Fixed chain unwrap only when free base and replace

codes/inc.asm

@@ -1,14 +1,10 @@
-#
-# 1 2 3 4 5 6 7 8
-# A B C D E F G H
-#
-
 define:
     0 [ABC][DE]
     1 [AB][CDE]
 
 data:
-    1011{FT} # {FT} is TUE BINDING hold
+    # {F} is TUE BINDING hold
+    1011{F}
 
 instructions:
     # mark last if is 1 if exist and replace this and open base C
@@ -21,19 +17,19 @@ instructions:
     #
     # if next bit is 1 it again replace this and open base C this is chain reaction
     #
-    {D*E*F*T*G*}   {D*E*A*B*C*H*}
+    {D*E*F*G*}   {D*E*A*B*C*H*}
 
     # remove all markers
-    {DEFTG}        {DEABCH}
+    {DEFG}        {DEABCH}
 
     # set 1 end this unvrap last 0
     {C*D*E*}
 
-    # shift 1 end to center of register cell if possible to by eble of unvrap by 0
+    # shift 1 end to center of register cell if possible. This allow unvrap by 0
     {B*C*D*}
 
     # set 0
-    {ABC} {DE}
+    {A*B*C*} {D*E*}
 
     # remove last 0
     {ABC}

codes/rule110.asm

@@ -9,6 +9,6 @@ instructions:
     {D*E*A*F*}      # mark 01
     {D*E*A*B*C*G*}  # mark 11
     {DEABCG}        # remove mark 11
-    {A*B*C*}{D*E*}  # write 0
+    {A*B*C*} {D*E*} # write 0
     {DEAF}          # remove mark 01
     {B*C*D*E*}      # write 1

src/SIMDDNA/register.py

@@ -53,7 +53,7 @@ class Register:
             for mol in IMols:
                 # remove all unstable binded chains binded on 1 base or lower
                 self.removeUnstable()
-        
+
     ##
     # remove unbinded chains from register (because new imol have bind on more posisin on register that older)
     # --
@@ -61,6 +61,7 @@ class Register:
     # ---
     # |||
     # ---- R
+    #
     def removeReplaced(self):
         while True:
             done = True
@@ -91,6 +92,7 @@ class Register:
     # ---
     #
     # ---- R
+    #
     def removeUnbinded(self):
         while True:
             done = True
@@ -104,7 +106,8 @@ class Register:
                             if not(self.mol.getBase(chainIB, pos) == molecule.nothing and self.mol.getBase(chainIA, pos) == molecule.nothing):
                                 bindScore -= 1
 
-                    if bindScore == 0:
+                    # chack if strand have any free binding base to strap it
+                    if bindScore == 0 and self.haveChainFreeBaseFor(chainIA, chainIB) and self.haveChainFreeBaseFor(chainIB, chainIA):
                         self.mol.removeChain(max(chainIA, chainIB))
                         self.mol.removeChain(min(chainIA, chainIB))
                         done = False
@@ -123,7 +126,7 @@ class Register:
             done = True
             # for all chains in register
             # primary detach newer 
-            for chainI in range(self.mol.chainsCount() - 1, 0, -1):
+            for chainI in range(1, self.mol.chainsCount()):
                 # for all bases in molecule
                 bindScore = 0
                 finalBindScore = 0
@@ -143,6 +146,16 @@ class Register:
             if done:
                 break
 
+    def haveChainFreeBaseFor(self, chainA, chainB):
+        for baseID in range(len(self.mol)):
+            if molecule.isComplementary(self.mol.getBase(chainA, baseID), self.mol.getBase(chainB, baseID)):
+                if not molecule.isComplementary(self.mol.getBase(chainA, baseID), self.mol.getBase(0, baseID)):
+                    return True
+                elif self.mol.bindedCountAt(baseID) >= 2:
+                    return True
+                
+        return False
+
     ##
     # try bind mol to all possible bindings
     # Added all imol bindings as new chains