Package org.openscience.cdk

Interface Summary

Interface	Description
DynamicFactory.CreationModifier<T>	An interface that allows posterior modification of an instance after it has been created.
DynamicFactory.Creator<T>	An interface that wraps object creation via the DynamicFactory.Creator.create(Object[]) method.
DynamicFactory.InterfaceProvider	An interface that can provide which interfaces the given class implements.
IImplementationSpecification	Interface that is used to describe the specification of a certain implementation of an algorithm.

Class Summary

Class	Description
AminoAcid	A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.
Association	Base class for storing interactions like hydrogen bonds and ionic interactions.
Atom	Represents the idea of an chemical atom.
AtomContainer	Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
AtomContainerSet	A set of AtomContainers.
AtomType	The base class for atom types.
BioPolymer	A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.
Bond	Implements the concept of a covalent bond between two or more atoms.
CDK	Helper class to provide general information about this CDK library.
CDKConstants	An interface providing predefined values for a number of constants used throughout the CDK.
ChemFile	A Object containing a number of ChemSequences.
ChemModel	An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.
ChemObject	The base class for all chemical objects in this cdk.
ChemSequence	A sequence of ChemModels, which can, for example, be used to store the course of a reaction.
ConformerContainer	A memory-efficient data structure to store conformers for a single molecule.
Crystal	Class representing a molecular crystal.
DefaultChemObjectBuilder	A factory class to provide implementation independent ICDKObjects.
DynamicFactory	A factory class for constructing ICDKObject and IChemObject implementations.
DynamicFactory.BasicCreator<T>	A simple creator that helps in creating an anonymous classes for a creator.
DynamicFactory.ConstructorKey	A class which encapsulates the information about an interface (of this implementation) and the parameter types of the constructor.
DynamicFactory.DefaultInterfaceProvider	A default interface provider implementation that simply returns the classes from Class.getInterfaces().
ElectronContainer	Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
Element	Implements the idea of an element in the periodic table.
EnzymeResidueLocator	Atom that represents part of an residue in an enzyme, like Arg255.
FragmentAtom	Class to represent an IPseudoAtom which embeds an IAtomContainer.
Isotope	Used to store and retrieve data of a particular isotope.
LonePair	A LonePair is an orbital primarily located with one Atom, containing two electrons.
Mapping	A Mapping is an relation between two ChemObjects in a non-chemical entity.
Monomer	A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.
PhysicalConstants	An class providing predefined properties of physical constants.
Polymer	Subclass of Molecule to store Polymer specific attributes that a Polymer has.
PseudoAtom	Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.
Reaction	Represents the idea of a chemical reaction.
ReactionScheme	Classes that extends the definition of reaction to a scheme.
ReactionSet	A set of reactions, for example those taking part in a reaction.
Ring	Class representing a ring structure in a molecule.
RingSet	Maintains a set of Ring objects.
SingleElectron	A Single Electron is an orbital which is occupied by only one electron.
Strand	A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.
Substance	An implementation of the ISubstance interface.
Vibration	A molecular vibration composed of a set of atom vectors.

Enum Summary

Enum	Description
ReactionRole