|
Class Summary |
| 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. |
| AtomParity |
Represents the concept of an atom parity identifying the stereochemistry
around an atom, given four neighbouring atoms. |
| 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 helper class to instantiate a ICDKObject for the original CDK
implementation. |
| 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. |
| Vibration |
A molecular vibration composed of a set of atom vectors. |