bug fixed

Author: mossbiscuits

model.csl

@@ -1,4 +1,4 @@
-CodY=20
+gbg = 50
 
 // get the probability by other means
 // here we just want a binary property

model.ragtimer

@@ -1,15 +1,11 @@
-codY    flache  SigD_hag    hag CodY_flache CodY_hag    CodY    SigD    Hag
-1   1   1   1   1   1   10  10  10
--1  -1  -1  -1  -1  -1  20  -1  -1
-R1  codY    >   codY    CodY    0.1
-R2  CodY    >   0   0.0002
-R3  flache  >   flache  SigD    1.0
-R4  SigD    >   0   0.0002
-R5  SigD_hag    >   SigD    hag Hag 1.0
-R6  Hag >   0   0.0002
-R7  SigD    hag >   SigD_hag    0.01
-R8  SigD_hag    >   SigD    hag 0.1
-R9  CodY    flache  >   CodY_flache 0.02
-R10 CodY_flache >   CodY    flache  0.1
-R11 CodY    hag >   CodY_hag    0.01
-R12 CodY_hag    >   CodY    hag 0.1
+r	l	rl	g	ga	gbg	gd
+50	2	0	50	0	0	0
+-1	-1	-1	-1	-1	50	-1
+r1	0	>	r	0.0038
+r2	r	>	0	0.0004
+r3	r	l	>	rl	l	0.042
+r4	rl	>	r	0.010
+r5	rl	g	>	ga	gbg	0.011
+r6	ga	>	gd	0.100
+r7	gbg	gd	>	g	1050
+r8	0	>	rl	3.21

model.sm

@@ -1,51 +1,31 @@
 ctmc
 
-const int var_bound = 20;
-
-const double k1  = 0.1;
-const double k2  = 0.0002;
-const double k3  = 1;
-const double k4  = 0.0002;
-const double k5  = 1;
-const double k6  = 0.0002;
-const double k7  = 0.01;
-const double k8  = 0.1;
-const double k9  = 0.02;
-const double k10 = 0.1;
-const double k11 = 0.01;
-const double k12 = 0.1;
-
-module motility
-
-codY : [0..var_bound] init 1;
-flache : [0..var_bound] init 1;
-SigD_hag : [0..var_bound] init 1;
-hag : [0..var_bound] init 1;
-CodY_flache : [0..var_bound] init 1;
-CodY_hag : [0..var_bound] init 1;
-CodY : [0..var_bound] init 10;
-SigD : [0..var_bound] init 10;
-Hag : [0..var_bound] init 10;
-
-[R1] codY>0 & CodY<var_bound -> (k1*codY) : (CodY'=CodY+1);
-[R2] CodY>0  -> (k2*CodY) : (CodY'=CodY-1);
-[R3] flache>0 & SigD<var_bound -> (k3*flache) : (SigD'=SigD+1);
-[R4] SigD>0 -> (k4*SigD) : (SigD'=SigD-1);
-[R5] SigD_hag>0 & SigD<var_bound & hag<var_bound & Hag<var_bound-> (k5*SigD_hag) : (SigD_hag'=SigD_hag-1)&(SigD'=SigD+1)&(hag'=hag+1)&(Hag'=Hag+1);
-[R6] Hag>0 -> (k6*Hag) : (Hag'=Hag-1);
-[R7] SigD>0 & hag>0 & SigD_hag<var_bound-> (k7*SigD*hag) : (SigD'=SigD-1)&(hag'=hag-1)&(SigD_hag'=SigD_hag+1);
-[R8] SigD_hag>0 & SigD<var_bound & hag<var_bound -> (k8*SigD_hag) : (SigD_hag'=SigD_hag-1)&(SigD'=SigD+1)&(hag'=hag+1);
-[R9] CodY>0 & flache>0 & CodY_flache<var_bound -> (k9*CodY*flache) : (CodY'=CodY-1)&(flache'=flache-1)&(CodY_flache'=CodY_flache+1);
-[R10] CodY_flache>0 & CodY<var_bound & flache<var_bound -> (k10*CodY_flache) : (CodY_flache'=CodY_flache-1)& (CodY'=CodY+1) & (flache'=flache+1);
-[R11] CodY>0 & hag>0 & CodY_hag<var_bound -> (k11*CodY*hag) : (CodY'=CodY-1)&(hag'=hag-1)&(CodY_hag'=CodY_hag+1);
-[R12] CodY_hag>0 & CodY<var_bound & hag<var_bound -> (k12*CodY_hag) : (CodY_hag'=CodY_hag-1)& (CodY'=CodY+1) & (hag'=hag+1);
-
-
-
-endmodule
-
-
-
-
-
-
+const double k1 = 0.0038; 
+const double k2 = 0.0004; 
+const double k3 = 0.042;
+const double k4 = 0.01;
+const double k5 = 0.011;
+const double k6 = 0.1;
+const double k7 = 1050;
+const double k8 = 3.21;
+
+module cycle
+
+	r   : int init 50;
+	l   : int init 2;
+	rl  : int init 0;
+	g   : int init 50;
+	ga  : int init 0;
+	gbg : int init 0;
+	gd  : int init 0;
+
+	[r1] true         -> k1            : (r' = r+1);
+	[r2] r>0          -> k2 * r        : (r' = r-1);
+	[r3] r>0 & l>0    -> k3 * l * r    : (r' = r-1) & (rl' = rl+1);
+	[r4] rl>0         -> k4 * rl       : (rl' = rl-1) & (r' = r+1);
+	[r5] rl>0 & g>0   -> k5 * rl * g   : (rl' = rl-1) & (g' = g-1)   & (ga' = ga+1) & (gbg' = gbg+1);
+	[r6] ga>0         -> k6 * ga       : (ga' = ga-1) & (gd' = gd+1);
+	[r7] gbg>0 & gd>0 -> k7 * gbg * gd : (gbg' = gbg-1) & (gd' = gd-1) & (g' = g+1);
+	[r8] true         -> k8            : (rl' = rl+1);
+
+endmodule

motility.csl

@@ -0,0 +1,6 @@
+CodY=20
+
+// get the probability by other means
+// here we just want a binary property
+// which we desire to reach 
+// (i.e. a bool that describes the failure state)

motility.ragtimer

@@ -0,0 +1,15 @@
+codY    flache  SigD_hag    hag CodY_flache CodY_hag    CodY    SigD    Hag
+1   1   1   1   1   1   10  10  10
+-1  -1  -1  -1  -1  -1  20  -1  -1
+r1  codY    >   codY    CodY    0.1
+r2  CodY    >   0   0.0002
+r3  flache  >   flache  SigD    1.0
+r4  SigD    >   0   0.0002
+r5  SigD_hag    >   SigD    hag Hag 1.0
+r6  Hag >   0   0.0002
+r7  SigD    hag >   SigD_hag    0.01
+r8  SigD_hag    >   SigD    hag 0.1
+r9  CodY    flache  >   CodY_flache 0.02
+r10 CodY_flache >   CodY    flache  0.1
+r11 CodY    hag >   CodY_hag    0.01
+r12 CodY_hag    >   CodY    hag 0.1

motility.sm

@@ -0,0 +1,51 @@
+ctmc
+
+const int var_bound = 20;
+
+const double k1  = 0.1;
+const double k2  = 0.0002;
+const double k3  = 1;
+const double k4  = 0.0002;
+const double k5  = 1;
+const double k6  = 0.0002;
+const double k7  = 0.01;
+const double k8  = 0.1;
+const double k9  = 0.02;
+const double k10 = 0.1;
+const double k11 = 0.01;
+const double k12 = 0.1;
+
+module motility
+
+codY : [0..var_bound] init 1;
+flache : [0..var_bound] init 1;
+SigD_hag : [0..var_bound] init 1;
+hag : [0..var_bound] init 1;
+CodY_flache : [0..var_bound] init 1;
+CodY_hag : [0..var_bound] init 1;
+CodY : [0..var_bound] init 10;
+SigD : [0..var_bound] init 10;
+Hag : [0..var_bound] init 10;
+
+[r1] codY>0 & CodY<var_bound -> (k1*codY) : (CodY'=CodY+1);
+[r2] CodY>0  -> (k2*CodY) : (CodY'=CodY-1);
+[r3] flache>0 & SigD<var_bound -> (k3*flache) : (SigD'=SigD+1);
+[r4] SigD>0 -> (k4*SigD) : (SigD'=SigD-1);
+[r5] SigD_hag>0 & SigD<var_bound & hag<var_bound & Hag<var_bound-> (k5*SigD_hag) : (SigD_hag'=SigD_hag-1)&(SigD'=SigD+1)&(hag'=hag+1)&(Hag'=Hag+1);
+[r6] Hag>0 -> (k6*Hag) : (Hag'=Hag-1);
+[r7] SigD>0 & hag>0 & SigD_hag<var_bound-> (k7*SigD*hag) : (SigD'=SigD-1)&(hag'=hag-1)&(SigD_hag'=SigD_hag+1);
+[r8] SigD_hag>0 & SigD<var_bound & hag<var_bound -> (k8*SigD_hag) : (SigD_hag'=SigD_hag-1)&(SigD'=SigD+1)&(hag'=hag+1);
+[r9] CodY>0 & flache>0 & CodY_flache<var_bound -> (k9*CodY*flache) : (CodY'=CodY-1)&(flache'=flache-1)&(CodY_flache'=CodY_flache+1);
+[r10] CodY_flache>0 & CodY<var_bound & flache<var_bound -> (k10*CodY_flache) : (CodY_flache'=CodY_flache-1)& (CodY'=CodY+1) & (flache'=flache+1);
+[r11] CodY>0 & hag>0 & CodY_hag<var_bound -> (k11*CodY*hag) : (CodY'=CodY-1)&(hag'=hag-1)&(CodY_hag'=CodY_hag+1);
+[r12] CodY_hag>0 & CodY<var_bound & hag<var_bound -> (k12*CodY_hag) : (CodY_hag'=CodY_hag-1)& (CodY'=CodY+1) & (hag'=hag+1);
+
+
+
+endmodule
+
+
+
+
+
+

new_rag_backup/depgraph.py

@@ -199,7 +199,8 @@ def buildGraph(recdepth, reactions, chemicals, initials, targets, parent, add_or
 		# Update required number of executions
 		reqExec = 0
 		for d in range(numChems):
-			print("DELTATARGET", d, "= ", deltaTarget[d])
+			if printing:
+				print("DELTATARGET", d, "= ", deltaTarget[d])
 			if deltaTarget[d] > 0:
 				for p in range(len(r.products)):
 					if chemicals[d] in r.products[p]:

new_rag_backup/reactions_v5.py

@@ -1293,7 +1293,7 @@ def randTest(runswanted, reactions1, prefix, prefix_index, loose=False, printing
                 reaction_exec_count[int(line[25])-1] += 1
         if line[0] == "t":
             if trace in tracelist:
-                print(f"***Run {count} was a duplicate and has been thrown out of {Options.traceList}")
+                print(f"***Run {count+1} was a duplicate and has been thrown out of {Options.traceList}")
             else:
                 tracelist.append(trace)
                 # tracelistfile.write(f"{prefixTrans}\t")    
@@ -1364,12 +1364,14 @@ def randTest(runswanted, reactions1, prefix, prefix_index, loose=False, printing
                         iterations[x].append(int(line[14]))
 
     if printing:
+        print(50*"-")
         print("\n\nAverage number of transitions in a trace is:", Totaltran/int(runswanted))
         print("The biggest number of transitions recorded in a trace is:", max(Totaltranlist))
         print("The smallest number of transitions recorded in a trace is:", min(Totaltranlist))
         print("\nAverage number of iterations needed in a trace is:", Totaliter/int(runswanted))
         print("The biggest number of iterations needed for a trace was:", max(Totaliterlist))
         print("The smallest number of iterations needed for a trace was:", min(Totaliterlist))
+        print(50*"-")
 
         for x in range(numOfReactions):
             print("\n\nAverage number of reaction", x+1, "executions in a trace is:", Total[x]/int(runswanted))