org.opentox.toxotis.core.component
Class Conformer

java.lang.Object
  extended by org.opentox.toxotis.core.OTComponent<T>
      extended by org.opentox.toxotis.core.OTOnlineResource<T>
          extended by org.opentox.toxotis.core.OTPublishable<T>
              extended by org.opentox.toxotis.core.DescriptorCaclulation<Compound>
                  extended by org.opentox.toxotis.core.component.Compound
                      extended by org.opentox.toxotis.core.component.Conformer
All Implemented Interfaces:
Serializable, IDescriptorCalculation, IOnlineResource, IOTComponent, IStAXWritable

public class Conformer
extends Compound

Conformers are compounds with 3D characteristics. Conformers don't play any significant role in ToxOtis till now since all chemical entities are cast as Compounds.

Author:
Pantelis Sopasakis, Charalampos Chomenides
See Also:
Serialized Form

Field Summary
 
Fields inherited from class org.opentox.toxotis.core.OTOnlineResource
XSD_DATATYPE_LINKS
 
Fields inherited from class org.opentox.toxotis.core.OTComponent
meta, RDF_ABOUT, RDF_RDF, RDF_RESOURCE, RDF_TYPE
 
Constructor Summary
Conformer()
           
Conformer(VRI uri)
           
 
Method Summary
 com.hp.hpl.jena.ontology.Individual asIndividual(com.hp.hpl.jena.ontology.OntModel model)
          The OpenTox component as an individual.
 VRI getCompoundUri()
           
 String getConformerId()
           
protected  Conformer loadFromRemote(VRI uri, AuthenticationToken token)
          This method is not implemented yet!
 
Methods inherited from class org.opentox.toxotis.core.component.Compound
getAssayProperty, getCasrn, getCompoundId, getConformers, getDepiction, getDepictionFromRemote, getEinecs, getInchi, getInchiKey, getIupacName, getMolecularStructure, getProperties, getPropertiesByOnt, getProperty, getProperty, getRegistrationDate, getSimilar, getSimilar, getSmiles, getSynonyms, listAvailableFeatures, listConformers, publishOnline, publishOnline, setCasrn, setConformers, setDepiction, setEinecs, setInchi, setInchiKey, setIupacName, setMolecularStructure, setRegistrationDate, setSmiles, setSynonyms, wrapInDataset, writeRdf
 
Methods inherited from class org.opentox.toxotis.core.DescriptorCaclulation
calculateDescriptors, calculateDescriptors, futureCDKPhysChemDescriptors, futureDescriptors, futureDescriptors, futureDescriptors, futureJoeLibDescriptors
 
Methods inherited from class org.opentox.toxotis.core.OTPublishable
publish, publish
 
Methods inherited from class org.opentox.toxotis.core.OTOnlineResource
download, download, download, download, downloadImage, loadFromRemote, loadFromRemote
 
Methods inherited from class org.opentox.toxotis.core.OTComponent
addOntologicalClasses, asOntModel, endRdfWriter, equals, getMeta, getOntologicalClasses, getUri, hashCode, initRdfWriter, isEnabled, setEnabled, setMeta, setOntologicalClasses, setUri, writeAnnotationProperty, writeClass, writeDatatypeProperty, writeMetaDataProperties, writeObjectProperty, writeRdf, writeRdf, writeSuperClassRelationships
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface org.opentox.toxotis.core.IOTComponent
addOntologicalClasses, asOntModel, getMeta, getOntologicalClasses, getUri, isEnabled, setEnabled, setMeta, setOntologicalClasses
 

Constructor Detail

Conformer

public Conformer()

Conformer

public Conformer(VRI uri)
          throws ToxOtisException
Throws:
ToxOtisException
Method Detail

getCompoundUri

public VRI getCompoundUri()

getConformerId

public String getConformerId()

asIndividual

public com.hp.hpl.jena.ontology.Individual asIndividual(com.hp.hpl.jena.ontology.OntModel model)
Description copied from interface: IOTComponent
The OpenTox component as an individual.

Specified by:
asIndividual in interface IOTComponent
Overrides:
asIndividual in class Compound
Parameters:
model - The ontological model to which the individual belongs.
Returns:
The OpenTox component as an individual of a data model.

loadFromRemote

protected Conformer loadFromRemote(VRI uri,
                                   AuthenticationToken token)
                            throws ServiceInvocationException
Description copied from class: Compound
This method is not implemented yet!

Overrides:
loadFromRemote in class Compound
Parameters:
uri - Identifier of the location from where the RDF document should be downloaded from and parsed into a Compound object.
token - Token provided
Returns:
Parsed instance of the component into an instance of Compound.
Throws:
ServiceInvocationException


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