fr.curie.BiNoM.pathways.biopax
Interface smallMolecule

All Superinterfaces:

entity, physicalEntity, com.ibm.adtech.jastor.Thing

All Known Implementing Classes:

smallMoleculeImpl

public interface smallMolecule
extends physicalEntity, com.ibm.adtech.jastor.Thing

Interface for smallMolecule ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.

(URI: http://www.biopax.org/release/biopax-level2.owl#smallMolecule)

RDF Schema Standard Properties
comment : Definition: Any bioactive molecule that is not a peptide, DNA, or RNA. Generally these are non-polymeric, but complex carbohydrates are not explicitly modeled as classes in this version of the ontology, thus are forced into this class. Comment: Recently, a number of small molecule databases have become available to cross-reference from this class. Examples: glucose, penicillin, phosphatidylinositol^^http://www.w3.org/2001/XMLSchema#string

Field Summary

static com.hp.hpl.jena.rdf.model.Property	CHEMICAL_DASH_FORMULAProperty The Jena Property for CHEMICAL_DASH_FORMULA
static com.hp.hpl.jena.rdf.model.Property	MOLECULAR_DASH_WEIGHTProperty The Jena Property for MOLECULAR_DASH_WEIGHT
static com.hp.hpl.jena.rdf.model.Property	STRUCTUREProperty The Jena Property for STRUCTURE
static com.hp.hpl.jena.rdf.model.Resource	TYPE The rdf:type for this ontology class

Fields inherited from interface fr.curie.BiNoM.pathways.biopax.entity

AVAILABILITYProperty, COMMENTProperty, DATA_DASH_SOURCEProperty, NAMEProperty, SHORT_DASH_NAMEProperty, SYNONYMSProperty, XREFProperty

Fields inherited from interface com.ibm.adtech.jastor.Thing

copyright

Method Summary

chemicalStructure	addSTRUCTURE() Adds an anonymous value for the 'STRUCTURE' property
void	addSTRUCTURE(chemicalStructure STRUCTURE) Adds a value for the 'STRUCTURE' property
chemicalStructure	addSTRUCTURE(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'STRUCTURE' property.
java.lang.String	getCHEMICAL_DASH_FORMULA() Gets the 'CHEMICAL_DASH_FORMULA' property value
java.lang.Double	getMOLECULAR_DASH_WEIGHT() Gets the 'MOLECULAR_DASH_WEIGHT' property value
java.util.Iterator	getSTRUCTURE() Get an Iterator the 'STRUCTURE' property values.
void	removeSTRUCTURE(chemicalStructure STRUCTURE) Removes a value for the 'STRUCTURE' property.
void	setCHEMICAL_DASH_FORMULA(java.lang.String CHEMICAL_DASH_FORMULA) Sets the 'CHEMICAL_DASH_FORMULA' property value
void	setMOLECULAR_DASH_WEIGHT(java.lang.Double MOLECULAR_DASH_WEIGHT) Sets the 'MOLECULAR_DASH_WEIGHT' property value

Methods inherited from interface fr.curie.BiNoM.pathways.biopax.entity

addAVAILABILITY, addCOMMENT, addDATA_DASH_SOURCE, addDATA_DASH_SOURCE, addDATA_DASH_SOURCE, addSYNONYMS, addXREF, addXREF, addXREF, getAVAILABILITY, getCOMMENT, getDATA_DASH_SOURCE, getNAME, getSHORT_DASH_NAME, getSYNONYMS, getXREF, removeAVAILABILITY, removeCOMMENT, removeDATA_DASH_SOURCE, removeSYNONYMS, removeXREF, setNAME, setSHORT_DASH_NAME

Methods inherited from interface com.ibm.adtech.jastor.Thing

clearCache, isRDFType, listStatements, model, registerListener, removeStatements, resource, unregisterListener, uri

Field Detail

TYPE

static final com.hp.hpl.jena.rdf.model.Resource TYPE

The rdf:type for this ontology class

MOLECULAR_DASH_WEIGHTProperty

static final com.hp.hpl.jena.rdf.model.Property MOLECULAR_DASH_WEIGHTProperty

The Jena Property for MOLECULAR_DASH_WEIGHT

(URI: http://www.biopax.org/release/biopax-level2.owl#MOLECULAR-WEIGHT)

RDF Schema Standard Properties
comment : Defines the molecular weight of the molecule, in daltons.@en

STRUCTUREProperty

static final com.hp.hpl.jena.rdf.model.Property STRUCTUREProperty

The Jena Property for STRUCTURE

(URI: http://www.biopax.org/release/biopax-level2.owl#STRUCTURE)

RDF Schema Standard Properties
comment : Defines the chemical structure and other information about this molecule, using an instance of class chemicalStructure.@en

CHEMICAL_DASH_FORMULAProperty

static final com.hp.hpl.jena.rdf.model.Property CHEMICAL_DASH_FORMULAProperty

The Jena Property for CHEMICAL_DASH_FORMULA

(URI: http://www.biopax.org/release/biopax-level2.owl#CHEMICAL-FORMULA)

RDF Schema Standard Properties
comment : The chemical formula of the small molecule. Note: chemical formula can also be stored in the STRUCTURE property (in CML). In case of disagreement between the value of this property and that in the CML file, the CML value takes precedence.^^http://www.w3.org/2001/XMLSchema#string

Method Detail

getMOLECULAR_DASH_WEIGHT

java.lang.Double getMOLECULAR_DASH_WEIGHT()
                                          throws com.ibm.adtech.jastor.JastorException

Gets the 'MOLECULAR_DASH_WEIGHT' property value

Returns:

Double

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

MOLECULAR_DASH_WEIGHTProperty

setMOLECULAR_DASH_WEIGHT

void setMOLECULAR_DASH_WEIGHT(java.lang.Double MOLECULAR_DASH_WEIGHT)
                              throws com.ibm.adtech.jastor.JastorException

Sets the 'MOLECULAR_DASH_WEIGHT' property value

Parameters:

{@link - java.lang.Double}

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

MOLECULAR_DASH_WEIGHTProperty

getSTRUCTURE

java.util.Iterator getSTRUCTURE()
                                throws com.ibm.adtech.jastor.JastorException

Get an Iterator the 'STRUCTURE' property values. This Iteartor may be used to remove all such values.

Returns:

Iterator of chemicalStructure

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

STRUCTUREProperty

addSTRUCTURE

void addSTRUCTURE(chemicalStructure STRUCTURE)
                  throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'STRUCTURE' property

Parameters:

The - chemicalStructure to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

STRUCTUREProperty

addSTRUCTURE

chemicalStructure addSTRUCTURE()
                               throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'STRUCTURE' property

Returns:

The anoymous chemicalStructure created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

STRUCTUREProperty

addSTRUCTURE

chemicalStructure addSTRUCTURE(com.hp.hpl.jena.rdf.model.Resource resource)
                               throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'STRUCTURE' property. This method is equivalent constructing a new instance of chemicalStructure with the factory and calling addSTRUCTURE(fr.curie.BiNoM.pathways.biopax.chemicalStructure STRUCTURE) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#chemicalStructure. That is, this method should not be used as a shortcut for creating new objects in the model.

Parameters:

The - om.hp.hpl.jena.rdf.model.Resource to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

STRUCTUREProperty

removeSTRUCTURE

void removeSTRUCTURE(chemicalStructure STRUCTURE)
                     throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'STRUCTURE' property. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Parameters:

The - chemicalStructure to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

STRUCTUREProperty

getCHEMICAL_DASH_FORMULA

java.lang.String getCHEMICAL_DASH_FORMULA()
                                          throws com.ibm.adtech.jastor.JastorException

Gets the 'CHEMICAL_DASH_FORMULA' property value

Returns:

String

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

CHEMICAL_DASH_FORMULAProperty

setCHEMICAL_DASH_FORMULA

void setCHEMICAL_DASH_FORMULA(java.lang.String CHEMICAL_DASH_FORMULA)
                              throws com.ibm.adtech.jastor.JastorException

Sets the 'CHEMICAL_DASH_FORMULA' property value

Parameters:

{@link - java.lang.String}

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

CHEMICAL_DASH_FORMULAProperty