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.
|
class |
DynamicFactory
A factory class for constructing
ICDKObject and IChemObject
implementations. |
Modifier and Type | Class and Description |
---|---|
class |
Aromaticity
A configurable model to perceive aromatic systems.
|
class |
AromaticityCalculator
Deprecated.
use
Aromaticity |
class |
CDKHueckelAromaticityDetector
Deprecated.
use
Aromaticity with the ElectronDonation.cdk() model |
class |
DoubleBondAcceptingAromaticityDetector
Deprecated.
use
Aromaticity with the ElectronDonation.cdkAllowingExocyclic() model |
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
[Gasteiger, J. and Marsili, M., Iterative partial equalization of orbital elektronegativity - a rapid access to atomic charges, Tetrahedron, 1980, 36:3219-3288].
|
class |
GasteigerPEPEPartialCharges
The calculation of the Gasteiger (PEPE) partial charges is based on
[Saller, H., Quantitative Emperische Modelle fur Elektronische Effekte in Pi-Systemen und fur die Chemische Reaktivitat, 1985, Thecn. Univ. Munchen].
|
class |
InductivePartialCharges
The calculation of the inductive partial atomic charges and equalization of
effective electronegativities is based on [Cherkasov, A., Inductive Electronegativity Scale. Iterative Calculation of Inductive Partial Charges, J. Chem. Inf. Comput. Sci., 2003, 43:2039-2047].
|
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 [Kang, Y.K. and Jhon, M.S., Additivity of Atomic Static Polarizabilities and Dispersion Coefficients, Theoretica Chimica Acta, 1982, 61:41-48] and [Gasteiger, J. and Hutchings, M.G., Quantitative Models of Gas-Phase Proton Transfer Reactions Involving Alcohols, Ethers, and their Thio analogs. Correlation Analyses Based on Residual Electronegativity and Effective Polarizability, J. Amer. Chem. Soc., 1984, 106:6489-6495]
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 |
Isotopes
List of isotopes.
|
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.
|
class |
XMLIsotopeFactory
Used to store and return data of a particular isotope.
|
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 |
Dictionary
Dictionary with entries.
|
class |
DictionaryDatabase
Database of dictionaries listing entries with compounds, fragments
and entities.
|
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.
|
class |
Entry
Entry in a Dictionary.
|
class |
EntryReact
Entry in a Dictionary for reactions.
|
class |
OWLFile
Dictionary with entries build from an OWL file.
|
class |
OWLReact
Dictionary with entries build from an OWL React.
|
Modifier and Type | Class and Description |
---|---|
class |
CDKException
Exception that is thrown by CDK classes when some problem has occured.
|
class |
Intractable
Indicates a computation did not complete within some predefined bound.
|
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 |
BitSetFingerprint |
class |
CircularFingerprinter
Circular fingerprints: for generating fingerprints that are functionally equivalent to ECFP-2/4/6 and FCFP-2/4/6
fingerprints, which are partially described by Rogers et al.
|
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 |
IntArrayCountFingerprint |
class |
KlekotaRothFingerprinter
SMARTS based substructure fingerprint based on
|
class |
LingoFingerprinter
An implementation of the LINGO fingerprint [Vidal, D. and Thormann, M. and Pons, M., LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities, J. Chem. Inf. Model., 2005, 45:386-393].
|
class |
MACCSFingerprinter
This fingerprinter generates 166 bit MACCS keys.
|
class |
PubchemFingerprinter
Generates a Pubchem fingerprint for a molecule.
|
class |
RandomNumber
Generates pseudorandom numbers using the MersenneTwister method from commons-math.
|
class |
ShortestPathFingerprinter
Generates a fingerprint for a given
IAtomContainer . |
class |
ShortestPathWalker |
class |
SignatureFingerprinter
An implementation of a
AtomSignature -based fingerprint. |
class |
SimpleAtomCanonicalizer
This code returns a sorted set of atoms for a container according to its
symbol and hybridization states.
|
class |
SimpleAtomComparator
This code returns a sorted set of atoms for a container according to its
symbol and hybridization states.
|
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
Deprecated.
Please use MolecularFormulaGenerator
|
class |
MolecularFormula
Class defining a molecular formula object.
|
class |
MolecularFormulaChecker
Validate a molecular formula given in IMolecularformula object.
|
class |
MolecularFormulaGenerator
This class generates molecular formulas within given mass range and elemental
composition.
|
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 [Bemis, G.W. and Murcko, M.A.
, The properties of known drugs. 1. Molecular Frameworks , Journal of Medicinal Chemistry, 1996, 39:2887-2893].
|
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.
|
class |
GeometryTools
A set of static utility classes for geometric calculations and operations.
|
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 [Cahn, R.S. and Ingold, C. and Prelog, V., Specification of Molecular Chirality, Angew. Chem. Int. Ed., 1966, 5:385-415].
|
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 [Zhao, Yuan H. and Abraham, Michael H. and Zissimos, Andreas M., Fast Calculation of van der Waals Volume as a Sum of Atomic and Bond Contributions and Its Application to Drug Compounds, The Journal of Organic Chemistry, 2003, 68:7368-7373].
|
Modifier and Type | Class and Description |
---|---|
class |
AllCycles
Compute all simple cycles (rings) in a graph.
|
class |
AllPairsShortestPaths
Utility to determine the shortest paths between all pairs of atoms in a
molecule.
|
class |
AtomContainerAtomPermutor
An atom container atom permutor that uses ranking and unranking to calculate
the next permutation in the series.
|
class |
AtomContainerBondPermutor
This class allows the user to iterate through the set of all possible
permutations of the bond order in a given atom container.
|
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 |
ConnectedComponents
Compute the connected components of an adjacency list.
|
class |
ConnectivityChecker
Tool class for checking whether the (sub)structure in an
AtomContainer is connected.
|
class |
Cycles
A utility class for storing and computing the cycles of a chemical graph.
|
class |
EssentialCycles
Determine the uniquely defined essential cycles of a graph.
|
class |
GraphUtil
Collection of static utilities for manipulating adjacency list
representations stored as a int[][].
|
class |
Matching
A matching is an independent edge set of a graph.
|
class |
MinimalPathIterator
Iterates over all shortest paths between two vertices in an undirected, unweighted graph.
|
class |
MinimumCycleBasis
Compute the minimum cycle basis (MCB) of a 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 |
Permutor
General permutation generator, that uses orderly generation by ranking and
unranking.
|
class |
RelevantCycles
Compute the relevant cycles (CR) of a graph.
|
class |
ShortestPaths
Find and reconstruct the shortest paths from a given start atom to any other
connected atom.
|
class |
SpanningTree
Spanning tree of a molecule.
|
class |
TripletShortCycles
Compute the shortest cycles through each vertex triple.
|
Modifier and Type | Class and Description |
---|---|
class |
CanonicalLabeler
Deprecated.
this labeller uses slow data structures and has been replaced -
Canon |
class |
ConjugatedPiSystemsDetector |
class |
InChINumbersTools
Tool for calculating atom numbers using the InChI algorithm.
|
class |
MorganNumbersTools
Compute the extended connectivity values (Morgan Numbers) [Morgan, H.L., The Generation of a Unique Machine Description for Chemical
Structures - A Technique Developed at Chemical Abstracts Service., J.Chem.Doc., 1965, 5:107-113].
|
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.
|
class |
TopologicalMatrix
Calculator for a topological 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 |
AbstractDiscretePartitionRefiner
Refines vertex partitions until they are discrete, and therefore equivalent
to permutations.
|
class |
AtomDiscretePartitionRefiner
A tool for determining the automorphism group of the atoms in a molecule, or
for checking for a canonical form of a molecule.
|
class |
BondDiscretePartitionRefiner
A tool for determining the automorphism group of the atoms in a molecule, or
for checking for a canonical form of a molecule.
|
class |
BondEquitablePartitionRefiner
Refiner for atom containers, which refines partitions of the bonds to
equitable partitions.
|
class |
DisjointSetForest
Implementation of a union-find data structure, largely copied from
code due to Derrick Stolee.
|
class |
Partition
A partition of a set of integers, such as the discrete partition {{1}, {2},
{3}, {4}} or the unit partition {{1, 2, 3, 4}} or an intermediate like {{1,
2}, {3, 4}}.
|
class |
Permutation
A permutation with some associated methods to multiply, invert, and convert
to cycle strings.
|
class |
PermutationGroup
A permutation group with a Schreier-Sims representation.
|
Modifier and Type | Class and Description |
---|---|
class |
BasicAtomEncoder
Enumeration of atom encoders for seeding atomic hash codes.
|
class |
HashGeneratorMaker
Fluent API for creating hash generators.
|
Modifier and Type | Class and Description |
---|---|
class |
DoubleBondElementEncoderFactory
Defines a stereo encoder factory for the hash code.
|
class |
GeometricCumulativeDoubleBondFactory
Stereo encoder factory for 2D and 3D cumulative double bonds.
|
class |
GeometricDoubleBondEncoderFactory
A stereo encoder factory encoding double bond configurations by 2D and 3D
coordinates.
|
class |
GeometricTetrahedralEncoderFactory
A stereo encoder factory for tetrahedral centres.
|
class |
TetrahedralElementEncoderFactory
Defines a stereo encoder factory for the hash code.
|
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
IAtomContainerSet or a IAtomContainer 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 [Dalby, A. and Nourse, J. G. and Hounshell, W. D. and
Gushurst, A. K. and Grier, D. L. and Leland, B. A. and
Laufer, J., Description of Several Chemical Structure File Formats Used by
Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255].
|
class |
MDLRXNReader
Reads a molecule from an MDL RXN file [Dalby, A. and Nourse, J. G. and Hounshell, W. D. and
Gushurst, A. K. and Grier, D. L. and Leland, B. A. and
Laufer, J., Description of Several Chemical Structure File Formats Used by
Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255].
|
class |
MDLRXNV2000Reader
Reads a molecule from an MDL RXN file [Dalby, A. and Nourse, J. G. and Hounshell, W. D. and
Gushurst, A. K. and Grier, D. L. and Leland, B. A. and
Laufer, J., Description of Several Chemical Structure File Formats Used by
Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255].
|
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 [Dalby, A. and Nourse, J. G. and Hounshell, W. D. and
Gushurst, A. K. and Grier, D. L. and Leland, B. A. and
Laufer, J., Description of Several Chemical Structure File Formats Used by
Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255]).
|
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 |
Mopac7Reader
Reads MOPAC output, extracts several electronic parameters and assigns them as a molecule
properties.
|
class |
MoSSOutputReader
Reader for MoSS output files [Unknown BibTeXML type: BOR2002] 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 ([Dalby, A. and Nourse, J. G. and Hounshell, W. D. and
Gushurst, A. K. and Grier, D. L. and Leland, B. A. and
Laufer, J., Description of Several Chemical Structure File Formats Used by
Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255]).
|
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 |
CMLModuleStack
Low weight 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 |
IteratingSDFReader
Iterating MDL SDF reader.
|
class |
IteratingSMILESReader
Iterating SMILES file reader.
|
Modifier and Type | Class and Description |
---|---|
class |
GaussianInputWriter
File writer thats generates input files for Gaussian calculation
jobs.
|
class |
Mopac7Writer
Prepares input file for running MOPAC.
|
Modifier and Type | Class and Description |
---|---|
class |
CDKOWLReader
Reads content from a CDK OWL serialization.
|
Modifier and Type | Class and Description |
---|---|
class |
AtomMatcher
Defines compatibility checking of atoms for (subgraph)-isomorphism mapping.
|
class |
BondMatcher
Defines compatibility checking of bonds for (subgraph)-isomorphism mapping.
|
class |
ComponentGrouping
A predicate for verifying component level grouping in query/target structure
matching.
|
class |
IsomorphismTester
A too simplistic implementation of an isomorphism test for chemical graphs.
|
class |
Mappings
A fluent interface for handling (sub)-graph mappings from a query to a target
structure.
|
class |
SmartsStereoMatch
Filters SMARTS matches for those that have valid stereochemistry
configuration.
|
class |
Ullmann
A structure pattern which utilises the Ullmann algorithm [Ullmann J R, An Algorithm for Subgraph Isomorphism, Journal of the Association for Computing Machinery, 1976, 23:?-?].
|
class |
VentoFoggia
A structure pattern which utilises the Vento-Foggia (VF) algorithm [Cordella Luigi P and Foggia Pasquale and Carlo Sansone and Vento Mario , A (Sub)Graph Isomorphism Algorithm for Matching Large Graphs, IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, 2004, 26:10].
|
Modifier and Type | Class and Description |
---|---|
class |
ExplicitConnectionAtom
Match an atom with the defined degree.
|
class |
RingMembershipAtom
This query is found in a specified number of ring.
|
class |
SmallestRingAtom
Match an atom in a specific size ring.
|
class |
TotalConnectionAtom
This matches an atom using total number of connections - referred to in
SMARTS as the connectivity.
|
class |
TotalRingConnectionAtom
This matcher checks the number of ring connections of the checked Atom with
other Atom's.
|
class |
TotalValencyAtom
This matcher checks the valence of the Atom.
|
Modifier and Type | Class and Description |
---|---|
class |
AtomPlacer
Methods for generating coordinates for atoms in various situations.
|
class |
HydrogenPlacer
This is a wrapper class for some existing methods in AtomPlacer.
|
class |
TemplateHandler
Helper class for Structure Diagram Generation.
|
Modifier and Type | Class and Description |
---|---|
class |
PDBAtomCustomizer
|
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
Deprecated.
|
class |
RandomNumbersTool
Class supplying useful methods to generate random numbers.
|
Modifier and Type | Class and Description |
---|---|
class |
AtomPlacer3D
Place aliphatic chains with Z matrix method.
|
class |
ForceFieldConfigurator
Reads in a force field configuration file, set the atom types into a vector, and the data into a hashtable
Therefore, it uses the class
MM2BasedParameterSetReader . |
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 [Aires-de-Sousa, J. and Hemmer, M.C. and Gasteiger, J., Prediction of 1H NMR Chemical Shifts Using Neural Networks, J. Chem. Inf. Mod., 2002, 74:80-90].
|
class |
RDFProtonDescriptor_GDR
This class calculates GDR proton descriptors used in neural networks for H1 NMR
shift [Aires-de-Sousa, J. and Hemmer, M.C. and Gasteiger, J., Prediction of 1H NMR Chemical Shifts Using Neural Networks, J. Chem. Inf. Mod., 2002, 74:80-90].
|
class |
RDFProtonDescriptor_GHR
This class calculates GHR proton descriptors used in neural networks for H1 NMR
shift [Aires-de-Sousa, J. and Hemmer, M.C. and Gasteiger, J., Prediction of 1H NMR Chemical Shifts Using Neural Networks, J. Chem. Inf. Mod., 2002, 74:80-90].
|
class |
RDFProtonDescriptor_GHR_topol
This class calculates GHR topological proton descriptors used in neural networks for H1 NMR
shift [Aires-de-Sousa, J. and Hemmer, M.C. and Gasteiger, J., Prediction of 1H NMR Chemical Shifts Using Neural Networks, J. Chem. Inf. Mod., 2002, 74:80-90].
|
class |
RDFProtonDescriptor_GSR
This class calculates GDR proton descriptors used in neural networks for H1 NMR
shift [Aires-de-Sousa, J. and Hemmer, M.C. and Gasteiger, J., Prediction of 1H NMR Chemical Shifts Using Neural Networks, J. Chem. Inf. Mod., 2002, 74:80-90].
|
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 [Ghose, A.K. and Crippen, G.M.
, Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships. I. Partition coefficients as a measure of hydrophobicity, Journal of Computational Chemistry, 1986, 7:565-577, Ghose, A.K. and Crippen, G.M.
, Atomic physicochemical parameters for three-dimensional-structure-directed quantitative structure-activity relationships. 2. Modeling dispersive and hydrophobic interactions, Journal of Chemical Information and Computer Science, 1987, 27:21-35].
|
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., The autocorrelation of a topological structure: A new molecular descriptor, Nouveau Journal de Chimie, 1980, ?:359-360].
|
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 |
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
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 [Liu, S. and Cao, C. and Li, Z.
, Approach to Estimation and Prediction for Normal
Boiling Point (NBP) of Alkanes Based on a Novel Molecular
Distance Edge (MDE) Vector, lambda, Journal of Chemical Information and Computer Sciences, 1998, 38:387-394].
|
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.
, Applications of the radius-diameter diagram to the classification of topological and geometrical shapes of chemical compounds, Journal of Chemical Information and Computer Science, 1992, 32:331-337])
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 |
TPSADescriptor
Calculation of topological polar surface area based on fragment
contributions (TPSA) [Ertl, P. and Rohde, B. and Selzer, P., Fast Calculation of Molecular Polar Surface Area as a Sum of
Fragment-Based Contributions and Its Application to the Prediction of
Drug Transport Properties, J. Med. Chem., 2000, 43:3714-3717].
|
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., New 3D Molecular Descriptors: The WHIM theory and QAR Applications, Persepectives in Drug Discovery and Design, 1998, ?:355-380].
|
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,
IAtomContainerSet, 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 [Bernstein, H.J., Manual RasMol 2.7.2.1 - CPK Colours].
|
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 |
Bounds
Defines a bound box element which the renderer can use to determine the true
drawing limits.
|
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
Compute the set of all rings in a molecule.
|
class |
Queue
Implementation of a Queue (FIFO stack).
|
class |
RingPartitioner
Partitions a RingSet into RingSets of connected rings.
|
class |
RingSearch
Efficiently search for atoms that are members of a ring.
|
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 [Faulon, J. L., Visco, D. P., and Pophale, R. S., The signature molecular descriptor. 1. Using extended
valence sequences in QSAR and QSPR studies., Journal of Chemical Information and Computer
Sciences, 2003, 43:707-720, Faulon, J. L., Collins, M. J., and Carr, R. D., The Signature Molecular Descriptor. 4. Canonizing Molecules
Using Extended Valence Sequences, Journal of Chemical Information and Computer
Sciences, 2004, 44:427-436] 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 [Faulon, J. L., Collins, M. J., and Carr, R. D., The Signature Molecular Descriptor. 4. Canonizing Molecules
Using Extended Valence Sequences, Journal of Chemical Information and Computer
Sciences, 2004, 44:427-436] 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 |
LingoSimilarity
A class to evaluate the similarity between two LINGO's as described in [Vidal, D. and Thormann, M. and Pons, M., LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities, J. Chem. Inf. Model., 2005, 45:386-393].
|
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
Generate a SMILES [Weininger, David, SMILES, a Chemical Language and Information System. 1.
Introduction to Methodology and Encoding Rules, Journal of Chemical Information and Computer
Sciences, 1988, 28:31-36, Weininger, David and Weininger, Arthur and Weininger, Joseph
L., SMILES 2. Algorithm for Generation of Unique SMILES
Notation, Journal of Chemical Information and Computer
Sciences, 1989, 29:97-101] string for a provided structure.
|
class |
SmilesParser
Read molecules and reactions from a SMILES [?Authors?, SMILES Tutorial] string.
|
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 |
AtomTypeAwareSaturationChecker
This class tries to figure out the bond order of the bonds that has the flag
SINGLE_OR_DOUBLE raised (i.e. |
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 [Bremser, W., HOSE - A Novel Substructure Code, Analytica Chimica Acta, 1978, 103:355-365].
|
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.
|
class |
MolecularFormulaSetManipulator
Class with convenience methods that provide methods to manipulate
MolecularFormulaSet's.
|
class |
MoleculeSetManipulator |
class |
ReactionManipulator |
class |
ReactionSchemeManipulator |
class |
ReactionSetManipulator |
class |
RingManipulator |
class |
RingSetManipulator |
class |
RingSizeComparator |
Modifier and Type | Class and Description |
---|---|
class |
PeriodicTable
Represents elements of the Periodic Table.
|
Modifier and Type | Class and Description |
---|---|
class |
ProblemMarker
Tool to mark IChemObject's as having a problem.
|
Copyright © 2014. All Rights Reserved.