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Added support for overhangs in molecule encoder

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This commit is contained in:
Lukáš Plevač 2023-11-28 13:15:51 +01:00
parent 06027bf7bd
commit e17800f1d4
1 changed files with 48 additions and 4 deletions
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52
src/SIMDDNA/molecule.py
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@ -332,12 +332,11 @@ def parse(notationStr):
# Encode molecule to ASCII reprezentation
# @param mol moleculte to encode
# @retun STR of ascii reprezentation
# @todo support for overhangs
#
def encode(mol):
outstr = ""
lastClose = ""
lastChain = -1
lastChain = None
lastBounded = None
for basePos in range(len(mol)):
@ -345,17 +344,62 @@ def encode(mol):
for chainID in range(1, mol.chainsCount()):
if isComplementary(mol.getBase(chainID, basePos), mol.getBase(0, basePos)):
if not lastBounded or lastBounded is None or lastChain != chainID:
# read post overhangs
postoverhang = ""
if lastChain is not None:
i = basePos
while i < len(mol):
if mol.getBase(lastChain, i) != nothing:
postoverhang += mol.getBase(lastChain, i)
i += 1
continue
break
if len(postoverhang) > 0:
postoverhang = f".<{postoverhang}>"
# read pre overhangs
overhang = ""
i = basePos
while i > 0:
i -= 1
if mol.getBase(chainID, i) != nothing:
overhang += mol.getBase(chainID, i)
continue
break
if len(overhang) > 0:
overhang = f"<{overhang[::-1]}>."
lastBounded = True
lastChain = chainID
outstr += lastClose + "["
outstr += lastClose + postoverhang + overhang + "["
lastClose = "]"
bounded = True
break
if (not bounded and lastBounded) or lastBounded is None:
# read post overhangs
overhang = ""
if lastChain is not None:
i = basePos
while i < len(mol):
if mol.getBase(lastChain, i) != nothing:
overhang += mol.getBase(lastChain, i)
i += 1
continue
break
if len(overhang) > 0:
overhang = f".<{overhang}>"
lastBounded = False
outstr += lastClose + "{"
lastChain = None
outstr += lastClose + overhang + "{"
lastClose = "}"
if mol.getBase(0, basePos) == nothing: