Package org.sigpath.datamodel

Core Data Model for representing SigPath Entities.

See:
Description

Interface Summary

ActivityMapping	Represents an Activity Mapping.
BioPolymer	Represents a biopolymer (Protein, DNA or RNA).
Chemical	Represents a chemical compound, either protein, DNA, complex, or small molecule.
Complex	Represents a complex of Chemicals.
ConcentrationMeasurement	Represents the measurement of the concentration of a chemical.
DNA	Represents a DNA molecule (no implementation available).
EnzymaticReaction	Represents an enzymatic reaction.
ExternalReferences	Keeps references to external databases.
Interaction
InteractionSites	Represents the site of an interaction between two molecules or more.
KineticInteraction	A sub-class of Interaction that is associated with a Kinetic.
LiteratureReference	Represents a primary Literature reference.
LiteratureReferences	Represents a set of references.
MacroMolecule	Represents a macromolecule(no implementation available).
Organism	Represents an organism.
Parameter	Represents a Parameter.
Protein	Represents a protein.
Reaction	Represents a chemical reaction.
ResidueRange	Represents a residue range.
RNA	Represents a DNA molecule (no implementation available).
SigPathEntity	Each entity in the data model derives from SigPathEntity.
SigPathFactory	Use instances of this factory to create instance of the SigPath data model.
SmallMolecule	Represents a small molecule.

Class Summary

ActivityMappingImpl	Maps activity to residues of a biopolymer.
BioPolymerImpl	Protein implementation.
ChangeLog	Change Log for SigPath Entities.
ChemicalImpl	Represents a chemical compound, either protein, DNA, complex, or small molecule.
ComplexImpl	Implements Complex.
ConcentrationMeasurementImpl	Implements ConcentrationMeasurement
Databases	Represents databases known to SigPath.
EnzymaticReactionImpl	Implements EnzymaticReaction.
ExternalReference	Keeps references to external databases.
ExternalReferencesImpl	Keeps references to external databases.
InteractionImpl
InteractionSitesImpl	Maps the site of an interaction to residues of a biopolymer.
Kinetic	General information about the kinetic of an interaction.
KineticCustom	A class to define custom kinetics.
KineticInteractionImpl	A special kinetic that use species and constant bindings for a full specification.
KineticMassAction	This kinetic implements mass action.
KineticMichaelisMenten	Irreversible Michaelis-Menten kinetic.
KineticReference	This class is used to make all inheriting class having the same export/import methods, unlike the KineticCustom class.
LiteratureReferenceImpl	Implements LiteratureReference.
LiteratureReferenceImplNonJdo	Implements LiteratureReference.
LiteratureReferencesImpl	Implements a set of references.
ModifiedEntityList	Represents a list of entities that have been modified since the initial import.
NamedChemical	Represents a Named Chemical.
NamedChemicalInteraction	Represents an interaction between two named-chemicals.
NavigatorFactoryImpl	Centralized class for creating SigPath Entities.
OrganismImpl	Implements Organism.
ParameterImpl	Implements a Parameter.
ProteinImpl	Protein implementation.
Query	Represents a SigPath Query.
ReactionImpl	Implements Reaction.
ReadOnlyIterator	An iterator with a noop remove method.
ResidueRangeImpl	Implements ResidueRange.
SigPathEntityImpl	Implements SigPathEntity.
SigPathFactoryImpl	Manage access to SigPath Entities.
SmallMoleculeImpl	Implements SmallMolecule.
SpidRange	Represents a range of spids.
Unit	Represents a unit.
UnitCoefficients
UserComment	User Comment for SigPath Entities.

Package org.sigpath.datamodel Description

Core Data Model for representing SigPath Entities.

SigPath Entities consists of Small Molecules, Proteins, DNA, RNA, etc. Each SigPath entity receives a unique Sigpath ID (SPID), and may also contain a number of external references and aliases.