Uses of Package
org.openscience.cdk

Packages that use org.openscience.cdk

Package	Description
org.openscience.cdk
org.openscience.cdk.debug
org.openscience.cdk.libio.md
org.openscience.cdk.pharmacophore
org.openscience.cdk.protein.data
org.openscience.cdk.qsar
org.openscience.cdk.reaction
org.openscience.cdk.templates

Classes in org.openscience.cdk used by org.openscience.cdk

Class and Description
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.
ChemObject The base class for all chemical objects in this cdk.
DynamicFactory.ConstructorKey A class which encapsulates the information about an interface (of this implementation) and the parameter types of the constructor.
DynamicFactory.CreationModifier An interface that allows posterior modification of an instance after it has been created.
DynamicFactory.Creator 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.
ElectronContainer Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
Element Implements the idea of an element in the periodic table.
Isotope Used to store and retrieve data of a particular isotope.
Monomer A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.
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.
ReactionRole
ReactionSet A set of reactions, for example those taking part in a reaction.

Classes in org.openscience.cdk used by org.openscience.cdk.debug

Class and Description
AminoAcid A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.
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.
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.
Crystal Class representing a molecular crystal.
ElectronContainer Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
Element Implements the idea of an element in the periodic table.
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.
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.

Classes in org.openscience.cdk used by org.openscience.cdk.libio.md

Class and Description
AtomContainer Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
ChemObject The base class for all chemical objects in this cdk.

Classes in org.openscience.cdk used by org.openscience.cdk.pharmacophore

Class and Description
Atom Represents the idea of an chemical atom.
AtomType The base class for atom types.
Bond Implements the concept of a covalent bond between two or more atoms.
ChemObject The base class for all chemical objects in this cdk.
ElectronContainer Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
Element Implements the idea of an element in the periodic table.
Isotope Used to store and retrieve data of a particular isotope.

Classes in org.openscience.cdk used by org.openscience.cdk.protein.data

Class and Description
Atom Represents the idea of an chemical atom.
AtomContainer Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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.
ChemObject The base class for all chemical objects in this cdk.
Element Implements the idea of an element in the periodic table.
Isotope Used to store and retrieve data of a particular isotope.
Monomer A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.
Polymer Subclass of Molecule to store Polymer specific attributes that a Polymer has.
Strand A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.

Classes in org.openscience.cdk used by org.openscience.cdk.qsar

Class and Description
IImplementationSpecification Interface that is used to describe the specification of a certain implementation of an algorithm.

Classes in org.openscience.cdk used by org.openscience.cdk.reaction

Class and Description
ChemObject The base class for all chemical objects in this cdk.
IImplementationSpecification Interface that is used to describe the specification of a certain implementation of an algorithm.
ReactionSet A set of reactions, for example those taking part in a reaction.

Classes in org.openscience.cdk used by org.openscience.cdk.templates

Class and Description
AminoAcid A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.