public interface Conversion extends Interaction
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. BiochemicalReaction
s will change the ModificationFeature
s on a
PhysicalEntity
, Transport
will change the Cellular Location and ComplexAssembly
will
change BindingFeature
s. 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.UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT
Modifier and Type | Method and Description |
---|---|
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.
|
Set<PhysicalEntity> |
getLeft()
The participants on the left side of the conversion interaction.
|
Set<Stoichiometry> |
getParticipantStoichiometry()
Stoichiometry of the left (
getLeft() ) and right(getRight() ) participants. |
Set<PhysicalEntity> |
getRight()
The participants on the right side of the conversion interaction.
|
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(Boolean spontaneous)
Specifies whether a conversion occurs spontaneously or not.
|
addInteractionType, addParticipant, getInteractionType, getParticipant, removeInteractionType, removeParticipant
getControlledOf, getPathwayComponentOf, getStepProcessOf
addAvailability, addDataSource, getAvailability, getDataSource, getParticipantOf, removeAvailability, removeDataSource
addEvidence, getEvidence, removeEvidence
addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setName, setStandardName
addXref, getXref, removeXref
addComment, getComment, removeComment
equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent
Set<PhysicalEntity> getLeft()
void addLeft(PhysicalEntity left)
left
- participants to be added to the left side of the conversion interaction.void removeLeft(PhysicalEntity left)
left
- participants to be removed from the left side of the conversion interaction.Set<Stoichiometry> getParticipantStoichiometry()
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.getLeft()
) and right(getRight()
) participants.void addParticipantStoichiometry(Stoichiometry stoichiometry)
stoichiometry
- to be addedvoid removeParticipantStoichiometry(Stoichiometry stoichiometry)
stoichiometry
- to be removedSet<PhysicalEntity> getRight()
void addRight(PhysicalEntity right)
right
- participants to be added to the right side of the conversion interaction.void removeRight(PhysicalEntity right)
right
- participants to be removed from the right side of the conversion interaction.Boolean getSpontaneous()
void setSpontaneous(Boolean spontaneous)
spontaneous
- Whether if this conversion is spontaneous.ConversionDirectionType getConversionDirection()
void setConversionDirection(ConversionDirectionType conversionDirection)
conversionDirection
- One of REVERSIBLE, LEFT-TO-RIGHT or RIGHT-TO-LEFT -- null for unknown.Copyright © 2015 BioPAX. All rights reserved.