Uses of Class
org.openscience.cdk.ChemObject

Packages that use ChemObject

Package	Description
org.openscience.cdk
org.openscience.cdk.debug
org.openscience.cdk.libio.md
org.openscience.cdk.pharmacophore
org.openscience.cdk.protein.data
org.openscience.cdk.reaction

Uses of ChemObject in org.openscience.cdk

Subclasses of ChemObject in org.openscience.cdk

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	Association Base class for storing interactions like hydrogen bonds and ionic interactions.
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	EnzymeResidueLocator Atom that represents part of an residue in an enzyme, like Arg255.
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	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.

Uses of ChemObject in org.openscience.cdk.debug

Subclasses of ChemObject in org.openscience.cdk.debug

Modifier and Type	Class and Description
class	DebugAminoAcid Debugging data class.
class	DebugAtom Debugging data class.
class	DebugAtomContainer Debugging data class.
class	DebugAtomContainerSet Debugging data class.
class	DebugAtomType Debugging data class.
class	DebugBioPolymer Debugging data class.
class	DebugBond Debugging data class.
class	DebugChemFile Debugging data class.
class	DebugChemModel Debugging data class.
class	DebugChemObject Debugging data class.
class	DebugChemSequence Debugging data class.
class	DebugCrystal Debugging data class.
class	DebugElectronContainer Debugging data class.
class	DebugElement Debugging data class.
class	DebugFragmentAtom Class to represent an IPseudoAtom which embeds an IAtomContainer.
class	DebugIsotope Debugging data class.
class	DebugLonePair Debugging data class.
class	DebugMapping Debugging data class.
class	DebugMonomer Debugging data class.
class	DebugPDBAtom Debugging data class.
class	DebugPDBMonomer Debugging data class.
class	DebugPDBPolymer Debugging data class.
class	DebugPDBStructure Debugging data class.
class	DebugPolymer Debugging data class.
class	DebugPseudoAtom Debugging data class.
class	DebugReaction Debugging data class.
class	DebugReactionScheme Debugging data class.
class	DebugReactionSet Debugging data class.
class	DebugRing Debugging data class.
class	DebugRingSet Debugging data class.
class	DebugSingleElectron Debugging data class.
class	DebugStrand Debugging data class.
class	DebugSubstance Debugging data class.

Uses of ChemObject in org.openscience.cdk.libio.md

Subclasses of ChemObject in org.openscience.cdk.libio.md

Modifier and Type	Class and Description
class	ChargeGroup A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule.
class	MDMolecule
class	Residue A residue is a named, numbered collection of atoms in an MDMolecule.

Uses of ChemObject in org.openscience.cdk.pharmacophore

Subclasses of ChemObject in org.openscience.cdk.pharmacophore

Modifier and Type	Class and Description
class	PharmacophoreAngleBond Represents an angle relationship between three pharmacophore groups.
class	PharmacophoreAtom A representation of a pharmacophore group.
class	PharmacophoreBond Represents a distance relationship between two pharmacophore groups.
class	PharmacophoreQueryAngleBond Represents a pharmacophore query angle constraint.
class	PharmacophoreQueryAtom Represents a query pharmacophore group.
class	PharmacophoreQueryBond Represents a pharmacophore query distance constraint.

Uses of ChemObject in org.openscience.cdk.protein.data

Subclasses of ChemObject in org.openscience.cdk.protein.data

Modifier and Type	Class and Description
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	PDBStrand An entry in the PDB database.
class	PDBStructure Holder for secundary protein structure elements.

Uses of ChemObject in org.openscience.cdk.reaction

Subclasses of ChemObject in org.openscience.cdk.reaction

Modifier and Type	Class and Description
class	ReactionChain Classes that extends the definition of reaction to a chain reaction.