;;
;; This file is for regression testing. DO NOT EVER CHANGE THIS FILE.
;;

(defdescription DNAReplication
	entities
		(
		;;;Main components
		molecule1	;; Original DNA molecule
		molecule2	;; Daughter Molecule
		molecule3	;; Daughter Molecule
		strand1		;; original strand becomes part of molecule2
		strand2		;; original strand becomes part of molecule3
		strand3		;; new strand part of molecule2
		strand4		;; new strand part of molecule2
		substrand1 	;; part(many) of strand 1
		substrand2 	;; part(many) of strand 2
		substrand3 	;; part(many) of strand 3
		substrand4 	;; part(many) of strand 4
		replication-site ;; sites(many) where replication starts.
		

		;;;Main Processes
		Replication	;; The entire process

		;;1st subprocess
		Initial-Strand-Separation-Process	
		initiator-protien	;; main enzyme in 1st subprocess

		;;initiator protien composed of the foll.
		topoisomerase1		
		gyrase1
		helicase1
		ssdna1-binding-protien

		
		Template-Directed-Bond-Formation13	;;lagging strand
		Template-Directed-Bond-Formation24	;; leading strand
		polymerase1
		
		
		;; polymerase is composed of the following.
		polymeraseI
		polymeraseIII
		
		
		RNAcreation24		;; leading strand
		rnapolymerase1		;;rnapolymerase is used in leading strand
		rnamolecule1

		RNAcreation13		;;lagging strand
		primase1		;;primase is used in leading strand
				
		Termination
		terminator-protien
		nuclease1
		ligase1
		)
	
	expressions
		(
		(symmetricPartTypes DNAMolecule DNAStrand)
	
		(isa molecule1 DNAMolecule)
		(parts molecule1 strand1)
		(parts molecule1 strand2)
		
		(isa strand1 DNAStrand)
		(isa strand2 DNAStrand)
		(isa strand1 Gene-HereditaryUnit)
		(isa strand2 Gene-HereditaryUnit)
		
		(isa substrand3 PhysicalPartOfObject)
		(isa substrand4 PhysicalPartOfObject)
		
		;;Strand have many substrand
;;		(parts (substrand1 Many-Quant) strand1)
;;		(parts (substrand2 Many-Quant) strand2)
;;		(parts (substrand3 Many-Quant) strand3)
;;		(parts (substrand4 Many-Quant) strand4)

		(parts substrand1 strand1)
		(parts substrand2 strand2)
		(parts substrand3 strand3)
		(parts substrand4 strand4)
		
		
		(isa replication-site SpatialThing-Localized)
		;; a DNA molecule has many replication sites
;;		(parts (replication-site Many-Quant) molecule1)
		(parts replication-site molecule1)
		
		(isa Replication ProcessingEvent)
		(isa Replication ChemicalReaction)
		(isa Replication CreationEvent)
		(isa Replication DestructionEvent)
		(isa Replication GeneticInformationTransferEvent)
		
		;; Each Initial-Strand-Separation-Process occurs at a single replication site	
		(firstSubEvents Replication Initial-Strand-Separation-Process)
		(isa Initial-Strand-Separation-Process ProcessingEvent)
		(isa Initial-Strand-Separation-Process UnwindingOfDNAHelix)
		(isa Initial-Strand-Separation-Process CreationEvent)
		(isa Initial-Strand-Separation-Process DestructionEvent)
		(inputsDestroyed Initial-Strand-Separation-Process molecule1)
		(outputsRemaining Initial-Strand-Separation-Process substrand1)
		(outputsRemaining Initial-Strand-Separation-Process substrand2)
		(isa substrand1 PhysicalPartOfObject)
		(isa substrand2 PhysicalPartOfObject)
		(isa initiator-protien Enzyme)
		(composedOf initiator-protien topoisomerase1)
		(composedOf initiator-protien gyrase1)
		(composedOf initiator-protien helicase1)
		(composedOf initiator-protien ssdna1-binding-protien)
		(isa topoisomerase1 Enzyme)
		(isa gyrase1 Enzyme)
		(isa helicase1 Enzyme)
		(isa ssdna1-binding-protien Enzyme)
		(catalyst Initial-Strand-Separation-Process initiator-protien)
		(initiator Initial-Strand-Separation-Process initiator-protien)
		
		;; Initial-Strand-Separation-Process occurs at every replication site
;;		(eventOccursAt Initial-Strand-Separation-Process (replication-site Every-NLAttr))		
		(eventOccursAt Initial-Strand-Separation-Process replication-site)		

;;		(eventResults (Initial-Strand-Separation-Process Every-NLAttr) (RNAcreation13 Many-Quant))
		(eventResults Initial-Strand-Separation-Process RNAcreation13)

;;		(eventResults (Initial-Strand-Separation-Process Every-NLAttr) RNAcreation24)
		(eventResults Initial-Strand-Separation-Process RNAcreation24)

		(subEvents Replication RNAcreation24)
		(isa RNAcreation24 CreationEvent)
		(inputs RNAcreation24 substrand2)
		(isa rnapolymerase1 Enzyme)
		(outputsCreated RNAcreation rnamoleclue1)
		(catalyst RNAcreation rnapolymerase1)
		(initiator RNAcreation rnapolymerase1)		

		(eventOccursAt RNACreation24 substrand2)
		(eventResults RNAcreation24 Template-Directed-Bond-Formation24)

		(subEvents Replication RNAcreation13)
		(isa RNAcreation13 CreationEvent)
		(inputs RNAcreation13 substrand1)
		(isa primase1 Enzyme)
		(outputsCreated RNAcreation rnamoleclue1)
		(isa rnamolecule1 RNAMolecule)
		(catalyst RNAcreation primase1)
		(initiator RNAcreation primase1)		

;;		(eventOccursAt (RNAcreation13 Many-Quant) substrand1)
;;		(eventResults (RNAcreation13 Every-NLAttr) Template-Directed-Bond-Formation13)
		(eventOccursAt RNAcreation13 substrand1)
		(eventResults RNAcreation13 Template-Directed-Bond-Formation13)


		(subEvents Replication Template-Directed-Bond-Formation24)
		(isa Template-Directed-Bond-Formation24 ProcessingEvent)
		(isa Template-Directed-Bond-Formation24 ConnectingTogether)
		(isa Template-Directed-Bond-Formation24 CreationEvent)
		(inputs Template-Directed-Bond-Formation24 rnamolecule1)
		(outputsCreated Template-directed-Bond-Formation24 substrand4) 
		(connectedTo strand2 substrand4)
		(templateGene Template-Directed-Bond-Formation24 strand2)
		(isa polymerase1 DNAPolymerase)
		(composedOf polymerase1 polymeraseI)
		(composedOf polymerase1 polymeraseIII)
		(isa polymeraseI Enzyme)
		(isa polymeraseIII Enzyme)
		(catalyst Template-Directed-Bond-Formation24 polymeraseIII)
		(initiator Template-Directed-Bond-Formation24 polymeraseIII)
		
		(subEvents Replication Template-Directed-Bond-Formation13)
		(isa Template-Directed-Bond-Formation13 ProcessingEvent)
		(isa Template-Directed-Bond-Formation13 ConnectingTogether)
		(isa Template-Directed-Bond-Formation13 CreationEvent)
		(inputs Template-Directed-Bond-Formation13 rnamolecule1)
		(outputsCreated Template-Directed-Bond-Formation13 substrand3)
		(connectedTo strand1 substrand3)	
		(templateGene Template-Directed-Bond-Formation13 strand1)		
		(templateGene Template-Directed-Bond-Formation strand2)
		(catalyst Template-Directed-Bond-Formation13 polymeraseIII)
		(initiator Template-Directed-Bond-Formation13 polymeraseIII)
		
		(lastSubEvents Replication Termination)
		(isa Termination ProcessingEvent)
		(isa Termination CreationEvent)
		(inputs Termination strand1)
		(inputs Termination strand2)
		(inputs Termination substrand3)
		(inputs Termination substrand4)
		(outputsCreated Termination molecule2)
		(outputsCreated Termination molecule3)
		(isa terminator-protien Enzyme)
		(composedOf terminator-protien nuclease1)
		(composedOf terminator-protien polymeraseI)
		(composedOf terminator-protien ligase1)
		(catalyst Terminator terminator-protien)
		(initiator Terminator terminator-protien)
		(isa molecule2 DNAMolecule)
			(connectedTo strand1 strand3)
			(parts molecule2 strand1)
			(parts molecule2 strand3)
		(isa molecule3 DNAMolecule)
			(connectedTo strand2 strand4)
			(parts molecule3 strand2)
			(parts molecule3 strand4)
		(isa strand3 DNAStrand)
		(isa strand4 DNAStrand)
		(isa strand3 Gene-HereditaryUnit)
		(isa strand4 Gene-HereditaryUnit)		
		))