Modifier and Type | Class and Description |
---|---|
class |
AminoAcid
A AminoAcid is Monomer which stores additional amino acid specific
informations, like the N-terminus atom.
|
class |
Association
Base class for storing interactions like hydrogen bonds and ionic interactions.
|
class |
Atom
Represents the idea of an chemical atom.
|
class |
AtomContainer
Base class for all chemical objects that maintain a list of Atoms and
ElectronContainers.
|
class |
AtomContainerSet
A set of AtomContainers.
|
class |
AtomType
The base class for atom types.
|
class |
BioPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store
additional informations about the Polymer which are connected to BioPolymers.
|
class |
Bond
Implements the concept of a covalent bond between two or more atoms.
|
class |
ChemFile
A Object containing a number of ChemSequences.
|
class |
ChemModel
An object containing multiple MoleculeSet and
the other lower level concepts like rings, sequences,
fragments, etc.
|
class |
ChemObject
The base class for all chemical objects in this cdk.
|
class |
ChemSequence
A sequence of ChemModels, which can, for example, be used to
store the course of a reaction.
|
class |
Crystal
Class representing a molecular crystal.
|
class |
ElectronContainer
Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
|
class |
Element
Implements the idea of an element in the periodic table.
|
class |
EnzymeResidueLocator
Atom that represents part of an residue in an enzyme, like Arg255.
|
class |
FragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.
|
class |
Isotope
Used to store and retrieve data of a particular isotope.
|
class |
LonePair
A LonePair is an orbital primarily located with one Atom, containing
two electrons.
|
class |
Mapping
A Mapping is an relation between two ChemObjects in a non-chemical
entity.
|
class |
Monomer
A Monomer is an AtomContainer which stores additional monomer specific
informations for a group of Atoms.
|
class |
Polymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
|
class |
PseudoAtom
Represents the idea of a non-chemical atom-like entity, like Me,
R, X, Phe, His, etc.
|
class |
Reaction
Represents the idea of a chemical reaction.
|
class |
ReactionScheme
Classes that extends the definition of reaction to a scheme.
|
class |
ReactionSet
A set of reactions, for example those taking part in a reaction.
|
class |
Ring
Class representing a ring structure in a molecule.
|
class |
RingSet
Maintains a set of Ring objects.
|
class |
SingleElectron
A Single Electron is an orbital which is occupied by only one electron.
|
class |
Strand
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
|
class |
Substance
An implementation of the
ISubstance interface. |
Modifier and Type | Method and Description |
---|---|
<T extends ICDKObject> |
DynamicFactory.implementorsOf(Class<T> intf)
Access the registered implementations for a given interface.
|
<T extends ICDKObject> |
DefaultChemObjectBuilder.newInstance(Class<T> clazz,
Object... params)
Creates a new instance of an
ICDKObject , using the constructor defined by the
given parameters. |
<T extends ICDKObject> |
DynamicFactory.ofClass(Class<T> intf)
Construct an implementation using the default constructor.
|
<T extends ICDKObject> |
DynamicFactory.ofClass(Class<T> intf,
Object... objects)
Construct an implementation using a constructor whose parameters match
that of the provided objects.
|
<T extends ICDKObject> |
DynamicFactory.register(Class<? extends T> impl)
Registers a class with the factory.
|
<S extends ICDKObject,T extends S> |
DynamicFactory.register(Class<S> intf,
Class<T> impl,
DynamicFactory.CreationModifier<T> modifier)
Explicitly register a concrete class with a provided interface and a
given modifier.
|
<S extends ICDKObject,T extends S> |
DynamicFactory.register(Class<S> intf,
Constructor<T> constructor)
Register a specific constructor with an explicit interface.
|
<S extends ICDKObject,T extends S> |
DynamicFactory.register(Class<S> intf,
Constructor<T> constructor,
DynamicFactory.CreationModifier<T> modifier)
Register a specific constructor with a creation modifier to an explicit
interface.
|
<T extends ICDKObject> |
DynamicFactory.register(Class<T> intf,
Class<? extends T> impl)
Explicitly register a concrete class with a provided interface.
|
Modifier and Type | Class and Description |
---|---|
class |
DebugAdductFormula
Debugging implementation of
IAdductFormula . |
class |
DebugAminoAcid
Debugging data class.
|
class |
DebugAtom
Debugging data class.
|
class |
DebugAtomContainer
Debugging data class.
|
class |
DebugAtomContainerSet
Debugging data class.
|
class |
DebugAtomType
Debugging data class.
|
class |
DebugBioPolymer
Debugging data class.
|
class |
DebugBond
Debugging data class.
|
class |
DebugChemFile
Debugging data class.
|
class |
DebugChemModel
Debugging data class.
|
class |
DebugChemObject
Debugging data class.
|
class |
DebugChemSequence
Debugging data class.
|
class |
DebugCrystal
Debugging data class.
|
class |
DebugElectronContainer
Debugging data class.
|
class |
DebugElement
Debugging data class.
|
class |
DebugFragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.
|
class |
DebugIsotope
Debugging data class.
|
class |
DebugLonePair
Debugging data class.
|
class |
DebugMapping
Debugging data class.
|
class |
DebugMolecularFormula
Debugging implementation of
IMolecularFormula . |
class |
DebugMolecularFormulaSet
Debugging implementation of
IMolecularFormulaSet . |
class |
DebugMonomer
Debugging data class.
|
class |
DebugPDBAtom
Debugging data class.
|
class |
DebugPDBMonomer
Debugging data class.
|
class |
DebugPDBPolymer
Debugging data class.
|
class |
DebugPDBStructure
Debugging data class.
|
class |
DebugPolymer
Debugging data class.
|
class |
DebugPseudoAtom
Debugging data class.
|
class |
DebugReaction
Debugging data class.
|
class |
DebugReactionScheme
Debugging data class.
|
class |
DebugReactionSet
Debugging data class.
|
class |
DebugRing
Debugging data class.
|
class |
DebugRingSet
Debugging data class.
|
class |
DebugSingleElectron
Debugging data class.
|
class |
DebugStrand
Debugging data class.
|
class |
DebugSubstance
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
<T extends ICDKObject> |
DebugChemObjectBuilder.newInstance(Class<T> clazz,
Object... params)
Creates a new instance of an
ICDKObject , using the constructor defined by the
given parameters. |
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 | Interface and Description |
---|---|
interface |
IAdductFormula
Class defining an adduct object in a MolecularFormula.
|
interface |
IAminoAcid
A AminoAcid is Monomer which stores additional amino acid specific
informations, like the N-terminus atom.
|
interface |
IAtom
Represents the idea of an chemical atom.
|
interface |
IAtomContainer
Base class for all chemical objects that maintain a list of Atoms and
ElectronContainers.
|
interface |
IAtomContainerSet
A set of AtomContainers.
|
interface |
IAtomType
The base class for atom types.
|
interface |
IBioPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store
additional informations about the Polymer which are connected to BioPolymers.
|
interface |
IBond
Implements the concept of a covalent bond between two or more atoms.
|
interface |
IChemFile
An
IChemObject containing a number of ChemSequences. |
interface |
IChemModel
An object containing multiple MoleculeSet and
the other lower level concepts like rings, sequences,
fragments, etc.
|
interface |
IChemObject
The base class for all chemical objects in this cdk.
|
interface |
IChemSequence
A sequence of ChemModels, which can, for example, be used to
store the course of a reaction.
|
interface |
ICrystal
Class representing a molecular crystal.
|
interface |
IDoubleBondStereochemistry
Stereochemistry specification for double bond stereochemistry.
|
interface |
IElectronContainer
Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
|
interface |
IElement
Implements the idea of an element in the periodic table.
|
interface |
IFragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.
|
interface |
IIsotope
Used to store and retrieve data of a particular isotope.
|
interface |
ILonePair
A LonePair is an orbital primarily located with one Atom, containing
two electrons.
|
interface |
IMapping
Represents a mapping of two atoms.
|
interface |
IMolecularFormula
Class defining a molecular formula object.
|
interface |
IMolecularFormulaSet
Class defining a molecular formula object.
|
interface |
IMonomer
A Monomer is an AtomContainer which stores additional monomer specific
informations for a group of Atoms.
|
interface |
IPDBAtom
A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.
|
interface |
IPDBMonomer
Represents the idea of an protein monomer as found in PDB files.
|
interface |
IPDBPolymer
A PDBPolymer is a subclass of a BioPolymer which is supposed to store
additional informations about the BioPolymer which are connected to BioPolymers.
|
interface |
IPDBStructure
Represents the idea of an chemical structure.
|
interface |
IPolymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
|
interface |
IPseudoAtom
Represents the idea of a non-chemical atom-like entity, like Me,
R, X, Phe, His, etc.
|
interface |
IReaction
Represents the idea of a chemical reaction.
|
interface |
IReactionScheme
Classes that implement this interface of a scheme.
|
interface |
IReactionSet
A set of reactions, for example those taking part in a reaction.
|
interface |
IRing
Class representing a ring structure in a molecule.
|
interface |
IRingSet
Maintains a set of Ring objects.
|
interface |
ISingleElectron
A Single Electron is an orbital which is occupied by only one electron.
|
interface |
IStereoElement
Represents the concept of a stereo element in the molecule.
|
interface |
IStrand
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
|
interface |
ISubstance
A chemical substance that consists of one or more chemical structures.
|
interface |
ITetrahedralChirality
Stereochemistry specification for quadrivalent atoms.
|
Modifier and Type | Method and Description |
---|---|
<T extends ICDKObject> |
IChemObjectBuilder.newInstance(Class<T> clazz,
Object... params)
Creates a new instance of an
ICDKObject , using the constructor defined by the
given parameters. |
Modifier and Type | Interface and Description |
---|---|
interface |
IQueryAtom
Defines the ability to be matched against
IAtom 's. |
interface |
IQueryAtomContainer
General concept of a IAtomContainer aimed at doing molecular subgraph
queries using the UniversalIsomorphismTester.
|
interface |
IQueryBond
Defines the abililty to be matched against IBond's.
|
interface |
IRGroupQuery
Interface definition for Rgroup query classes.
|
Modifier and Type | Class and Description |
---|---|
class |
CTFileQueryBond
Captures query bond types defined in the CTFile.
|
class |
InverseSymbolSetQueryAtom
A QueryAtom that matches all symbols but those in this container.
|
class |
OrderQueryBond |
class |
OrderQueryBondOrderOnly
IQueryBond that matches IBond object only based on bond order, and
disregarding any aromaticity flag. |
class |
QueryAtom |
class |
QueryAtomContainer |
class |
QueryBond
Implements the concept of a "query bond" between two or more atoms.
|
class |
QueryChemObject |
class |
RGroupQuery
Represents information contained in a Symyx RGfile (R-group query file).
It contains a root structure (the scaffold if you like), a map with R-group definitions (each of which can contain multiple substitutes) and a map with attachment points. |
class |
SymbolAndChargeQueryAtom |
class |
SymbolChargeIDQueryAtom |
class |
SymbolQueryAtom |
class |
SymbolSetQueryAtom
A QueryAtom that matches all symbols in this container.
|
Modifier and Type | Class and Description |
---|---|
class |
AliphaticAtom
This matcher any non-aromatic atom.
|
class |
AliphaticSymbolAtom
This smarts atom matches aliphatic atom with element symbol specified.
|
class |
AnyAtom
This matcher any Atom including explicit hydrogens.
|
class |
AnyOrderQueryBond
This matches a bond of any order.
|
class |
AromaticAtom
This matcher any aromatic atom.
|
class |
AromaticOrSingleQueryBond
This matches an aromatic or a single bond, used when no bond is specified between an atom.
|
class |
AromaticQueryBond
This matches an aromatic bond.
|
class |
AromaticSymbolAtom
This class matches aromatic atom with element symbol specified.
|
class |
AtomicNumberAtom
This matches an atom using the atomic number.
|
class |
ChiralityAtom
This matches an atom with chirality property.
|
class |
ExplicitConnectionAtom
Match an atom with the defined degree.
|
class |
FormalChargeAtom
This matcher checks the formal charge of the Atom.
|
class |
HybridizationNumberAtom
This matcher checks the hybridization state of an atom.
|
class |
HydrogenAtom
This matches Hydrogen atoms.
|
class |
ImplicitHCountAtom
This matcher checks the number of implicit hydrogens of the Atom.
|
class |
LogicalOperatorAtom
This class matches a logical operator that connects two query atoms.
|
class |
LogicalOperatorBond
This class matches a logical operator that connects two query bonds.
|
class |
MassAtom
This class matches an atom based on the atomic mass.
|
class |
NonCHHeavyAtom
This matcher any heavy atom that is not C or H.
|
class |
PeriodicGroupNumberAtom
This matcher checks the periodic group number of an atom.
|
class |
ReactionRoleQueryAtom
Matches atoms with a particular role in a reaction.
|
class |
RecursiveSmartsAtom
This matches recursive smarts atoms.
|
class |
RingBond
This smarts bond matches any bond that is in a ring.
|
class |
RingIdentifierAtom
This encapsulates an atom with a ring identifier, with an optional ring
bond specified.
|
class |
RingMembershipAtom
This query is found in a specified number of ring.
|
class |
SmallestRingAtom
Match an atom in a specific size ring.
|
class |
SMARTSAtom
Abstract smarts atom.
|
class |
SMARTSBond
Abstract smarts bond.
|
class |
StereoBond
This query bond indicates a particular geometric stereo configuration.
|
class |
TotalConnectionAtom
This matches an atom using total number of connections - referred to in
SMARTS as the connectivity.
|
class |
TotalHCountAtom
SMARTS query atom for matching the total hydrogen count.
|
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 |
ChargeGroup
A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule.
|
class |
MDMolecule |
class |
Residue
A residue is a named, numbered collection of atoms in an MDMolecule.
|
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 |
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.
|
Modifier and Type | Class and Description |
---|---|
class |
PDBAtom
Represents the idea of an atom as used in PDB files.
|
class |
PDBMonomer
Represents the idea of an monomer as used in PDB files.
|
class |
PDBPolymer
An entry in the PDB database.
|
class |
PDBStrand
An entry in the PDB database.
|
class |
PDBStructure
Holder for secundary protein structure elements.
|
Modifier and Type | Class and Description |
---|---|
class |
ReactionChain
Classes that extends the definition of reaction to a chain reaction.
|
Modifier and Type | Method and Description |
---|---|
<T extends ICDKObject> |
SilentChemObjectBuilder.newInstance(Class<T> clazz,
Object... params)
Creates a new instance of an
ICDKObject , using the constructor defined by the
given parameters. |
Modifier and Type | Class and Description |
---|---|
class |
DoubleBondStereochemistry
Stereochemistry specification for double bonds.
|
class |
ExtendedTetrahedral
Extended tetrahedral configuration.
|
class |
TetrahedralChirality
Stereochemistry specification for quadrivalent atoms.
|
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