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Converted the dictionary corona to a class coronaDNA #54

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Converted the dictionary corona to a class coronaDNA #54

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4ac84b2
Update corona.py
Lajellu Mar 12, 2021
2641cf4
Create opt.py
Lajellu Mar 12, 2021
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96 changes: 51 additions & 45 deletions corona.py
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Expand Up @@ -12,8 +12,6 @@
# copy machine -- https://www.uniprot.org/uniprot/Q0ZJN1
# zhanglab breaks this down into many more proteins

corona = {}

# begin: 266 base pairs "untranslated"
# https://en.wikipedia.org/wiki/Five_prime_untranslated_region

Expand Down Expand Up @@ -43,47 +41,55 @@
# 16 = 2'-O-methyltransferase (2'-O-MT)
# https://en.wikipedia.org/wiki/MRNA_(nucleoside-2%27-O-)-methyltransferase

# in front "the untranslated leader sequence that ends with the Transcription Regulation Sequence"
corona['untranslated_region'] = cc[0:265]

corona['orf1a'] = translate(cc[266-1:13483], True)

# cc[266-1+4398*3:13468] = 'TTT_TTA_AAC' aka 'X_XXY_YYZ'
# https://en.wikipedia.org/wiki/Ribosomal_frameshift
# Programmed −1 Ribosomal Frameshifting
# TODO: add this to the translate function with automatic detection
corona['orf1b'] = translate(cc[13468-1:21555], False).strip("*") # chop off the stop, note this doesn't have a start

# exploit vector, this attaches to ACE2. also called "surface glycoprotein"
# https://www.ncbi.nlm.nih.gov/Structure/pdb/6VYB -- open state
# https://www.ncbi.nlm.nih.gov/Structure/pdb/6VXX -- closed state
# 1273 amino acids
# S1 = 14-685
# S2 = 686-1273
# S2' = 816-1273
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750777/
corona['spike_glycoprotein'] = translate(cc[21563-1:25384], True)

# Forms homotetrameric potassium sensitive ion channels (viroporin) and may modulate virus release.
corona['orf3a'] = translate(cc[25393-1:26220], True)

# these two things stick out, used in assembly aka they package the virus
corona['envelope_protein'] = translate(cc[26245-1:26472], True) # also known as small membrane
corona['membrane_glycoprotein'] = translate(cc[26523-1:27191], True)

corona['orf6'] = translate(cc[27202-1:27387], True)

corona['orf7a'] = translate(cc[27394-1:27759], True)
corona['orf7b'] = translate(cc[27756-1:27887], True) # is this one real?

corona['orf8'] = translate(cc[27894-1:28259], True)

# https://en.wikipedia.org/wiki/Capsid
# Packages the positive strand viral genome RNA into a helical ribonucleocapsid
# Includes the "internal" protein (from Coronavirus Pathogenesis)
# https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/human-coronavirus-oc43
corona['nucleocapsid_phosphoprotein'] = translate(cc[28274-1:29533], True)

# might be called the internal protein (Coronavirus Pathogenesis)
corona['orf10'] = translate(cc[29558-1:29674], True)
class coronaDNA:
def __init__(self):
# in front "the untranslated leader sequence that ends with the Transcription Regulation Sequence"
self.untranslated_region = cc[0:265]

self.orf1a = translate(cc[266-1:13483], True)

# cc[266-1+4398*3:13468] = 'TTT_TTA_AAC' aka 'X_XXY_YYZ'
# https://en.wikipedia.org/wiki/Ribosomal_frameshift
# Programmed −1 Ribosomal Frameshifting
# TODO: add this to the translate function with automatic detection
self.orf1b = translate(cc[13468-1:21555], False).strip("*") # chop off the stop, note this doesn't have a start

# exploit vector, this attaches to ACE2. also called "surface glycoprotein"
# https://www.ncbi.nlm.nih.gov/Structure/pdb/6VYB -- open state
# https://www.ncbi.nlm.nih.gov/Structure/pdb/6VXX -- closed state
# 1273 amino acids
# S1 = 14-685
# S2 = 686-1273
# S2' = 816-1273
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750777/
self.spike_glycoprotein = translate(cc[21563-1:25384], True)

# Forms homotetrameric potassium sensitive ion channels (viroporin) and may modulate virus release.
self.orf3a = translate(cc[25393-1:26220], True)

# these two things stick out, used in assembly aka they package the virus
self.envelope_protein = translate(cc[26245-1:26472], True) # also known as small membrane
self.membrane_glycoprotein = translate(cc[26523-1:27191], True)
self.orf6 = translate(cc[27202-1:27387], True)
self.orf7a = translate(cc[27394-1:27759], True)
self.orf7b = translate(cc[27756-1:27887], True) # is this one real?
self.orf8 = translate(cc[27894-1:28259], True)

# https://en.wikipedia.org/wiki/Capsid
# Packages the positive strand viral genome RNA into a helical ribonucleocapsid
# Includes the "internal" protein (from Coronavirus Pathogenesis)
# https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/human-coronavirus-oc43
self.nucleocapsid_phosphoprotein = translate(cc[28274-1:29533], True)

# might be called the internal protein (Coronavirus Pathogenesis)
self.orf10 = translate(cc[29558-1:29674], True)

def __del__(self):
print('Destructor called, coronaDNA object deleted.')

# Instantiate a new instance of the corona DNA class
coronaDNAIns = coronaDNA()

# Then delete the instance
del coronaDNAIns

2 changes: 1 addition & 1 deletion opt.py
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@@ -1,7 +1,7 @@
#!/usr/bin/env python3
from lib import cc as virus
from vaccine.load import dat as vaccine
from corona import corona
from corona import coronaDNA

virus = virus.replace("T", "U")
vaccine = vaccine.replace("Ψ", "U")
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