
AtomContainerRenderer
A general renderer for
IAtomContainer s. |
class |
BoundsCalculator
Utility class for calculating the 2D bounding rectangles (bounds)
of various IChemObject subtypes - IChemModel, IReactionSet, IReaction,
IMoleculeSet, and IAtomContainer.
|
class |
ChemModelRenderer
|
class |
MoleculeSetRenderer
|
class |
ReactionRenderer
|
class |
ReactionSetRenderer
|
class |
RendererModel
Model for
IRenderer that contains settings for drawing objects. |
Modifier and Type | Class and Description |
---|---|
class |
CDK2DAtomColors
Gives a short table of atom colors for 2D display.
|
class |
CDKAtomColors
Gives a short table of atom colors for 3D display.
|
class |
CPKAtomColors
Colors atoms using CPK color scheme .
|
class |
PartialAtomicChargeColors
Class defining the color which with atoms are colored.
|
class |
RasmolColors
Atom coloring following RasMol/Chime Color scheme
http://www.umass.edu/microbio/rasmol/rascolor.htm.
|
Modifier and Type | Class and Description |
---|---|
class |
ArrowElement
IRenderingElement for linear arrows. |
class |
AtomSymbolElement
A text element with added information.
|
class |
ElementGroup
A group of rendering elements, of any type.
|
class |
GeneralPath
A path of rendering elements from the elements.path package.
|
class |
LineElement
A line between two points.
|
class |
OvalElement
An oval element (should) have both a width and a height.
|
class |
PathElement
A path composed of points.
|
class |
RectangleElement
A rectangle, with width and height.
|
class |
RingElement
A ring is just a circle - in other words, an oval whose width and height are
the same.
|
class |
TextElement
Text element as used in the chemical drawing.
|
class |
TextGroupElement
A group of text elements, particularly the element symbol (eg: "C")
surrounded by other annotations such as mass number, charge, etc.
|
class |
WedgeLineElement
A 'wedge' is a triangle aligned along a bond that indicates stereochemistry.
|
Modifier and Type | Class and Description |
---|---|
class |
CubicTo
A cubic curve in the path.
|
class |
LineTo
A line element in the path.
|
class |
MoveTo
A MoveTo path element moves the drawing 'pen' without making any lines or
curves and is commonly used to start a path or make gaps in the path.
|
class |
QuadTo
Make a quadratic curve in the path.
|
Modifier and Type | Class and Description |
---|---|
class |
AWTFontManager
AWT-specific font manager.
|
Modifier and Type | Class and Description |
---|---|
class |
AtomContainerBoundsGenerator
IGenerator that draws a rectangular around the IAtomContainer . |
class |
AtomMassGenerator
IGenerator that can render mass number information of atoms. |
class |
AtomNumberGenerator
IGenerator for IAtomContainer s that will draw atom numbers
for the atoms. |
class |
BasicAtomGenerator
Generates basic
IRenderingElement s for atoms in an atom container. |
class |
BasicBondGenerator
Generator for elements from bonds.
|
class |
BasicGenerator
Combination generator for basic drawing of molecules.
|
class |
BasicSceneGenerator
This generator does not create any elements, but acts as a holding place
for various generator parameters used by most drawings, such as the zoom,
background color, margin, etc.
|
class |
BoundsGenerator
Produce a bounding rectangle for various chem objects.
|
class |
ExtendedAtomGenerator
A generator for atoms with mass, charge, etc.
|
class |
LonePairGenerator
Generate the symbols for lone pairs.
|
class |
MappingGenerator
IGenerator that will show how atoms map between the reactant and
product side. |
class |
ProductsBoxGenerator
Generate the symbols for radicals.
|
class |
RadicalGenerator
Generate the symbols for radicals.
|
class |
ReactantsBoxGenerator
Generate the symbols for radicals.
|
class |
ReactionArrowGenerator
Generate the arrow for a reaction.
|
class |
ReactionBoxGenerator
Generate the symbols for radicals.
|
class |
ReactionPlusGenerator
Generate the arrow for a reaction.
|
class |
ReactionSceneGenerator
Generator for general reaction scene components.
|
class |
RingGenerator
Generates just the aromatic indicators for rings : circles, or light-gray
inner bonds, depending on the value of CDKStyleAromaticity.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractGeneratorParameter<T>
Abstract class to provide the base functionality for
IGeneratorParameter implementations. |
Modifier and Type | Class and Description |
---|---|
class |
AbstractAWTDrawVisitor
Partial implementation of the
IDrawVisitor interface for the AWT
widget toolkit, allowing molecules to be rendered with toolkits based on
AWT, like the Java reference graphics platform Swing. |
class |
AWTDrawVisitor
Implementation of the
IDrawVisitor interface for the AWT
widget toolkit, allowing molecules to be rendered with toolkits based on
AWT, like the Java reference graphics platform Swing. |
Modifier and Type | Class and Description |
---|---|
class |
AllRingsFinder
Finds the Set of all Rings.
|
class |
AllRingsFinderMod
Finds the Set of all Rings.
|
class |
Path
Implementation of a Path as needed by .
|
class |
Queue
Implementation of a Queue (FIFO stack).
|
class |
RingPartitioner
Partitions a RingSet into RingSets of connected rings.
|
class |
SSSRFinder
Finds the Smallest Set of Smallest Rings.
|
Modifier and Type | Class and Description |
---|---|
class |
CycleBasis
A minimum basis of all cycles in a graph.
|
class |
SimpleCycle
A cycle in a graph G is a subgraph in which every vertex has even degree.
|
Modifier and Type | Class and Description |
---|---|
class |
AtomSignature
The signature for a molecule rooted at a particular
atom.
|
class |
MoleculeFromSignatureBuilder
Builds a molecule from a signature.
|
class |
MoleculeSignature
A molecule signature is a way to produce
AtomSignature s and to get
the canonical signature string for a molecule. |
class |
Orbit
A list of atom indices, and the label of the orbit.
|
class |
SignatureQuotientGraph
A signature quotient graph has a vertex for every signature symmetry class
and an edge for each bond in the molecule between atoms in their class.
|
Modifier and Type | Class and Description |
---|---|
class |
AdductFormula
Class defining an adduct object in a MolecularFormula.
|
class |
MolecularFormula
Class defining a molecular formula object.
|
class |
MolecularFormulaSet
Class defining an set object of MolecularFormulas.
|
Modifier and Type | Class and Description |
---|---|
class |
DistanceMoment
Fast similarity measure for 3D structures.
|
class |
Tanimoto
Calculates the Tanimoto coefficient for a given pair of two
fingerprint bitsets or real valued feature vectors.
|
Modifier and Type | Class and Description |
---|---|
class |
DeduceBondSystemTool
Tool that tries to deduce bond orders based on connectivity and hybridization
for a number of common ring systems of up to seven-membered rings.
|
class |
FixBondOrdersTool
Class to Fix bond orders at present for Aromatic Rings only.
|
class |
InvPair
This is used to hold the invariance numbers for the canonical labeling of
IAtomContainer s. |
class |
SmilesGenerator
Generates SMILES strings .
|
class |
SmilesParser
Parses a SMILES string and an AtomContainer.
|
Modifier and Type | Class and Description |
---|---|
class |
SMARTSQueryTool
This class provides a easy to use wrapper around SMARTS matching functionality.
|
Modifier and Type | Class and Description |
---|---|
class |
Isomorphism
This class implements the Isomorphism- a multipurpose structure comparison tool.
|
Modifier and Type | Class and Description |
---|---|
class |
DefaultBondMatcher
Checks if a bond is matching between query and target molecules.
|
class |
DefaultMCSPlusAtomMatcher
Checks if atom is matching between query and target molecules.
|
class |
DefaultRGraphAtomMatcher
Checks if atom is matching between query and target molecules.
|
class |
DefaultVFAtomMatcher
Checks if atom is matching between query and target molecules.
|
class |
DefaultVFBondMatcher
Checks if a bond is matching between query and target molecules.
|
Modifier and Type | Class and Description |
---|---|
class |
McGregor
Class which reports MCS solutions based on the McGregor algorithm
published in 1982.
|
class |
McGregorChecks
Class to perform check/methods for McGregor class.
|
class |
McgregorHelper
Helper Class for McGregor algorithm.
|
class |
QueryProcessor
Class to handle mappings of query molecule.
|
class |
TargetProcessor
Class to handle mappings of target molecule based on the query.
|
Modifier and Type | Class and Description |
---|---|
class |
BKKCKCF
This class implements Bron-Kerbosch clique detection algorithm as it is
described in [F.
|
class |
ExactMapping
This class handles MCS between two identical molecules.
|
class |
GenerateCompatibilityGraph
This class generates compatibility graph between query and target molecule.
|
class |
MCSPlus
This class handles MCS plus algorithm which is a combination of
c-clique algorithm and McGregor algorithm.
|
class |
MCSPlusHandler
This class acts as a handler class for MCSPlus algorithm.
|
Modifier and Type | Class and Description |
---|---|
class |
CDKMCS
This class implements atom multipurpose structure comparison tool.
|
class |
CDKMCSHandler
This class acts as a handler class for
CDKMCS algorithm. |
class |
CDKRGraph
This class implements the Resolution Graph (CDKRGraph).
|
class |
CDKRMap
An CDKRMap implements the association between an edge (bond) in G1 and an edge
(bond) in G2, G1 and G2 being the compared graphs in a RGraph context.
|
class |
CDKRMapHandler
This algorithm derives from the algorithm described in
[Tonnelier, C.
|
class |
CDKRNode
Node of the resolution graphe (RGraph) An CDKRNode represents an association
betwwen two edges of the source graphs G1 and G2 that are compared.
|
class |
CDKSubGraphHandler
This class acts as a handler class for
CDKMCS algorithm. |
Modifier and Type | Class and Description |
---|---|
class |
SingleMapping
This class handles single atom mapping.
|
class |
SingleMappingHandler
This is a handler class for single atom mapping
(
SingleMapping ). |
Modifier and Type | Class and Description |
---|---|
class |
VFlibMCSHandler
This class should be used to find MCS between query
graph and target graph.
|
class |
VFlibSubStructureHandler
This is an ultra fast method to report if query
is a substructure for target molecule.
|
class |
VFlibTurboHandler
This is an ultra fast method to report if query
is a substructure for target molecule.
|
Modifier and Type | Class and Description |
---|---|
class |
EdgeBuilder
Class for building/storing edges (bonds) in the graph with bond
query capabilities.
|
class |
NodeBuilder
Class for building/storing nodes (atoms) in the graph with atom
query capabilities.
|
class |
VFQueryBuilder
Class for parsing and generating query graph.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IEdge
Interface for the Edges (bonds) in graph.
|
interface |
IMapper
Interface for the mappings (mapped objects).
|
interface |
INode
Interface for the Node (atomss) in graph.
|
interface |
IQuery
Interface for the query molecule/graph.
|
interface |
IQueryCompiler
Interface for the query graph generator.
|
interface |
IState
Interface for the storing the states of the mapping in the VF algorithm.
|
Modifier and Type | Class and Description |
---|---|
class |
Match
Holds matching query and target nodes.
|
class |
VFMapper
This class finds MCS between query and target molecules
using VF2 algorithm.
|
class |
VFMCSMapper
This class finds MCS between query and target molecules
using VF2 algorithm.
|
class |
VFState
This class finds mapping states between query and target
molecules.
|
Modifier and Type | Class and Description |
---|---|
class |
QueryCompiler
This class creates an template for MCS/substructure query.
|
Modifier and Type | Class and Description |
---|---|
class |
ChemicalFilters
Class that ranks MCS final solution according to the chemical rules.
|
class |
PostFilter
Class that cleans redundant mappings from the solution set.
|
Modifier and Type | Class and Description |
---|---|
class |
TimeOut
Class that manages MCS timeout.
|
Modifier and Type | Class and Description |
---|---|
class |
BinaryTree
Class to construct a Binary tree for McGregor search.
|
class |
BondEnergy
Helper class defining the energy for a bond type.
|
class |
FinalMappings
Class that stores raw mapping(s) after each algorithm is executed.
|
class |
LabelContainer
Class that handles atoms and assignes an integer lable to them.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractMCS
Interface for all MCS algorithms.
|
class |
AbstractMCSAlgorithm
Interface for MCS search algorithm.
|
class |
AbstractSubGraph
Interface class for reporting only substructure searches.
|
class |
Algorithm
This class represents various algorithm type supported by SMSD.
|
interface |
IFinalMapping
Interface for mappings.
|
interface |
IMCSBase
Interface that holds basic core interface for all MCS algorithm.
|
Modifier and Type | Class and Description |
---|---|
class |
BondEnergies
Class that stores bond breaking/formation energy between two atoms.
|
class |
ExtAtomContainerManipulator
Class that handles some customised features for SMSD atom containers.
|
class |
MoleculeSanityCheck
Class that cleans a molecule before MCS search.
|
class |
MolHandler
Class that handles molecules for MCS search.
|
class |
TimeManager
Class that handles execution time of the MCS search.
|
Modifier and Type | Class and Description |
---|---|
class |
DoubleBondStereochemistry
Stereochemistry specification for double bonds.
|
class |
StereoTool
Methods to determine or check the stereo class of a set of atoms.
|
class |
TetrahedralChirality
Stereochemistry specification for quadrivalent atoms.
|
Modifier and Type | Class and Description |
---|---|
class |
InChITautomerGenerator
Creates tautomers for a given input molecule, based on the mobile H atoms listed in the InChI.
|
Modifier and Type | Class and Description |
---|---|
class |
AtomicProperties
Provides atomic property values for descriptor calculations.
|
class |
CDKHydrogenAdder
Adds implicit hydrogens based on atom type definitions.
|
class |
CDKValencyChecker
Assumes CDK atom types to be detected and adds missing hydrogens based on the
atom typing.
|
class |
DeAromatizationTool
Methods that takes a ring of which all bonds are aromatic, and assigns single
and double bonds.
|
class |
ElementComparator
Compares elements based on the order commonly used in
molecular formula.
|
class |
FormatStringBuffer
A class for formatting output similar to the C printf command.
|
class |
HOSECodeGenerator
Generates HOSE codes .
|
class |
IDCreator
Class that provides methods to give unique IDs to ChemObjects.
|
class |
IonizationPotentialTool
This class contains the necessary information to predict ionization
potential energy.
|
class |
LoggingTool
Useful for logging messages.
|
class |
LoggingToolFactory
Factory used to instantiate a
ILoggingTool . |
class |
SaturationChecker
Provides methods for checking whether an atoms valences are saturated with
respect to a particular atom type.
|
class |
StructureResonanceGenerator
This class try to generate resonance structure for a determinate molecule.
|
class |
SystemOutLoggingTool
Implementation of the
ILoggingTool interface that sends output to
the System .out channel. |
Modifier and Type | Class and Description |
---|---|
class |
AtomContainerDiff
Compares two
IAtomContainer classes. |
class |
AtomDiff
Compares two
IAtom classes. |
class |
AtomTypeDiff
Compares two
IAtomType classes. |
class |
BondDiff
Compares two
IBond classes. |
class |
ChemObjectDiff
Compares two
IChemObject classes. |
class |
ElectronContainerDiff
Compares two
IChemObject classes. |
class |
ElementDiff
Compares two
IElement classes. |
class |
IsotopeDiff
Compares two
IIsotope classes. |
class |
LonePairDiff
Compares two
ILonePair classes. |
class |
SingleElectronDiff
Compares two
ISingleElectron classes. |
Modifier and Type | Class and Description |
---|---|
class |
AbstractDifference
Difference between two IChemObjects.
|
class |
AbstractDifferenceList
Diff between two IChemObjects.
|
class |
AtomTypeHybridizationDifference
IDifference between two IAtomType.Hybridization s. |
class |
BondOrderDifference
IDifference between two IBond.Order s. |
class |
BooleanArrayDifference
Difference between two boolean[]'s.
|
class |
BooleanDifference
IDifference between two Boolean s. |
class |
ChemObjectDifference
IDifference between two IChemObject s. |
class |
DoubleDifference
IDifference between two Double . |
class |
IntegerDifference
IDifference between two Integer . |
class |
Point2dDifference
Difference between two boolean[]'s.
|
class |
Point3dDifference
Difference between two boolean[]'s.
|
class |
StringDifference
IDifference between two String . |
Modifier and Type | Class and Description |
---|---|
class |
AminoAcidManipulator
Class with convenience methods that provide methods to manipulate
AminoAcid's.
|
class |
AtomContainerComparator
Compares two IAtomContainers for order with the following criteria with decreasing priority:
|
class |
AtomContainerManipulator
Class with convenience methods that provide methods to manipulate
AtomContainer's.
|
class |
AtomContainerSetManipulator |
class |
AtomTypeManipulator
Class with utilities for the
AtomType class. |
class |
BondManipulator
Class with convenience methods that provide methods to manipulate
AtomContainer's.
|
class |
ChemFileManipulator
Class with convenience methods that provide methods from
methods from ChemObjects within the ChemFile.
|
class |
ChemModelManipulator
Class with convenience methods that provide methods from
methods from ChemObjects within the ChemModel.
|
class |
ChemSequenceManipulator
Class with convenience methods that provide methods from
methods from ChemObjects within the ChemSequence.
|
class |
MolecularFormulaManipulator
Class with convenience methods that provide methods to manipulate
IMolecularFormula 's. |
class |
MolecularFormulaRangeManipulator
Class with convenience methods that provide methods to manipulate
MolecularFormulaRange's.
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class |
MolecularFormulaSetManipulator
Class with convenience methods that provide methods to manipulate
MolecularFormulaSet's.
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class |
MoleculeSetManipulator |
class |
ReactionManipulator |
class |
ReactionSchemeManipulator |
class |
ReactionSetManipulator |
class |
RingManipulator |
class |
RingSetManipulator |
class |
RingSizeComparator |
Modifier and Type | Class and Description |
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class |
PeriodicTable
Represents elements of the Periodic Table.
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Modifier and Type | Class and Description |
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class |
ProblemMarker
Tool to mark IChemObject's as having a problem.
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