SigPath

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.


SigPath

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