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	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	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	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	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	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	Description
class	ReactionChain	Classes that extends the definition of reaction to a chain reaction.