lukasplevac/POC1-SIMD-DNA
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Fixed chain unwrap only when free base and replace

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This commit is contained in:
Lukáš Plevač 2023-11-21 20:51:51 +01:00
parent d232355349
commit 9d8ffb7ee6
3 changed files with 23 additions and 14 deletions
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16
codes/inc.asm
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@ -1,14 +1,10 @@
#
# 1 2 3 4 5 6 7 8
# A B C D E F G H
#
define: define:
0 [ABC][DE] 0 [ABC][DE]
1 [AB][CDE] 1 [AB][CDE]
data: data:
1011{FT} # {FT} is TUE BINDING hold # {F} is TUE BINDING hold
1011{F}
instructions: instructions:
# mark last if is 1 if exist and replace this and open base C # 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 # 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 # remove all markers
{DEFTG} {DEABCH} {DEFG} {DEABCH}
# set 1 end this unvrap last 0 # set 1 end this unvrap last 0
{C*D*E*} {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*} {B*C*D*}
# set 0 # set 0
{ABC} {DE} {A*B*C*} {D*E*}
# remove last 0 # remove last 0
{ABC} {ABC}

17
src/SIMDDNA/register.py
View File

@ -61,6 +61,7 @@ class Register:
# --- # ---
# ||| # |||
# ---- R # ---- R
#
def removeReplaced(self): def removeReplaced(self):
while True: while True:
done = True done = True
@ -91,6 +92,7 @@ class Register:
# --- # ---
# #
# ---- R # ---- R
#
def removeUnbinded(self): def removeUnbinded(self):
while True: while True:
done = 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): if not(self.mol.getBase(chainIB, pos) == molecule.nothing and self.mol.getBase(chainIA, pos) == molecule.nothing):
bindScore -= 1 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(max(chainIA, chainIB))
self.mol.removeChain(min(chainIA, chainIB)) self.mol.removeChain(min(chainIA, chainIB))
done = False done = False
@ -123,7 +126,7 @@ class Register:
done = True done = True
# for all chains in register # for all chains in register
# primary detach newer # 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 # for all bases in molecule
bindScore = 0 bindScore = 0
finalBindScore = 0 finalBindScore = 0
@ -143,6 +146,16 @@ class Register:
if done: if done:
break 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 # try bind mol to all possible bindings
# Added all imol bindings as new chains # Added all imol bindings as new chains