Uses of Interface
org.openscience.cdk.interfaces.ICDKObject
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Uses of ICDKObject in org.openscience.cdk
Classes in org.openscience.cdk that implement ICDKObject Modifier and Type Class 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
AtomRef
An atom ref, references a CDKIAtom
indirectly.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
BondRef
A bond ref, references a CDKIBond
indirectly.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 theISubstance
interface.Methods in org.openscience.cdk with type parameters of type ICDKObject Modifier and Type Method Description <T extends ICDKObject>
Set<Class<?>>DynamicFactory. implementorsOf(Class<T> intf)
Access the registered implementations for a given interface.<T extends ICDKObject>
TDefaultChemObjectBuilder. newInstance(Class<T> clazz, Object... params)
Creates a new instance of anICDKObject
, using the constructor defined by the given parameters.<T extends ICDKObject>
TDynamicFactory. ofClass(Class<T> intf)
Construct an implementation using the default constructor.<T extends ICDKObject>
TDynamicFactory. ofClass(Class<T> intf, Object... objects)
Construct an implementation using a constructor whose parameters match that of the provided objects.<T extends ICDKObject>
booleanDynamicFactory. register(Class<? extends T> impl)
Registers a class with the factory.<S extends ICDKObject,T extends S>
booleanDynamicFactory. 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>
booleanDynamicFactory. register(Class<S> intf, Constructor<T> constructor)
Register a specific constructor with an explicit interface.<S extends ICDKObject,T extends S>
booleanDynamicFactory. 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>
booleanDynamicFactory. register(Class<T> intf, Class<? extends T> impl)
Explicitly register a concrete class with a provided interface. -
Uses of ICDKObject in org.openscience.cdk.debug
Classes in org.openscience.cdk.debug that implement ICDKObject Modifier and Type Class Description class
DebugAdductFormula
Debugging implementation ofIAdductFormula
.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 ofIMolecularFormula
.class
DebugMolecularFormulaSet
Debugging implementation ofIMolecularFormulaSet
.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.Methods in org.openscience.cdk.debug with type parameters of type ICDKObject Modifier and Type Method Description <T extends ICDKObject>
TDebugChemObjectBuilder. newInstance(Class<T> clazz, Object... params)
Creates a new instance of anICDKObject
, using the constructor defined by the given parameters. -
Uses of ICDKObject in org.openscience.cdk.formula
Classes in org.openscience.cdk.formula that implement ICDKObject Modifier and Type Class 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. -
Uses of ICDKObject in org.openscience.cdk.interfaces
Subinterfaces of ICDKObject in org.openscience.cdk.interfaces Modifier and Type Interface 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
AnIChemObject
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<F extends IChemObject,C extends IChemObject>
Representation of stereochemical configuration.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.Methods in org.openscience.cdk.interfaces with type parameters of type ICDKObject Modifier and Type Method Description <T extends ICDKObject>
TIChemObjectBuilder. newInstance(Class<T> clazz, Object... params)
Creates a new instance of anICDKObject
, using the constructor defined by the given parameters. -
Uses of ICDKObject in org.openscience.cdk.isomorphism.matchers
Subinterfaces of ICDKObject in org.openscience.cdk.isomorphism.matchers Modifier and Type Interface Description interface
IQueryAtom
Defines the ability to be matched againstIAtom
'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.Classes in org.openscience.cdk.isomorphism.matchers that implement ICDKObject Modifier and Type Class Description class
CTFileQueryBond
Deprecated.UseExpr.Type.SINGLE_OR_AROMATIC
etc.class
InverseSymbolSetQueryAtom
Deprecated.class
OrderQueryBond
Deprecated.class
OrderQueryBondOrderOnly
Deprecated.Usenew QueryBond(beg, end, ORDER, bord)
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
Deprecated.class
SymbolChargeIDQueryAtom
class
SymbolQueryAtom
Deprecated.class
SymbolSetQueryAtom
Deprecated.Usenew Expr(Element, 6).and(new Expr(Element, 8))
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Uses of ICDKObject in org.openscience.cdk.isomorphism.matchers.smarts
Classes in org.openscience.cdk.isomorphism.matchers.smarts that implement ICDKObject Modifier and Type Class Description class
AliphaticAtom
Deprecated.class
AliphaticSymbolAtom
Deprecated.class
AnyAtom
Deprecated.class
AnyOrderQueryBond
Deprecated.class
AromaticAtom
Deprecated.class
AromaticOrSingleQueryBond
Deprecated.class
AromaticQueryBond
Deprecated.class
AromaticSymbolAtom
Deprecated.class
AtomicNumberAtom
Deprecated.class
ChiralityAtom
Deprecated.class
ExplicitConnectionAtom
Deprecated.class
FormalChargeAtom
Deprecated.class
HybridizationNumberAtom
Deprecated.class
HydrogenAtom
Deprecated.class
ImplicitHCountAtom
Deprecated.class
LogicalOperatorAtom
Deprecated.class
LogicalOperatorBond
Deprecated.class
MassAtom
Deprecated.class
NonCHHeavyAtom
Deprecated.class
OrderQueryBond
Deprecated.class
PeriodicGroupNumberAtom
Deprecated.class
ReactionRoleQueryAtom
Deprecated.class
RecursiveSmartsAtom
Deprecated.class
RingBond
Deprecated.class
RingIdentifierAtom
Deprecated.class
RingMembershipAtom
Deprecated.class
SmallestRingAtom
Deprecated.class
SMARTSAtom
Deprecated.class
SMARTSBond
Deprecated.class
StereoBond
Deprecated.class
TotalConnectionAtom
Deprecated.class
TotalHCountAtom
Deprecated.class
TotalRingConnectionAtom
Deprecated.class
TotalValencyAtom
Deprecated. -
Uses of ICDKObject in org.openscience.cdk.libio.md
Classes in org.openscience.cdk.libio.md that implement ICDKObject Modifier and Type Class 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. -
Uses of ICDKObject in org.openscience.cdk.pharmacophore
Classes in org.openscience.cdk.pharmacophore that implement ICDKObject Modifier and Type Class 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. -
Uses of ICDKObject in org.openscience.cdk.protein.data
Classes in org.openscience.cdk.protein.data that implement ICDKObject Modifier and Type Class 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. -
Uses of ICDKObject in org.openscience.cdk.reaction
Classes in org.openscience.cdk.reaction that implement ICDKObject Modifier and Type Class Description class
ReactionChain
Classes that extends the definition of reaction to a chain reaction. -
Uses of ICDKObject in org.openscience.cdk.silent
Classes in org.openscience.cdk.silent that implement ICDKObject Modifier and Type Class Description class
AdductFormula
Class defining an adduct object in a MolecularFormula.class
AminoAcid
A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.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
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
MolecularFormula
Class defining a molecular formula object.class
MolecularFormulaSet
Class defining an set object of MolecularFormulas.class
Monomer
A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.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
PDBStructure
Holder for secundary protein structure elements.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 theISubstance
interface.Methods in org.openscience.cdk.silent with type parameters of type ICDKObject Modifier and Type Method Description <T extends ICDKObject>
TSilentChemObjectBuilder. newInstance(Class<T> clazz, Object... params)
Creates a new instance of anICDKObject
, using the constructor defined by the given parameters. -
Uses of ICDKObject in org.openscience.cdk.stereo
Classes in org.openscience.cdk.stereo that implement ICDKObject Modifier and Type Class Description class
Atropisomeric
Restricted axial rotation around Aryl-Aryl bonds.class
DoubleBondStereochemistry
Stereochemistry specification for double bonds.class
ExtendedCisTrans
Extended Cis/Trans double bond configuration.class
ExtendedTetrahedral
Extended tetrahedral configuration.class
Octahedral
Represents an octahedral configuration of an atom six neighbors.class
SquarePlanar
Describes square planar configuration.class
TetrahedralChirality
Stereochemistry specification for tetravalent atoms.class
TrigonalBipyramidal
Describes a trigonal-bipyramidal configuration.
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