Package | Description |
---|---|
org.openscience.cdk.silent |
Modifier and Type | Class and Description |
---|---|
class |
AminoAcid
A AminoAcid is Monomer which stores additional amino acid specific
informations, like the N-terminus atom.
|
class |
Atom
Represents the idea of an chemical atom.
|
class |
AtomContainer
Base class for all chemical objects that maintain a list of Atoms and
ElectronContainers.
|
class |
AtomContainerSet
A set of AtomContainers.
|
class |
AtomType
The base class for atom types.
|
class |
BioPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store
additional informations about the Polymer which are connected to BioPolymers.
|
class |
Bond
Implements the concept of a covalent bond between two or more atoms.
|
class |
ChemFile
A Object containing a number of ChemSequences.
|
class |
ChemModel
An object containing multiple MoleculeSet and
the other lower level concepts like rings, sequences,
fragments, etc.
|
class |
ChemSequence
A sequence of ChemModels, which can, for example, be used to
store the course of a reaction.
|
class |
Crystal
Class representing a molecular crystal.
|
class |
ElectronContainer
Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
|
class |
Element
Implements the idea of an element in the periodic table.
|
class |
FragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.
|
class |
Isotope
Used to store and retrieve data of a particular isotope.
|
class |
LonePair
A LonePair is an orbital primarily located with one Atom, containing
two electrons.
|
class |
Mapping
A Mapping is an relation between two ChemObjects in a non-chemical
entity.
|
class |
Monomer
A Monomer is an AtomContainer which stores additional monomer specific
informations for a group of Atoms.
|
class |
PDBAtom
Represents the idea of an atom as used in PDB files.
|
class |
PDBMonomer
Represents the idea of an monomer as used in PDB files.
|
class |
PDBPolymer
An entry in the PDB database.
|
class |
PDBStructure
Holder for secundary protein structure elements.
|
class |
Polymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
|
class |
PseudoAtom
Represents the idea of a non-chemical atom-like entity, like Me,
R, X, Phe, His, etc.
|
class |
Reaction
Represents the idea of a chemical reaction.
|
class |
ReactionScheme
Classes that extends the definition of reaction to a scheme.
|
class |
ReactionSet
A set of reactions, for example those taking part in a reaction.
|
class |
Ring
Class representing a ring structure in a molecule.
|
class |
RingSet
Maintains a set of Ring objects.
|
class |
SingleElectron
A Single Electron is an orbital which is occupied by only one electron.
|
class |
Strand
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
|
class |
Substance
An implementation of the
ISubstance interface. |
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