Rack#

class biopax-explorer.pattern.rack.Rack[source]#

Bases: object

A reference list of Patterns related to BIOPAX use cases.

Methods

controlsMetabolicCatalysisBothComplex([enl])	Pattern for a Protein controlling a reaction whose participant is a small molecule.
controlsMetabolicCatalysisBothSimple([enl])	Pattern for a Protein controlling a reaction whose participant is a small molecule.
controlsMetabolicCatalysisControlledComplex([enl])	Pattern for a Protein controlling a reaction whose participant is a small molecule.
controlsMetabolicCatalysisControllerComplex([enl])	Pattern for a Protein controlling a reaction whose participant is a small molecule.
inspect(fct)	Inspect function signature.
stateChangeSimple([label, enl])	Pattern for a Conversion has an input PhysicalEntity (except Complex) and another output PhysicalEntity (except Complex) that belongs to the same EntityReference
usedToProduceBothComplex([enl])	Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule.
usedToProduceLeftComplex([enl])	Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule.
usedToProduceNoComplex([enl])	Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule.
usedToProduceRightComplex([enl])	Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule.

bindsTo
controlsExpressionWithConversion
controlsExpressionWithTemplateReac
controlsMetabolicCatalysis
controlsPhosphorylation
controlsPhosphorylationBothComplex
controlsPhosphorylationBothComplexAndComplexController
controlsPhosphorylationControllerAndLeftComplex
controlsPhosphorylationControllerAndRightComplex
controlsPhosphorylationControllerComplex
controlsPhosphorylationLeftComplex
controlsPhosphorylationRightComplex
controlsPhosphorylationRightSimple
controlsStateChange
controlsStateChangeBothComplex
controlsStateChangeComplexController
controlsStateChangeComplexControllerAndBothComplex
controlsStateChangeSimple
inComplexWith
inSameActiveComplex
inSameActiveComplexMolecularInteraction
inSameActiveComplexOtherInteraction
inSameComplex
inSameComplexEffectingControl
modifierConv
modifierConvComplex
modifierConvNoComplex
molecularInteraction
molecularInteractionComplex
molecularInteractionNoComplex
notBlackboxComplexInComplex
reactsWith
reactsWithComplex
reactsWithNoComplex
stateChange
stateChangeComplex
stateChangeNoComplex
usedToProduce

Methods Summary

bindsTo([entity_node_list])
controlsExpressionWithConversion([...])
controlsExpressionWithTemplateReac([...])
controlsMetabolicCatalysis()	rtype: Pattern
controlsMetabolicCatalysisBothComplex([enl])	Pattern for a Protein controlling a reaction whose participant is a small molecule.
controlsMetabolicCatalysisBothSimple([enl])	Pattern for a Protein controlling a reaction whose participant is a small molecule.
controlsMetabolicCatalysisControlledComplex([enl])	Pattern for a Protein controlling a reaction whose participant is a small molecule.
controlsMetabolicCatalysisControllerComplex([enl])	Pattern for a Protein controlling a reaction whose participant is a small molecule.
controlsPhosphorylation()	rtype: Pattern
controlsPhosphorylationBothComplex([enl])
controlsPhosphorylationBothComplexAndComplexController([enl])
controlsPhosphorylationControllerAndLeftComplex([enl])
controlsPhosphorylationControllerAndRightComplex([enl])
controlsPhosphorylationControllerComplex([enl])
controlsPhosphorylationLeftComplex([enl])
controlsPhosphorylationRightComplex([enl])
controlsPhosphorylationRightSimple([enl])
controlsStateChange()	rtype: Pattern
controlsStateChangeBothComplex([...])
controlsStateChangeComplexController([...])
controlsStateChangeComplexControllerAndBothComplex([...])
controlsStateChangeSimple([entity_node_list])
inComplexWith([entity_node_list])
inSameActiveComplex()	rtype: Pattern
inSameActiveComplexMolecularInteraction([...])
inSameActiveComplexOtherInteraction([...])
inSameComplex([entity_node_list])
inSameComplexEffectingControl([entity_node_list])	rtype: Pattern
inspect(fct)	Inspect function signature.
modifierConv()	rtype: Pattern
modifierConvComplex([entity_node_list])
modifierConvNoComplex([entity_node_list])
molecularInteraction()	rtype: Pattern
molecularInteractionComplex([entity_node_list])
molecularInteractionNoComplex([entity_node_list])
notBlackboxComplexInComplex([entity_node_list])
reactsWith()	rtype: Pattern
reactsWithComplex([enl])
reactsWithNoComplex([enl])
stateChange([label])	rtype: Pattern
stateChangeComplex([label, enl])
stateChangeNoComplex([label, entity_node_list])
stateChangeSimple([label, enl])	Pattern for a Conversion has an input PhysicalEntity (except Complex) and another output PhysicalEntity (except Complex) that belongs to the same EntityReference
usedToProduce()	rtype: Pattern
usedToProduceBothComplex([enl])	Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule.
usedToProduceLeftComplex([enl])	Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule.
usedToProduceNoComplex([enl])	Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule.
usedToProduceRightComplex([enl])	Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule.

Methods Documentation

bindsTo(entity_node_list=None)[source]#

controlsExpressionWithConversion(entity_node_list=None)[source]#

controlsExpressionWithTemplateReac(entity_node_list=None)[source]#

controlsMetabolicCatalysis()[source]#

Return type:

Pattern

controlsMetabolicCatalysisBothComplex(enl=None)[source]#

Pattern for a Protein controlling a reaction whose participant is a small molecule. The controller and the participant are both in a Complex

controlsMetabolicCatalysisBothSimple(enl=None)[source]#

Pattern for a Protein controlling a reaction whose participant is a small molecule. The controller and the participant is not a Complex

controlsMetabolicCatalysisControlledComplex(enl=None)[source]#

Pattern for a Protein controlling a reaction whose participant is a small molecule. The participant is in a Complex

controlsMetabolicCatalysisControllerComplex(enl=None)[source]#

Pattern for a Protein controlling a reaction whose participant is a small molecule. The controller is in a Complex

controlsPhosphorylation()[source]#

Return type:

Pattern

controlsPhosphorylationBothComplex(enl=None)[source]#

controlsPhosphorylationBothComplexAndComplexController(enl=None)[source]#

controlsPhosphorylationControllerAndLeftComplex(enl=None)[source]#

controlsPhosphorylationControllerAndRightComplex(enl=None)[source]#

controlsPhosphorylationControllerComplex(enl=None)[source]#

controlsPhosphorylationLeftComplex(enl=None)[source]#

controlsPhosphorylationRightComplex(enl=None)[source]#

controlsPhosphorylationRightSimple(enl=None)[source]#

controlsStateChange()[source]#

Return type:

Pattern

controlsStateChangeBothComplex(entity_node_list=None)[source]#

controlsStateChangeComplexController(entity_node_list=None)[source]#

controlsStateChangeComplexControllerAndBothComplex(entity_node_list=None)[source]#

controlsStateChangeSimple(entity_node_list=None)[source]#

inComplexWith(entity_node_list=None)[source]#

inSameActiveComplex()[source]#

Return type:

Pattern

inSameActiveComplexMolecularInteraction(entity_node_list=None)[source]#

inSameActiveComplexOtherInteraction(entity_node_list=None)[source]#

inSameComplex(entity_node_list=None)[source]#

inSameComplexEffectingControl(entity_node_list=None)[source]#

Return type:

Pattern

inspect(fct)[source]#

Inspect function signature.

modifierConv()[source]#

Return type:

Pattern

modifierConvComplex(entity_node_list=None)[source]#

modifierConvNoComplex(entity_node_list=None)[source]#

molecularInteraction()[source]#

Return type:

Pattern

molecularInteractionComplex(entity_node_list=None)[source]#

molecularInteractionNoComplex(entity_node_list=None)[source]#

notBlackboxComplexInComplex(entity_node_list=None)[source]#

reactsWith()[source]#

Return type:

Pattern

reactsWithComplex(enl=None)[source]#

reactsWithNoComplex(enl=None)[source]#

stateChange(label=None)[source]#

Return type:

Pattern

stateChangeComplex(label=None, enl=None)[source]#

stateChangeNoComplex(label=None, entity_node_list=None)[source]#

stateChangeSimple(label=None, enl=None)[source]#

Pattern for a Conversion has an input PhysicalEntity (except Complex) and another output PhysicalEntity (except Complex) that belongs to the same EntityReference

Args:

label (str): input name

usedToProduce()[source]#

Return type:

Pattern

usedToProduceBothComplex(enl=None)[source]#

Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule. Complex at left and at right

usedToProduceLeftComplex(enl=None)[source]#

Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule. Complex at left

usedToProduceNoComplex(enl=None)[source]#

Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule.

usedToProduceRightComplex(enl=None)[source]#

Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule. Complex at right