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
ICDKObject s. |
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. |
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