Package org.openscience.cdk.silent

Class Summary

Class	Description
AdductFormula	Class defining an adduct object in a MolecularFormula.
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.
MolecularFormula	Class defining a molecular formula object.
MolecularFormulaSet	Class defining an set object of MolecularFormulas.
Monomer	A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.
PDBAtom	Represents the idea of an atom as used in PDB files.
PDBMonomer	Represents the idea of an monomer as used in PDB files.
PDBPolymer	An entry in the PDB database.
PDBStructure	Holder for secundary protein structure elements.
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.
SilentChemObjectBuilder	A factory class to provide implementation independent ICDKObjects.
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.