Package org.openscience.cdk.interfaces

Interface Summary

Interface	Description
IAdductFormula	Class defining an adduct object in a MolecularFormula.
IAminoAcid	A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.
IAtom	Represents the idea of an chemical atom.
IAtomContainer	Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
IAtomContainerSet	A set of AtomContainers.
IAtomType	The base class for atom types.
IBioPolymer	A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.
IBond	Implements the concept of a covalent bond between two or more atoms.
ICDKObject	The base class for all data objects in this CDK.
IChemFile	An IChemObject containing a number of ChemSequences.
IChemModel	An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.
IChemObject	The base class for all chemical objects in this cdk.
IChemObjectBuilder	A helper class to instantiate a ICDKObject instance for a specific implementation.
IChemObjectChangeEvent	Event fired by CDK IChemObject classes to their registered listeners in case something changed within them.
IChemObjectListener	Classes implementing this interface must implement this method such that they react appropriately to changes in the object they are interested in.
IChemSequence	A sequence of ChemModels, which can, for example, be used to store the course of a reaction.
ICrystal	Class representing a molecular crystal.
IDoubleBondStereochemistry	Stereochemistry specification for double bond stereochemistry.
IElectronContainer	Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
IElement	Implements the idea of an element in the periodic table.
IFragmentAtom	Class to represent an IPseudoAtom which embeds an IAtomContainer.
IIsotope	Used to store and retrieve data of a particular isotope.
ILonePair	A LonePair is an orbital primarily located with one Atom, containing two electrons.
IMapping	Represents a mapping of two atoms.
IMolecularFormula	Class defining a molecular formula object.
IMolecularFormulaSet	Class defining a molecular formula object.
IMonomer	A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.
IPDBAtom	A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.
IPDBMonomer	Represents the idea of an protein monomer as found in PDB files.
IPDBPolymer	A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.
IPDBStructure	Represents the idea of an chemical structure.
IPolymer	Subclass of Molecule to store Polymer specific attributes that a Polymer has.
IPseudoAtom	Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.
IReaction	Represents the idea of a chemical reaction.
IReactionScheme	Classes that implement this interface of a scheme.
IReactionSet	A set of reactions, for example those taking part in a reaction.
IRing	Class representing a ring structure in a molecule.
IRingSet	Maintains a set of Ring objects.
ISetting	A simple setting that can be managed by the SettingManager.
ISingleElectron	A Single Electron is an orbital which is occupied by only one electron.
IStereoElement<F extends IChemObject,C extends IChemObject>	Representation of stereochemical configuration.
IStrand	A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.
ISubstance	A chemical substance that consists of one or more chemical structures.
ITetrahedralChirality	Stereochemistry specification for quadrivalent atoms.

Enum Summary

Enum	Description
IAtomType.Hybridization	An enum for the different hybridization states.
IBond.Order	A list of permissible bond orders.
IBond.Stereo	Enumeration of possible stereo types of two-atom bonds.
IDoubleBondStereochemistry.Conformation	Enumeration that defines the two possible values for this stereochemistry type.
IReaction.Direction	Permissible reaction directions.
ITetrahedralChirality.Stereo	Enumeration that defines the two possible chiralities for this stereochemistry type.