| AminoAcid |
A AminoAcid is Monomer which stores additional amino acid specific
informations, like the N-terminus atom.
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| Association |
Base class for storing interactions like hydrogen bonds and ionic interactions.
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| Atom |
Represents the idea of an chemical atom.
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| AtomContainer |
This class should not be used directly.
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| AtomContainerLegacy |
Base class for all chemical objects that maintain a list of Atoms and
ElectronContainers.
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| AtomContainerSet |
A set of AtomContainers.
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| AtomRef |
An atom ref, references a CDK IAtom indirectly. |
| AtomType |
The base class for atom types.
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| BioPolymer |
A BioPolymer is a subclass of a Polymer which is supposed to store
additional informations about the Polymer which are connected to BioPolymers.
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| Bond |
Implements the concept of a covalent bond between two or more atoms.
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| BondRef |
A bond ref, references a CDK IBond indirectly. |
| CDK |
Helper class to provide general information about this CDK library.
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| CDKConstants |
An interface providing predefined values for a number of
constants used throughout the CDK.
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| ChemFile |
A Object containing a number of ChemSequences.
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| ChemModel |
An object containing multiple MoleculeSet and
the other lower level concepts like rings, sequences,
fragments, etc.
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| ChemObject |
The base class for all chemical objects in this cdk.
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| ChemSequence |
A sequence of ChemModels, which can, for example, be used to
store the course of a reaction.
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| ConformerContainer |
A memory-efficient data structure to store conformers for a single molecule.
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| Crystal |
Class representing a molecular crystal.
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| DefaultChemObjectBuilder |
A factory class to provide implementation independent ICDKObjects. |
| DynamicFactory |
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| DynamicFactory.BasicCreator<T> |
A simple creator that helps in creating an anonymous classes for a
creator.
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| DynamicFactory.ConstructorKey |
A class which encapsulates the information about an interface (of this
implementation) and the parameter types of the constructor.
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| DynamicFactory.DefaultInterfaceProvider |
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| ElectronContainer |
Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
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| Element |
Implements the idea of an element in the periodic table.
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| EnzymeResidueLocator |
Atom that represents part of an residue in an enzyme, like Arg255.
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| FragmentAtom |
Class to represent an IPseudoAtom which embeds an IAtomContainer.
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| Isotope |
Used to store and retrieve data of a particular isotope.
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| LonePair |
A LonePair is an orbital primarily located with one Atom, containing
two electrons.
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| Mapping |
A Mapping is an relation between two ChemObjects in a non-chemical
entity.
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| Monomer |
A Monomer is an AtomContainer which stores additional monomer specific
informations for a group of Atoms.
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| PhysicalConstants |
An class providing predefined properties of physical constants.
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| Polymer |
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
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| PseudoAtom |
Represents the idea of a non-chemical atom-like entity, like Me,
R, X, Phe, His, etc.
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| Reaction |
Represents the idea of a chemical reaction.
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| ReactionScheme |
Classes that extends the definition of reaction to a scheme.
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| ReactionSet |
A set of reactions, for example those taking part in a reaction.
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| Ring |
Class representing a ring structure in a molecule.
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| RingSet |
Maintains a set of Ring objects.
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| SingleElectron |
A Single Electron is an orbital which is occupied by only one electron.
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| Strand |
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
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| Substance |
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| Vibration |
A molecular vibration composed of a set of atom vectors.
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