; Bacterial RNA transcription scenario from Alberts 7.1.4
; Dec 18, 2000
;  modified Feb 14, 2001

; disclaimer: due to non-KM stuff, this scenario has not been tested/debugged

; ########## DNA ##########

; There is a representation of DNA in the component library that's still
; being worked out. This is not it. This version of DNA has just what's 
; needed for the RNA transcription scenario.

; Changes to conform to the new ADL (Jim):
; subevent-order has been removed
; subevent -> sub-steps
; each sub-step has an event-to-do and a next-step.

(DNA has
     (superclasses (Nucleic-Acid))
     (required-slot ())
     (primary-slot ())
     (secondary-slot ())
     (cmap-correspondance ()))

(every DNA has
  (shape (*helix))

  (has-part 
    ((a DNA-Strand called "S1" with
       (region 
         ((a DNA-5-End with
            (is-at 
              ((the DNA-3-End region of 
                 ((the has-part of Self) called "S2")))))
          (a DNA-3-End with
            (is-at 
              ((the DNA-5-End region of 
                 ((the has-part of Self) called "S2"))))))))
     (a DNA-Strand called "S2" with
       (region 
         ((a DNA-5-End with
            (is-at 
              ((the DNA-3-End region of 
                 ((the has-part of Self) called "S1")))))
          (a DNA-3-End with
            (is-at 
              ((the DNA-5-End region of 
                 ((the has-part of Self) called "S1")))))))))))


; ########## DNA-Strand ##########

(DNA-Strand has
         (superclasses (Nucleic-Acid))
         (required-slot ())
         (primary-slot ())
         (secondary-slot ())
         (cmap-correspondence ())
         (test-case ()))

(every DNA-Strand has
       (views ((a View with
                     (as ((a Sequence with
                             (basic-unit (Deoxyribonucleotide))))))))

       (has-part ((at-least 1 Gene-Coding-Region)))

       (region ((a DNA-5-End with
                   (is-opposite ((the DNA-3-End region of Self))))
                (a DNA-3-End with
                   (is-opposite ((the DNA-5-End region of Self)))))))


; ########## Sequence ##########

(Sequence has
         (superclasses (Entity))
         (required-slot (basic-unit))
         (primary-slot ())
         (secondary-slot ())
         (cmap-correspondence ())
         (test-case ()))

(every Sequence has
       (basic-unit (Entity))
       (the-seq ((:seq (an instance of (Self basic-unit)) 
                       (an instance of (Self basic-unit))))))

; A sequence has at least two elements (instances of whatever the basic-unit
; class is). More elements can be added to the chain by appending


; ########## Append ##########

(Append has
        (superclasses (Create))
        (required-slot (object destination result))
        (primary-slot ())
        (secondary-slot ())
        (cmap-correspondence ())
        (test-case ()))

(every Append has
       (object ((an instance of (the basic-unit of (the destination of Self)))))
       (destination ((a Sequence)))
       (result ((a Sequence with
                   (the-seq (((the the-seq of (the destination of Self)))
                               append
                              (:seq (the object of Self))))))))


; ########## Gene-Coding-Regin ##########

(Gene-Coding-Region has
         (superclasses (Nucleic-Acid))
         (required-slot ())
         (primary-slot ())
         (secondary-slot ())
         (cmap-correspondence ())
         (test-case ()))

(every Gene-Coding-Region has
       (has-part ((a Promoter)
                  (a Terminator))))


; ########## Operon ##########

(Operon has
         (superclasses (Gene-Coding-Region))
         (required-slot ())
         (primary-slot ())
         (secondary-slot ())
         (cmap-correspondence ())
         (test-case ()))

(every Operon has
   (has-part 
      ((a Operon-Coding-Region with
         (location 
            ((a Place with
                (is-between ((:args (the Promoter has-part of Self)
                                    (the Terminator has-part of Self)))))))))))


; ########## Promoter ##########

(Promoter has
         (superclasses (Regulatory-Region))
         (required-slot ())
         (primary-slot ())
         (secondary-slot ())
         (cmap-correspondence ())
         (test-case ()))

(every Promoter has
       (views ((a View with
                     (as ((a Sequence with
                             (basic-unit (Deoxyribonucleotide)))))))))


; ########## Terminator ##########

(Terminator has
         (superclasses (Regulatory-Region))
         (required-slot ())
         (primary-slot ())
         (secondary-slot ())
         (cmap-correspondence ())
         (test-case ()))

(every Terminator has
       (views ((a View with
                     (as ((a Sequence with
                             (basic-unit (Deoxyribonucleotide)))))))))


; ########## Operon-Coding-Region ##########

(Operon-Coding-Region has
         (superclasses (Gene-Coding-Region))
         (required-slot ())
         (primary-slot ())
         (secondary-slot ())
         (cmap-correspondence ())
         (test-case ()))

(every Operon-Coding-Region has
       (views ((a View with
                     (as ((a Sequence with
                             (basic-unit (Deoxyribonucleotide))))))))
       (has-part ((at-least 2 Gene))))


; ########## Bacterial-RNA-Transcription ##########

; Here is the transcription scenario itself. There are some not-KM
; elements in here. Also, slots that begin with "the-" are merely
; shorthand used locally. For example, by using a slot "the-DNA"
; whose value is "((the DNA is-part-of* of (the object of Self)))"
; I can refer to the DNA as simply "(the the-DNA of Self)".

; This encoding of the scenario simplifies the transcription by
; assuming that the polymerase unbonds one pair of deoxyribonuc's,
; then transcribes one of them, then bonds them again, instead of
; unzipping some distance downstream.

(Bacterial-RNA-Transcription has
        (superclasses    (RNA-Transcription))
        (required-slot   (object result source destination instrument))
        (primary-slot    ())
        (cmap-correspondence ()))

(every Bacterial-RNA-Transcription has
       (object ((a Operon-Coding-Region)))
       (the-DNA ((the DNA is-part-of* of (the object of Self))))
       (result ((a RNA-Transcript)))
       (source ((the Promoter has-part of (the object of Self))))
       (destination ((the Terminator has-part of (the object of Self))))
       (instrument ((a RNA-Polymerase)))

       (pcs-list ((:triple (the RNA-Polymerase instrument of Self)
                           agent-of
                           (a Find-Promoter with 
                              (object ((the source of Self)))))
                  (:triple (the RNA-Polymerase instrument of Self)
                           object-of
                           (a Be-Attached-To with
                              (destination (the the-DNA of Self))
                              (intensity (*strong))))))


				; The expression (theN N of ...) refers to the Nth element in the 
				; sequence (= Nth iteration of the loop) that the Operon-Coding-Region 
				; inherits as a has-part by being modeled as a Sequence (with a View).

       (the-Next-S1-Deoxyribonucleotide ( ; <===
				 (theN N of ; <===
				       (the the-seq of ; <===
					  (the Operon-Coding-Region has-part* of ; <===
					       (the DNA-Strand called "S1" has-part of ; <===
						  the the-DNA of Self)))))) ; <===
       (the-Next-S2-Deoxyribonucleotide ( ; <===
				 (theN N of ; <===
				       (the the-seq of ; <===
					  (the Operon-Coding-Region has-part* of ; <===
					       (the DNA-Strand called "S2" has-part of ; <===
						  the the-DNA of Self)))))) ; <===

       (sub-steps

        ;; loop until the location of the RNA-Polymerase instrument is
        ;; the location of the Terminator

        ((a step called "Unzip-DNA" with
	  (event-to-do ((the-class Unbond with
			       (object ((the the-Next-S1-Deoxyribonucleotide of Self)
				      (the the-Next-S2-Deoxyribonucleotide of Self)))
			       (agent ((the RNA-Polymerase instrument of Self))))))
	  (next-step (((the sub-steps of Self) called "Move-to-DNA"))))

         (a step called "Move-To-DNA" with
	  (event-to-do ((the-class Move with
			       (object ((a Ribonucleotide)))
			       (destination ((the the-Next-S1-Deoxyribonucleotide of Self))))))
	  (next-step (((the sub-steps of Self) called "Ribonucleotide-Bond"))))
         
         (a step called "Ribonucleotide-Bond" with
	  (event-to-do ((the-class Hydrogen-Bond with
			       (object ((the Ribonucleotide object of
					 ((the Move subevent of Self) called "Move-To-DNA"))
				      (the the-Next-S1-Deoxyribonucleotide of Self))))))
	  (next-step (((the Append sub-steps of Self)))))
         
         (a step with
	  (event-to-do ((the-class Append with
			       (object (
				      (the Ribonucleotide object of
					 ((the Move subevent of Self) called "Move-To-DNA"))))
			       (destination ((the RNA-Transcript result of Self))) ; <===
			       (result ((the RNA-Transcript result of Self)))))) ; <===
	  (next-steps (((the sub-steps of Self) called "Release-Ribonucleotide"))))

         (a step called "Release-Ribonucleotide" with
	  (event-to-do ((the-class Unbond with
			       (object (
				      (the Ribonucleotide object of
					 ((the Move subevent of Self) called "Move-To-DNA"))
				      (the the-Next-S1-Deoxyribonucleotide of Self))))))
	  (next-step (((the sub-steps of Self) called "Move-Downstream"))))

         (a step called "Move-Downstream" with
	  (event-to-do ((the-class Move with
			       (object ((the RNA-Polymerase instrument of Self)))
			       (direction (*downstream))
			       (away-from ((the source of Self)))
			       (toward ((the destination of Self))))))
	  (next-step (((the sub-steps of Self) called "Zip-DNA"))))

         (a step called "Zip-DNA" with
	  (event-to-do ((the-class Hydrogen-Bond with
			       (object ((the the-Next-S1-Deoxyribonucleotide of Self)
				      (the the-Next-S2-Deoxyribonucleotide of Self)))
			       (agent ((the RNA-Polymerase instrument of Self))))))
	  (test ('((the N of Self) = 10)))
            (next-step ((:args t ((the sub-steps of Self) called "Release-Sigma-Factor"))
                        (:args NIL ((the sub-steps of Self) called "Unzip-DNA")))))

		       ; if N = 10 do this Detach (it's only done once)

        (a step called "Release-Sigma-Factor" with
	 (event-to-do ((the-class Detach with
			      (object ((a Sigma-Factor)))	; there should be only one
			      (source ((the RNA-Polymerase instrument of Self))))))
	 (next-step (((the sub-steps of Self) called "Release-RNA-Polymerase"))))

        (a step called "Release-RNA-Polymerase" with
	 (event-to-do ((the-class Detach with
			      (object ((the RNA-Polymerase instrument of Self)))
			      (source ((the the-DNA of Self))))))
	 (next-step (((the sub-steps of Self) called "Release-RNA-Transcript"))))

        (a step called "Release-RNA-Transcript" with
	 (event-to-do ((the-class Detach with
			      (object ((the RNA-Transcript result of Self)))
			      (source ((the RNA-Polymerase instrument of Self))))))))))


; ########## Find-Promoter ##########

(Find-Promoter has
        (required-slot   (agent object))
        (primary-slot    ())
        (cmap-correspondence ()))


(every Find-Promoter has
       (agent ((a RNA-Polymerase)))
       (object ((a Promoter)))
       (the-DNA ((the DNA is-part-of* of (the Promoter object of Self))))

       (sub-steps ((a step called "Move-To-DNA" with
		  (event-to-do ((the-class Move with
				       (object ((the RNA-Polymerase agent of Self)))
				       (destination ((the the-DNA of Self))))))
		  (next-step ((the Make-Contact sub-steps of self))))
                  (a step with
		 (event-to-do ((the-class Make-Contact with
				      (object ((the RNA-Polymerase agent of Self)
					     (the the-DNA of Self))))))
		 (next-step ((the Attach sub-steps of Self))))
                  (a step with
		 (event-to-do ((the-class Attach with
				      (object ((the RNA-Polymerase agent of Self)))
				      (destination ((the the-DNA of Self)))
				      (intensity (*weak)))))
		 (next-step ((the Move sub-steps of Self
			        called "Move-Along-DNA"))))
                  (a step called "Move-Along-DNA" with
		 (event-to-do ((the-class Move with
				      (object ((the RNA-Polymerase agent of Self)))
				      (path ((the the-DNA of Self)))
				      (destination ((the Promoter object of Self)))
				      (rate (*quickly)))))
		 (next-step ((the Recognize sub-steps of Self))))
                  (a step with
		 (event-to-do ((the-class Recognize with
				      (pcs-list
				       ((:triple 
				         (the agent of (the Recognize subevent of Self))
				         object-of
				         (a Be-Attached-To to with
					  (destination 
					   ((the RNA-Polymerase agent of Self)))))))
				      (object ((the Promoter object of Self)))
				      (agent ((a Sigma-Factor)))
				      (del-list
				       ((:triple 
				         (the Be-Attached-To object-of of
					    (the RNA-Polymerase agent of Self))
				         intensity
				         (*weak))))
				      (add-list
				       ((:triple 
				         (the Be-Attached-To object-of of
					    (the RNA-Polymerase agent of Self))
				         intensity
				         (*strong)))))))))))