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Author: eukaryo

directpath-comparison-experiment.py

@@ -1,5 +1,5 @@
 
-import re
+import re, random
 from czno import getMinBarrierPathDijkstra, basePairList, energyOfStr
 from previous_direct_methods import MorganHiggs1998GreedyDirect, Voss2004GreedyDirect
 
@@ -19,8 +19,8 @@ def InterpretDatasetFile(filename):
             if re.fullmatch(r"^[ACGU]+$", line) is not None:
                 if len(structures) >= 1:
                     dataset.append([seq, structures])
-                    seq = line
-                    structures = []
+                seq = line
+                structures = []
             elif re.fullmatch(r"^[(.)]+$", line) is not None:
                 structures.append(line)
             else:
@@ -40,15 +40,15 @@ def DirectPathSingleExperiment(sequence, structure1, structure2):
 
     pathway1 = getMinBarrierPathDijkstra(sequence, structure1, structure2)
     result.append(PathwayToBarrier(sequence, pathway1))
-    
+
     pathway2 = MorganHiggs1998GreedyDirect(sequence, structure1, structure2)
     result.append(PathwayToBarrier(sequence, pathway2))
 
     pathway3 = Voss2004GreedyDirect(sequence, structure1, structure2)
     result.append(PathwayToBarrier(sequence, pathway3))
 
     best_value4 = float("inf")
-    for i in range(1000):
+    for i in range(10):
         pathway4 = Voss2004GreedyDirect(sequence, structure1, structure2, 10, i)
         best_value4 = min(best_value4, PathwayToBarrier(sequence, pathway4))
     result.append(best_value4)
@@ -58,11 +58,17 @@ def DirectPathSingleExperiment(sequence, structure1, structure2):
 
 if __name__ == '__main__':
     dataset = InterpretDatasetFile("s151-localminima-dataset.txt")
+
     for data in dataset:
-        for i in range(len(data[1])):
-            for j in range(i+1, len(data[1])):
-                hamdist = HammingDistance(data[1][i], data[1][j])
-                if 5 <= hamdist and hamdist <= 20:
-                    result = DirectPathSingleExperiment(data[0], data[1][i], data[1][j])
+        starts = random.sample(data[1], min(1, len(data[1])))
+        for i in range(len(starts)):
+            g1 = list(set(data[1]) - set(starts)) + starts[i+1:]
+            g2 = [HammingDistance(starts[i],g1[x]) for x in range(len(g1))]
+            g3 = [g1[x] for x in range(len(g1)) if 5 <= g2[x] and g2[x] <= 15]
+            goals = random.sample(g3, min(1, len(g3)))
+            for j in range(len(goals)):
+                hamdist = HammingDistance(starts[i], goals[j])
+                if 5 <= hamdist and hamdist <= 15:
+                    result = DirectPathSingleExperiment(data[0], starts[i], goals[j])
                     print(str(len(data[0]))+" "+str(hamdist)+" "+" ".join([str(x) for x in result]))
 

previous_direct_methods.py

@@ -47,4 +47,5 @@ def Voss2004GreedyDirect(sequence, structure1, structure2, k = 1, seed = 12345):
         PossibleNextStateAndEnergy = [(energyOfStr(sequence, x), x) for x in PossibleNextState]
         NextState = random.choice(sorted(PossibleNextStateAndEnergy)[0:k])[1]
         answer.append(NextState)
+        A = set(basePairList(NextState))
     return answer