org.sigpath.datamodel
Interface Chemical

All Superinterfaces:

Collectable, SigPathEntity

All Known Subinterfaces:

BioPolymer, Complex, DNA, MacroMolecule, Protein, RNA, SmallMolecule

All Known Implementing Classes:

BioPolymerImpl, ChemicalImpl, ComplexImpl, NamedChemical, ProteinImpl, SmallMoleculeImpl

public interface Chemical
extends SigPathEntity

Represents a chemical compound, either protein, DNA, complex, or small molecule. Subclasses are provided which classify Chemicals into more specific categories.

Method Summary

boolean	contains(Chemical part) Does the chemical contain this part.
Collection	getBecomes() Gets information about what this chemical can become.
Collection	getComesFrom() Gets information about what chemical does this chemical comes from.
Organism	getOrganism() Returns the organism which produces this chemical.
Set	involvedIn() Returns the set of reactions in which this chemical is involved.
boolean	isBackgroundInformation() Is this chemical background information.
void	setInvolvedIn(EnzymaticReaction er, boolean state) Makes or destroy the "involved in" association to an enzymatic reaction.
void	setInvolvedIn(NamedChemicalInteraction nci, boolean state) Makes or destroys the "involved in" association to a Named Chemical Interaction.
void	setInvolvedIn(Reaction reaction, boolean state) Makes or destroy the "involved in" association to a reaction.
void	setOrganism(Organism o) Sets the organism which produces this chemical.

Methods inherited from interface org.sigpath.datamodel.SigPathEntity

addAlias, addAliases, addReview, addUserComment, changeAlias, getAliases, getAliasesCollection, getAliasesIterator, getChangeLog, getCombinedStringLength, getComments, getDescription, getExternalReferences, getForwardReferences, getLiteratureReferences, getName, getReviews, getSpid, getUserComments, isExportable, removeAlias, removeAliases, removeReviews, setAliases, setAliasesCollection, setChangeLog, setComments, setDescription, setExportable, setName, setSpid

Methods inherited from interface org.sigpath.datamodel.lset.Collectable

getCollections

Method Detail

contains

boolean contains(Chemical part)

Does the chemical contain this part. A complex contains each monomer and their parts, and other molecules contains themselves.

Returns:

True if the entity contains this part. False otherwise.

getOrganism

Organism getOrganism()

Returns the organism which produces this chemical.

setOrganism

void setOrganism(Organism o)

Sets the organism which produces this chemical.

getComesFrom

Collection getComesFrom()

Gets information about what chemical does this chemical comes from. A source of a chemical is a molecule which can be transformed to produce the chemical.

Returns:

Collection of ComesFromInfo instances (one for each direct source).

See Also:

ComesFromInfo

getBecomes

Collection getBecomes()

Gets information about what this chemical can become.

Returns:

Collection of BecomesInfo instances.

involvedIn

Set involvedIn()

Returns the set of reactions in which this chemical is involved. A chemical is involved in a reaction if it appears on the left side or right of the reaction, or serves as an enzyme in an enzymatic reaction.

setInvolvedIn

void setInvolvedIn(Reaction reaction,
                   boolean state)

Makes or destroy the "involved in" association to a reaction. Involved in association describe the fact that chemical a is/is not involved in reaction r. a.setInvolvedIn(r, "true") means that the chemical a is involved in reaction r. In this case, involvedIn() will return a collection that contains r.

Parameters:

reaction - Reaction in which this chemical is involved.

state - True when the chemical is involved in the reaction, set otherwise.

See Also:

involvedIn()

setInvolvedIn

void setInvolvedIn(EnzymaticReaction er,
                   boolean state)

Makes or destroy the "involved in" association to an enzymatic reaction. Involved in association describe the fact that chemical a is/is not involved in an enzymatic reaction er. a.setInvolvedIn(er, "true") means that the chemical a is involved in er. * In this case, involvedIn() will return a collection that contains er.

Parameters:

er - EnzymaticReaction in which this chemical is involved.

state - True when the chemical is involved in the enzymatic reaction, False otherwise.

See Also:

involvedIn()

setInvolvedIn

void setInvolvedIn(NamedChemicalInteraction nci,
                   boolean state)

Makes or destroys the "involved in" association to a Named Chemical Interaction. Involved in association describes the fact that the chemical a is/is not involved in the interaction nci. a.setInvolvedIn(er, "true") means that the chemical a is involved in nci. In this case, involvedIn() will return a collection that contains nci.

Parameters:

nci - NamedChemicalInteraction in which this chemical is involved.

state - True when the chemical is involved in the Named Chemical Interaction, False otherwise.

See Also:

involvedIn()

isBackgroundInformation

boolean isBackgroundInformation()

Is this chemical background information. A chemical is background information if it not the result of the transformation of another chemical described in sigpath. Background information is usually imported from other biological databases than SigPath, and have appropriate links (database, accession codes pairs).