First working

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "svg.preview.background": "custom"
+}

exmaple.asm

@@ -1,16 +0,0 @@
-//
-// Example NOT program
-//
-
-data:
-    //   ->
-    //   ||
-    // ---- 
-    <AB>[CD]
-
-instructions:
-    // -----
-    // -----
-    {A*B*C*D*E*}; <ABCDE>
-    // --
-    {A*B*}

rule110.asm

@@ -0,0 +1,14 @@
+define:
+    0 [ABC][DE]
+    1 {A}[BCDE]
+
+data:
+    1001111010
+
+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
+    {DEAF}          # remove mark 01
+    {B*C*D*E*}      # write 1

src/SIMDDNA/ascii.py

@@ -8,7 +8,9 @@ def toBindingLen(chainID, curPOS, molecule):
     for basePos in range(curPOS, len(molecule)):
         if molecule.getBase(chainID, basePos) != nothing:
             if isComplementary(molecule.getBase(chainID, basePos), molecule.getBase(0, basePos)):
-                return toBLen
+                #if only this binded here
+                if molecule.bindedCountAt(basePos) == 1:
+                    return toBLen
             
         toBLen += 1
 
@@ -18,7 +20,8 @@ def toBindingLen(chainID, curPOS, molecule):
     for basePos in range(curPOS, -1, -1):
         if molecule.getBase(chainID, basePos) != nothing:
             if isComplementary(molecule.getBase(chainID, basePos), molecule.getBase(0, basePos)):
-                return toBLen
+                if molecule.bindedCountAt(basePos) == 1:
+                    return toBLen
             
         toBLen -= 1
 
@@ -50,10 +53,8 @@ def showMolecule(molecule, spacing = ""):
 
             if lenToBinding is None:
                 print(f"Warning: no binded for chain {chainID}")
+
             elif lenToBinding == 0:
-                if bounded:
-                    print(f"Warning: two or more posible bindings on base {basePos}")
-                    
                 bounded     = True
                     
                 Invlines[1] += "|"

src/SIMDDNA/molecule.py

@@ -84,6 +84,14 @@ class Molecule:
     def getBase(self, chainID, baseID):
         return self.chains[chainID][baseID]
     
+    def bindedCountAt(self, baseID):
+        binding = 0
+        for chain in self.chains:
+            if isComplementary(self.chains[0][baseID], chain[baseID]):
+                binding += 1
+
+        return binding
+    
     def charAddBase(self, chainID, char, isBackward = False):
         if isBackward:
             if len(self.chains[chainID]) == 0 or self.getBase(chainID, 0) != nothing:

src/SIMDDNA/register.py

@@ -9,42 +9,104 @@ class Register:
         self.mol = mol
 
     def inscription(self, IMols):
-        for _ in range(1):
+        for mol in IMols:
-            used = False
+            self.doAllBinding(mol)
-            for imol in IMols:
+            self.removeUnbinded()
-                bindIndex, unbindChain = self.getNearestBinding(imol)
+            self.removeReplaced()
+            self.removeUnstable()
+        
+    def removeReplaced(self):
+        while True:
+            done = True
+            # for all chains in register
+            # primary detach newer 
+            for chainI in range(self.mol.chainsCount() - 1, 0, -1):
+                # for all bases in molecule
+                binded = False
+                for pos in range(len(self.mol)):
+                    if molecule.isComplementary(self.mol.getBase(chainI, pos), self.mol.getBase(0, pos)) and self.mol.bindedCountAt(pos) == 1: # binde minimaly once
 
-                if unbindChain is not None:
+                        binded = True
-                    used = True
+                        break
-                    self.mol.removeChain(unbindChain)
 
-                if bindIndex is not None:
+                if not(binded):
-                    used = True
+                    self.mol.removeChain(chainI)
-                    chain = self.mol.addChain()
+                    done = False
-                    self.mol.padChain(chain, bindIndex)
+                    break
-                    self.mol.chain2chain(chain, imol.getChain(0))
-                    self.mol.endPad()
 
-            if not used:
+            
+            if done:
                 break
 
-    def getNearestBinding(self, imol):
+    def removeUnbinded(self):
+        while True:
+            done = True
+            # for all chains in register
+            for chainIA in range(1, self.mol.chainsCount()):
+                for chainIB in range(1, self.mol.chainsCount()):
+                    # for all bases in molecule
+                    bindScore = 0
+                    for pos in range(len(self.mol)):
+                        if not(molecule.isComplementary(self.mol.getBase(chainIA, pos), self.mol.getBase(chainIB, pos))):
+                            if not(self.mol.getBase(chainIB, pos) == molecule.nothing and self.mol.getBase(chainIA, pos) == molecule.nothing):
+                                bindScore -= 1
+
+                    if bindScore == 0:
+                        self.mol.removeChain(max(chainIA, chainIB))
+                        self.mol.removeChain(min(chainIA, chainIB))
+                        done = False
+                        break
+
+                if not(done):
+                    break
+            
+            if done:
+                break
+
+    def removeUnstable(self):
+        while True:
+            done = True
+            # for all chains in register
+            # primary detach newer 
+            for chainI in range(self.mol.chainsCount() - 1, 0, -1):
+                # for all bases in molecule
+                bindScore = 0
+                for pos in range(len(self.mol)):
+                    if molecule.isComplementary(self.mol.getBase(chainI, pos), self.mol.getBase(0, pos)) and self.mol.bindedCountAt(pos) == 1: # binde minimaly once
+                        bindScore += 1
+
+                if bindScore < 2:
+                    self.mol.removeChain(chainI)
+                    done = False
+                    break
+
+            
+            if done:
+                break
+
+    def doAllBinding(self, imol):
+        # for all chains in register
         for chainI in range(self.mol.chainsCount()):
+            # for all possible aligment in molecule
             for aligment in range(len(self.mol)):
+                # calculate align score for all possible aligments
                 align_score = 0
                 for baseID in range(min(len(imol), len(self.mol) - aligment)):
                     if molecule.isComplementary(self.mol.getBase(chainI, baseID + aligment), imol.getBase(0, baseID)):
                         align_score += 1
-                    elif align_score > 0:
+                    elif align_score < 2:
+                        align_score = 0
+                    
+                    # this will definitly bind
+                    if align_score >= 2:
                         break
 
                 # ok now finded binding
                 if align_score >= 2:
-                    if chainI == 0:
+                    chain = self.mol.addChain()
-                        return aligment, None
+                    self.mol.padChain(chain, aligment)
-
+                    self.mol.chain2chain(chain, imol.getChain(0))
-
+                    self.mol.endPad()
-        return None, None
     
     def show(self):
         return self.mol.rawPrint()
@@ -58,8 +120,11 @@ print("Before")
 print("---------------------------------\n")
 
 # create register
+num1 = "{A}[BCDE]"
+num0 = "[ABC][DE]"
+
 myreg = Register(molecule.parse(
-    "{EEEBCDEEEBCD}"
+    num1 + num0 + num0 + num1 + num1 + num1 + num1 + num0 + num1 + num0
 ))
 
 myreg.asciiShow()
@@ -76,11 +141,40 @@ print("---------------------------------\n")
 
 # do instruction
 # remove
+
 myreg.inscription([
-    molecule.parse("{A*B*C*D*A*}")
+    molecule.parse("{D*E*A*F*}")
 ])
 
+myreg.asciiShow("")
 
-myreg.show()
+myreg.inscription([
+    molecule.parse("{D*E*A*B*C*G*}")
+])
 
-myreg.asciiShow()
+myreg.asciiShow("")
+
+myreg.inscription([
+    molecule.parse("{DEABCG}")
+])
+
+myreg.asciiShow("")
+
+myreg.inscription([
+    molecule.parse("{A*B*C*}"),
+    molecule.parse("{D*E*}")
+])
+
+myreg.asciiShow("")
+
+myreg.inscription([
+    molecule.parse("{DEAF}")
+])
+
+myreg.asciiShow("")
+
+myreg.inscription([
+    molecule.parse("{B*C*D*E*}")
+])
+
+myreg.asciiShow("")

src/SIMDDNA/svg.py

@@ -0,0 +1,42 @@
+import svgwrite
+
+# Vytvoření nového SVG dokumentu
+svg_document = svgwrite.Drawing('complementary_strands.svg', profile='tiny', size=(400, 60))
+
+# Nukleotidy pro první vlákno
+strand1 = "ATGCTAAGCTAGCTA"
+
+# Funkce pro získání komplementárního nukleotidu
+def get_complementary_base(base):
+    if base == 'A':
+        return 'T'
+    elif base == 'T':
+        return 'A'
+    elif base == 'C':
+        return 'G'
+    elif base == 'G':
+        return 'C'
+    else:
+        return base
+
+# Nukleotidy pro druhé komplementární vlákno
+strand2 = ''.join([get_complementary_base(base) for base in strand1])
+
+# Barvy pro jednotlivé nukleotidy
+color_map = {'A': 'blue', 'T': 'red', 'C': 'green', 'G': 'yellow'}
+
+# Vykreslení prvního vlákna
+for i, base in enumerate(strand1):
+
+    baseSize = 30
+    
+    x1 = i  * baseSize
+    y1 = 10
+    x2 = x1 + baseSize
+    y2 = 10
+
+    svg_document.add(svgwrite.shapes.Line(start=(x1, y1), end=(x2, y2), stroke=color_map[base], stroke_width=2))
+    svg_document.add(svgwrite.text.Text(base, insert=(x1 + baseSize / 2 - 12 / 2, y1), font_size=12, fill=color_map[base]))
+
+# Uložení SVG dokumentu
+svg_document.save()