org.biopax.paxtools.model.level3
Interface Conversion

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, Entity, Interaction, Level3Element, Named, Observable, Process, java.io.Serializable, XReferrable

All Known Subinterfaces:

BiochemicalReaction, ComplexAssembly, Degradation, Transport, TransportWithBiochemicalReaction

All Known Implementing Classes:

BiochemicalReactionImpl, ComplexAssemblyImpl, ConversionImpl, DegradationImpl, TransportImpl, TransportWithBiochemicalReactionImpl

public interface Conversion
extends Interaction

Definition: An interaction in which molecules of one or more PhysicalEntity pools are physically transformed and become a member of one or more other PhysicalEntity pools.

Rationale: Conversion and pools of entities are two central abstractions of chemistry. They can be quantized with rate and concentration respectively. A conversion in BioPAX, similar to chemistry, is stoichiometric and closed world, i.e. it is assumed that all of the participants are listed. These properties are due to the law of mass conservation. This differs from Control for example where multiple entities might be controlling the controlled and everything that is not listed is assumed to be unknown. Conversions in BioPAX can be reversible -- the property names Left and Right were preferred specifically because they are direction neutral as opposed to substrate and product or input and output.

Usage: Subclasses of conversion represent different types of transformation reflected by the properties of different physicalEntity. BiochemicalReactions will change the ModificationFeatures on a PhysicalEntity, Transport will change the Cellular Location and ComplexAssembly will change BindingFeatures. Generic Conversion class should only be used when the modification does not fit into a any of these classes.

Example: Opening of a voltage gated channel.

Nested Class Summary

Nested classes/interfaces inherited from interface org.biopax.paxtools.model.BioPAXElement

BioPAXElement.Key

Field Summary

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

void	addLeft(PhysicalEntity left) Adds a participant to the left side of the conversion interaction.
void	addParticipantStoichiometry(Stoichiometry stoichiometry) This method adds a stoichiometry for one of the participants of this conversion.
void	addRight(PhysicalEntity right) Adds a participant to the right side of the conversion interaction.
ConversionDirectionType	getConversionDirection() This property represents the direction of the reaction.
java.util.Set<PhysicalEntity>	getLeft() The participants on the left side of the conversion interaction.
java.util.Set<Stoichiometry>	getParticipantStoichiometry() Stoichiometry of the left (getLeft()) and right(getRight()) participants.
java.util.Set<PhysicalEntity>	getRight() The participants on the right side of the conversion interaction.
java.lang.Boolean	getSpontaneous() Specifies whether a conversion occurs spontaneously or not.
void	removeLeft(PhysicalEntity left) Removes a participant from the left side of the conversion interaction.
void	removeParticipantStoichiometry(Stoichiometry stoichiometry) This method removes a stoichiometry for one of the participants of this conversion.
void	removeRight(PhysicalEntity right) Removes a participant from the right side of the conversion interaction.
void	setConversionDirection(ConversionDirectionType conversionDirection) This property represents the direction of the reaction.
void	setSpontaneous(java.lang.Boolean spontaneous) Specifies whether a conversion occurs spontaneously or not.

Methods inherited from interface org.biopax.paxtools.model.level3.Interaction

addInteractionType, addParticipant, getInteractionType, getParticipant, removeInteractionType, removeParticipant

Methods inherited from interface org.biopax.paxtools.model.level3.Process

getControlledOf, getPathwayComponentOf, getStepProcessOf

Methods inherited from interface org.biopax.paxtools.model.level3.Entity

addAvailability, addDataSource, getAvailability, getDataSource, getParticipantOf, removeAvailability, removeDataSource

Methods inherited from interface org.biopax.paxtools.model.level3.Observable

addEvidence, getEvidence, removeEvidence

Methods inherited from interface org.biopax.paxtools.model.level3.Named

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setStandardName

Methods inherited from interface org.biopax.paxtools.model.level3.XReferrable

addXref, getXref, removeXref

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent

Method Detail

getLeft

java.util.Set<PhysicalEntity> getLeft()

The participants on the left side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the left property may be either reactants or products. left is a sub-property of participants.

Returns:

The participants on the left side of the conversion interaction.

addLeft

void addLeft(PhysicalEntity left)

Adds a participant to the left side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the left property may be either reactants or products. left is a sub-property of participants.

Parameters:

left - participants to be added to the left side of the conversion interaction.

removeLeft

void removeLeft(PhysicalEntity left)

Removes a participant from the left side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the left property may be either reactants or products. left is a sub-property of participants.

Parameters:

left - participants to be removed from the left side of the conversion interaction.

getParticipantStoichiometry

java.util.Set<Stoichiometry> getParticipantStoichiometry()

Stoichiometry of the left (getLeft()) and right(getRight()) participants. Note: This is a "bridge" workaround for the n-ary relationship problem. There is no default stoichiometry ( e.g. 1). Leaving this out will create reactions with unknown stoichiometry. It is a best practice to define the stoichiometry of each participant. It is invalid to define more than one stoichiometry per participant. It is invalid to reuse stoichiometry instances across conversions.

Returns:

Stoichiometry of the left (getLeft()) and right(getRight()) participants.

addParticipantStoichiometry

void addParticipantStoichiometry(Stoichiometry stoichiometry)

This method adds a stoichiometry for one of the participants of this conversion.

Parameters:

stoichiometry - to be added

removeParticipantStoichiometry

void removeParticipantStoichiometry(Stoichiometry stoichiometry)

This method removes a stoichiometry for one of the participants of this conversion.

Parameters:

stoichiometry - to be removed

getRight

java.util.Set<PhysicalEntity> getRight()

The participants on the right side of the conversion interaction. Since conversion interactions may proceed in either the right-to-right or right-to-right direction, occupants of the right property may be either reactants or products. right is a sub-property of participants.

Returns:

The participants on the right side of the conversion interaction.

addRight

void addRight(PhysicalEntity right)

Adds a participant to the right side of the conversion interaction. Since conversion interactions may proceed in either the right-to-right or right-to-right direction, occupants of the right property may be either reactants or products. right is a sub-property of participants.

Parameters:

right - participants to be added to the right side of the conversion interaction.

removeRight

void removeRight(PhysicalEntity right)

Removes a participant from the right side of the conversion interaction. Since conversion interactions may proceed in either the right-to-right or right-to-right direction, occupants of the right property may be either reactants or products. right is a sub-property of participants.

Parameters:

right - participants to be removed from the right side of the conversion interaction.

getSpontaneous

java.lang.Boolean getSpontaneous()

Specifies whether a conversion occurs spontaneously or not.

If the spontaneity is not known,this property should not be specified.

Returns:

whether if this conversion is spontaneous.

setSpontaneous

void setSpontaneous(java.lang.Boolean spontaneous)

Specifies whether a conversion occurs spontaneously or not.

If the spontaneity is not known,this property should not be specified.

Parameters:

spontaneous - Whether if this conversion is spontaneous.

getConversionDirection

ConversionDirectionType getConversionDirection()

This property represents the direction of the reaction. If a reaction will run in a single direction under all biological contexts then it is considered irreversible and has a direction. Otherwise it is reversible.

Returns:

One of REVERSIBLE, LEFT-TO-RIGHT or RIGHT-TO-LEFT

setConversionDirection

void setConversionDirection(ConversionDirectionType conversionDirection)

This property represents the direction of the reaction. If a reaction will run in a single direction under all biological contexts then it is considered irreversible and has a direction. Otherwise it is reversible.

Parameters:

conversionDirection - One of REVERSIBLE, LEFT-TO-RIGHT or RIGHT-TO-LEFT -- null for unknown.